0s autopkgtest [13:18:06]: starting date and time: 2025-05-03 13:18:06+0000 0s autopkgtest [13:18:06]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [13:18:06]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.b87b_8nw/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:coot --apt-upgrade coot --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=coot/1.1.15+dfsg-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-4.secgroup --name adt-questing-amd64-coot-20250503-131806-juju-7f2275-prod-proposed-migration-environment-20-aa1b250e-dc29-4e37-a66f-b5653cff6573 --image adt/ubuntu-questing-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 36s autopkgtest [13:18:42]: testbed dpkg architecture: amd64 36s autopkgtest [13:18:42]: testbed apt version: 3.0.0 36s autopkgtest [13:18:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup 36s autopkgtest [13:18:42]: testbed release detected to be: None 37s autopkgtest [13:18:43]: updating testbed package index (apt update) 37s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 37s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 37s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 37s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 37s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1597 kB] 38s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [150 kB] 38s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [38.8 kB] 38s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 Packages [202 kB] 38s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/main i386 Packages [145 kB] 38s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 Packages [1515 kB] 38s Get:11 http://ftpmaster.internal/ubuntu questing-proposed/universe i386 Packages [615 kB] 38s Get:12 http://ftpmaster.internal/ubuntu questing-proposed/multiverse i386 Packages [25.3 kB] 38s Get:13 http://ftpmaster.internal/ubuntu questing-proposed/multiverse amd64 Packages [54.1 kB] 38s Fetched 4453 kB in 1s (6208 kB/s) 38s Reading package lists... 39s autopkgtest [13:18:45]: upgrading testbed (apt dist-upgrade and autopurge) 39s Reading package lists... 39s Building dependency tree... 39s Reading state information... 39s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 40s Starting 2 pkgProblemResolver with broken count: 0 40s Done 40s Entering ResolveByKeep 40s 40s Calculating upgrade... 40s The following packages will be upgraded: 40s debianutils ed libmbim-glib4 libmbim-proxy libnftnl11 libnvme1t64 40s libperl5.40 libqmi-glib5 libqmi-proxy perl perl-base perl-modules-5.40 40s python3-lazr.restfulclient 40s 13 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 40s Need to get 11.7 MB of archives. 40s After this operation, 168 kB disk space will be freed. 40s Get:1 http://ftpmaster.internal/ubuntu questing/main amd64 debianutils amd64 5.22 [93.0 kB] 40s Get:2 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 libperl5.40 amd64 5.40.1-3 [4877 kB] 40s Get:3 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 perl amd64 5.40.1-3 [262 kB] 40s Get:4 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 perl-base amd64 5.40.1-3 [1840 kB] 40s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 perl-modules-5.40 all 5.40.1-3 [3217 kB] 40s Get:6 http://ftpmaster.internal/ubuntu questing/main amd64 ed amd64 1.21.1-1 [57.2 kB] 40s Get:7 http://ftpmaster.internal/ubuntu questing/main amd64 libnftnl11 amd64 1.2.9-1 [69.1 kB] 40s Get:8 http://ftpmaster.internal/ubuntu questing/main amd64 libmbim-proxy amd64 1.32.0-1 [6276 B] 40s Get:9 http://ftpmaster.internal/ubuntu questing/main amd64 libmbim-glib4 amd64 1.32.0-1 [233 kB] 40s Get:10 http://ftpmaster.internal/ubuntu questing/main amd64 libnvme1t64 amd64 1.13-2 [84.2 kB] 40s Get:11 http://ftpmaster.internal/ubuntu questing/main amd64 libqmi-proxy amd64 1.36.0-1 [6220 B] 40s Get:12 http://ftpmaster.internal/ubuntu questing/main amd64 libqmi-glib5 amd64 1.36.0-1 [920 kB] 40s Get:13 http://ftpmaster.internal/ubuntu questing/main amd64 python3-lazr.restfulclient all 0.14.6-3 [51.0 kB] 41s Fetched 11.7 MB in 0s (41.8 MB/s) 41s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 80514 files and directories currently installed.) 41s Preparing to unpack .../debianutils_5.22_amd64.deb ... 41s Unpacking debianutils (5.22) over (5.21) ... 41s Setting up debianutils (5.22) ... 41s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 80514 files and directories currently installed.) 41s Preparing to unpack .../libperl5.40_5.40.1-3_amd64.deb ... 41s Unpacking libperl5.40:amd64 (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 41s Preparing to unpack .../perl_5.40.1-3_amd64.deb ... 41s Unpacking perl (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 41s Preparing to unpack .../perl-base_5.40.1-3_amd64.deb ... 41s Unpacking perl-base (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 41s Setting up perl-base (5.40.1-3) ... 41s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 80514 files and directories currently installed.) 41s Preparing to unpack .../0-perl-modules-5.40_5.40.1-3_all.deb ... 41s Unpacking perl-modules-5.40 (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 41s Preparing to unpack .../1-ed_1.21.1-1_amd64.deb ... 42s Unpacking ed (1.21.1-1) over (1.21-1) ... 42s Preparing to unpack .../2-libnftnl11_1.2.9-1_amd64.deb ... 42s Unpacking libnftnl11:amd64 (1.2.9-1) over (1.2.8-1) ... 42s Preparing to unpack .../3-libmbim-proxy_1.32.0-1_amd64.deb ... 42s Unpacking libmbim-proxy (1.32.0-1) over (1.31.2-0ubuntu4) ... 42s Preparing to unpack .../4-libmbim-glib4_1.32.0-1_amd64.deb ... 42s Unpacking libmbim-glib4:amd64 (1.32.0-1) over (1.31.2-0ubuntu4) ... 42s Preparing to unpack .../5-libnvme1t64_1.13-2_amd64.deb ... 42s Unpacking libnvme1t64 (1.13-2) over (1.11.1-2) ... 42s Preparing to unpack .../6-libqmi-proxy_1.36.0-1_amd64.deb ... 42s Unpacking libqmi-proxy (1.36.0-1) over (1.35.6-1) ... 42s Preparing to unpack .../7-libqmi-glib5_1.36.0-1_amd64.deb ... 42s Unpacking libqmi-glib5:amd64 (1.36.0-1) over (1.35.6-1) ... 42s Preparing to unpack .../8-python3-lazr.restfulclient_0.14.6-3_all.deb ... 42s Unpacking python3-lazr.restfulclient (0.14.6-3) over (0.14.6-2) ... 42s Setting up libnftnl11:amd64 (1.2.9-1) ... 42s Setting up libnvme1t64 (1.13-2) ... 42s Setting up ed (1.21.1-1) ... 42s Setting up perl-modules-5.40 (5.40.1-3) ... 42s Setting up python3-lazr.restfulclient (0.14.6-3) ... 42s Setting up libmbim-glib4:amd64 (1.32.0-1) ... 42s Setting up libmbim-proxy (1.32.0-1) ... 42s Setting up libperl5.40:amd64 (5.40.1-3) ... 42s Setting up perl (5.40.1-3) ... 42s Setting up libqmi-glib5:amd64 (1.36.0-1) ... 42s Setting up libqmi-proxy (1.36.0-1) ... 42s Processing triggers for install-info (7.1.1-1) ... 42s Processing triggers for libc-bin (2.41-6ubuntu1) ... 42s Processing triggers for man-db (2.13.0-1) ... 43s Reading package lists... 43s Building dependency tree... 43s Reading state information... 43s Starting pkgProblemResolver with broken count: 0 43s Starting 2 pkgProblemResolver with broken count: 0 43s Done 43s Solving dependencies... 43s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 45s autopkgtest [13:18:51]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Sun Apr 6 15:05:05 UTC 2025 46s autopkgtest [13:18:52]: @@@@@@@@@@@@@@@@@@@@ apt-source coot 50s Get:1 http://ftpmaster.internal/ubuntu questing-proposed/universe coot 1.1.15+dfsg-1 (dsc) [2998 B] 50s Get:2 http://ftpmaster.internal/ubuntu questing-proposed/universe coot 1.1.15+dfsg-1 (tar) [89.2 MB] 50s Get:3 http://ftpmaster.internal/ubuntu questing-proposed/universe coot 1.1.15+dfsg-1 (diff) [53.6 kB] 50s gpgv: Signature made Wed Apr 2 13:41:35 2025 UTC 50s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 50s gpgv: issuer "merkys@debian.org" 50s gpgv: Can't check signature: No public key 50s dpkg-source: warning: cannot verify inline signature for ./coot_1.1.15+dfsg-1.dsc: no acceptable signature found 51s autopkgtest [13:18:57]: testing package coot version 1.1.15+dfsg-1 52s autopkgtest [13:18:58]: build not needed 59s autopkgtest [13:19:05]: test command1: preparing testbed 59s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s Starting pkgProblemResolver with broken count: 0 60s Starting 2 pkgProblemResolver with broken count: 0 60s Done 60s The following NEW packages will be installed: 60s adwaita-icon-theme coot coot-data coot-doc dconf-gsettings-backend 60s dconf-service fontconfig fontconfig-config fonts-freefont-ttf 60s fonts-noto-core fonts-noto-mono gir1.2-freedesktop gir1.2-gdkpixbuf-2.0 60s gir1.2-graphene-1.0 gir1.2-gtk-4.0 gir1.2-harfbuzz-0.0 gir1.2-pango-1.0 60s gtk-update-icon-cache hicolor-icon-theme libamd-comgr2 libamdhip64-5 60s libasound2-data libasound2t64 libblas3 libboost-iostreams1.83.0 60s libboost-numpy1.83.0 libboost-python1.83.0 libboost-serialization1.83.0 60s libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libccp4-data 60s libccp4c0t64 libclipper2 libcoordgen3 libcootapi-dev libcootapi1.1 60s libcpdb-frontend2t64 libcpdb2t64 libdatrie1 libdconf1 libdeflate0 libepoxy0 60s libevent-pthreads-2.1-7t64 libfabric1 libfontconfig1 libgdk-pixbuf-2.0-0 60s libgdk-pixbuf2.0-common libgfortran5 libgles2 libglvnd0 libgomp1 60s libgraphene-1.0-0 libgraphite2-3 libgsl28 libgslcblas0 libgtk-4-1 60s libgtk-4-common libharfbuzz-gobject0 libharfbuzz-subset0 libharfbuzz0b 60s libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 60s libibumad3 libinchi1.07 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 60s libllvm17t64 libmaeparser1 libmmdb2-0 libmunge2 libogg0 libopenmpi40 60s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpangoxft-1.0-0 60s libpciaccess0 libpixman-1-0 libpmix2t64 libpsm-infinipath1 libpsm2-2 60s librdkit1t64 librdmacm1t64 libsharpyuv0 libssm2 libthai-data libthai0 60s libtiff6 libucx0 libvorbis0a libvorbisfile3 libvulkan1 libwayland-client0 60s libwayland-egl1 libwebp7 libxcb-render0 libxcb-shm0 libxcursor1 libxdamage1 60s libxfixes3 libxft2 libxi6 libxinerama1 libxnvctrl0 libxrandr2 libxrender1 60s ocl-icd-libopencl1 python3-numpy python3-numpy-dev python3-rdkit rdkit-data 60s refmac-dictionary sfftw2 ttf-bitstream-vera 60s 0 upgraded, 121 newly installed, 0 to remove and 0 not upgraded. 60s Need to get 172 MB of archives. 60s After this operation, 838 MB of additional disk space will be used. 60s Get:1 http://ftpmaster.internal/ubuntu questing/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-5 [148 kB] 60s Get:2 http://ftpmaster.internal/ubuntu questing/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 60s Get:3 http://ftpmaster.internal/ubuntu questing/main amd64 libgfortran5 amd64 15-20250404-0ubuntu1 [926 kB] 60s Get:4 http://ftpmaster.internal/ubuntu questing/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 60s Get:5 http://ftpmaster.internal/ubuntu questing/main amd64 python3-numpy amd64 1:2.2.3+ds-5 [5702 kB] 60s Get:6 http://ftpmaster.internal/ubuntu questing/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [8004 B] 60s Get:7 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 60s Get:8 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 60s Get:9 http://ftpmaster.internal/ubuntu questing/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 60s Get:10 http://ftpmaster.internal/ubuntu questing/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 60s Get:11 http://ftpmaster.internal/ubuntu questing/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 60s Get:12 http://ftpmaster.internal/ubuntu questing/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 60s Get:13 http://ftpmaster.internal/ubuntu questing/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 60s Get:14 http://ftpmaster.internal/ubuntu questing/main amd64 libtiff6 amd64 4.7.0-3ubuntu1 [204 kB] 60s Get:15 http://ftpmaster.internal/ubuntu questing/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [161 kB] 60s Get:16 http://ftpmaster.internal/ubuntu questing/main amd64 gtk-update-icon-cache amd64 4.18.4+ds-1 [54.1 kB] 60s Get:17 http://ftpmaster.internal/ubuntu questing/main amd64 hicolor-icon-theme all 0.18-2 [13.3 kB] 60s Get:18 http://ftpmaster.internal/ubuntu questing/main amd64 adwaita-icon-theme all 48.0-1 [578 kB] 60s Get:19 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-noto-mono all 20201225-2 [435 kB] 60s Get:20 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-noto-core all 20201225-2 [13.3 MB] 61s Get:21 http://ftpmaster.internal/ubuntu questing/universe amd64 ttf-bitstream-vera all 1.10-8.2 [244 kB] 61s Get:22 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 coot-data all 1.1.15+dfsg-1 [11.8 MB] 61s Get:23 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-freefont-ttf all 20211204+svn4273-2 [5641 kB] 61s Get:24 http://ftpmaster.internal/ubuntu questing/main amd64 fontconfig-config amd64 2.15.0-2.2ubuntu1 [37.8 kB] 61s Get:25 http://ftpmaster.internal/ubuntu questing/main amd64 libfontconfig1 amd64 2.15.0-2.2ubuntu1 [164 kB] 61s Get:26 http://ftpmaster.internal/ubuntu questing/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 61s Get:27 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 61s Get:28 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 61s Get:29 http://ftpmaster.internal/ubuntu questing/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 61s Get:30 http://ftpmaster.internal/ubuntu questing/main amd64 libcairo2 amd64 1.18.4-1 [662 kB] 61s Get:31 http://ftpmaster.internal/ubuntu questing/main amd64 libcairo-gobject2 amd64 1.18.4-1 [127 kB] 61s Get:32 http://ftpmaster.internal/ubuntu questing/main amd64 gir1.2-freedesktop amd64 1.84.0-1 [65.0 kB] 61s Get:33 http://ftpmaster.internal/ubuntu questing/main amd64 gir1.2-gdkpixbuf-2.0 amd64 2.42.12+dfsg-2 [9388 B] 61s Get:34 http://ftpmaster.internal/ubuntu questing/main amd64 libgraphene-1.0-0 amd64 1.10.8-5 [46.0 kB] 61s Get:35 http://ftpmaster.internal/ubuntu questing/main amd64 gir1.2-graphene-1.0 amd64 1.10.8-5 [11.1 kB] 61s Get:36 http://ftpmaster.internal/ubuntu questing/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 61s Get:37 http://ftpmaster.internal/ubuntu questing/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 61s Get:38 http://ftpmaster.internal/ubuntu questing/main amd64 libharfbuzz-gobject0 amd64 10.2.0-1 [34.6 kB] 61s Get:39 http://ftpmaster.internal/ubuntu questing/main amd64 gir1.2-harfbuzz-0.0 amd64 10.2.0-1 [45.1 kB] 61s Get:40 http://ftpmaster.internal/ubuntu questing/main amd64 fontconfig amd64 2.15.0-2.2ubuntu1 [180 kB] 61s Get:41 http://ftpmaster.internal/ubuntu questing/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 61s Get:42 http://ftpmaster.internal/ubuntu questing/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 61s Get:43 http://ftpmaster.internal/ubuntu questing/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 61s Get:44 http://ftpmaster.internal/ubuntu questing/main amd64 libpango-1.0-0 amd64 1.56.3-1 [256 kB] 61s Get:45 http://ftpmaster.internal/ubuntu questing/main amd64 libpangoft2-1.0-0 amd64 1.56.3-1 [52.9 kB] 61s Get:46 http://ftpmaster.internal/ubuntu questing/main amd64 libpangocairo-1.0-0 amd64 1.56.3-1 [29.1 kB] 61s Get:47 http://ftpmaster.internal/ubuntu questing/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 61s Get:48 http://ftpmaster.internal/ubuntu questing/main amd64 libpangoxft-1.0-0 amd64 1.56.3-1 [21.1 kB] 61s Get:49 http://ftpmaster.internal/ubuntu questing/main amd64 gir1.2-pango-1.0 amd64 1.56.3-1 [34.6 kB] 61s Get:50 http://ftpmaster.internal/ubuntu questing/main amd64 libcairo-script-interpreter2 amd64 1.18.4-1 [67.2 kB] 61s Get:51 http://ftpmaster.internal/ubuntu questing/main amd64 libcpdb2t64 amd64 2.0~b7-0ubuntu3 [31.8 kB] 61s Get:52 http://ftpmaster.internal/ubuntu questing/main amd64 libcpdb-frontend2t64 amd64 2.0~b7-0ubuntu3 [21.5 kB] 61s Get:53 http://ftpmaster.internal/ubuntu questing/main amd64 libepoxy0 amd64 1.5.10-2 [218 kB] 61s Get:54 http://ftpmaster.internal/ubuntu questing/main amd64 libharfbuzz-subset0 amd64 10.2.0-1 [553 kB] 61s Get:55 http://ftpmaster.internal/ubuntu questing/main amd64 libvulkan1 amd64 1.4.304.0-1 [147 kB] 61s Get:56 http://ftpmaster.internal/ubuntu questing/main amd64 libwayland-client0 amd64 1.23.1-3 [29.7 kB] 61s Get:57 http://ftpmaster.internal/ubuntu questing/main amd64 libwayland-egl1 amd64 1.23.1-3 [6168 B] 61s Get:58 http://ftpmaster.internal/ubuntu questing/main amd64 libxfixes3 amd64 1:6.0.0-2build1 [10.8 kB] 61s Get:59 http://ftpmaster.internal/ubuntu questing/main amd64 libxcursor1 amd64 1:1.2.3-1 [23.1 kB] 61s Get:60 http://ftpmaster.internal/ubuntu questing/main amd64 libxdamage1 amd64 1:1.1.6-1build1 [6150 B] 61s Get:61 http://ftpmaster.internal/ubuntu questing/main amd64 libxi6 amd64 2:1.8.2-1 [32.4 kB] 61s Get:62 http://ftpmaster.internal/ubuntu questing/main amd64 libxinerama1 amd64 2:1.1.4-3build1 [6396 B] 61s Get:63 http://ftpmaster.internal/ubuntu questing/main amd64 libxrandr2 amd64 2:1.5.4-1 [19.6 kB] 61s Get:64 http://ftpmaster.internal/ubuntu questing/main amd64 libglvnd0 amd64 1.7.0-1build1 [69.6 kB] 61s Get:65 http://ftpmaster.internal/ubuntu questing/main amd64 libgles2 amd64 1.7.0-1build1 [17.1 kB] 61s Get:66 http://ftpmaster.internal/ubuntu questing/main amd64 libdconf1 amd64 0.40.0-5 [39.8 kB] 61s Get:67 http://ftpmaster.internal/ubuntu questing/main amd64 dconf-service amd64 0.40.0-5 [28.4 kB] 61s Get:68 http://ftpmaster.internal/ubuntu questing/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [22.7 kB] 61s Get:69 http://ftpmaster.internal/ubuntu questing/main amd64 libgtk-4-common all 4.18.4+ds-1 [1514 kB] 61s Get:70 http://ftpmaster.internal/ubuntu questing/main amd64 libgtk-4-1 amd64 4.18.4+ds-1 [3605 kB] 61s Get:71 http://ftpmaster.internal/ubuntu questing/main amd64 gir1.2-gtk-4.0 amd64 4.18.4+ds-1 [220 kB] 61s Get:72 http://ftpmaster.internal/ubuntu questing/universe amd64 rdkit-data all 202409.6-2 [12.6 MB] 62s Get:73 http://ftpmaster.internal/ubuntu questing/main amd64 libboost-python1.83.0 amd64 1.83.0-4.2ubuntu1 [314 kB] 62s Get:74 http://ftpmaster.internal/ubuntu questing/universe amd64 libboost-numpy1.83.0 amd64 1.83.0-4.2ubuntu1 [243 kB] 62s Get:75 http://ftpmaster.internal/ubuntu questing/universe amd64 libboost-serialization1.83.0 amd64 1.83.0-4.2ubuntu1 [344 kB] 62s Get:76 http://ftpmaster.internal/ubuntu questing/universe amd64 libcoordgen3 amd64 3.0.2-1 [215 kB] 62s Get:77 http://ftpmaster.internal/ubuntu questing/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-4.2ubuntu1 [260 kB] 62s Get:78 http://ftpmaster.internal/ubuntu questing/universe amd64 libinchi1.07 amd64 1.07.3+dfsg-1 [702 kB] 62s Get:79 http://ftpmaster.internal/ubuntu questing/universe amd64 libmaeparser1 amd64 1.3.1-1build1 [90.2 kB] 62s Get:80 http://ftpmaster.internal/ubuntu questing/universe amd64 librdkit1t64 amd64 202409.6-2 [6204 kB] 62s Get:81 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-rdkit amd64 202409.6-2 [4987 kB] 62s Get:82 http://ftpmaster.internal/ubuntu questing/universe amd64 refmac-dictionary all 5.41-3 [16.7 MB] 62s Get:83 http://ftpmaster.internal/ubuntu questing/main amd64 libasound2-data all 1.2.13-1build1 [21.1 kB] 62s Get:84 http://ftpmaster.internal/ubuntu questing/main amd64 libasound2t64 amd64 1.2.13-1build1 [437 kB] 62s Get:85 http://ftpmaster.internal/ubuntu questing/universe amd64 libccp4-data all 8.0.0-4 [65.2 kB] 62s Get:86 http://ftpmaster.internal/ubuntu questing/universe amd64 libccp4c0t64 amd64 8.0.0-4 [104 kB] 62s Get:87 http://ftpmaster.internal/ubuntu questing/universe amd64 libmmdb2-0 amd64 2.0.22-1 [363 kB] 62s Get:88 http://ftpmaster.internal/ubuntu questing/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [7966 B] 62s Get:89 http://ftpmaster.internal/ubuntu questing/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.4 [179 kB] 62s Get:90 http://ftpmaster.internal/ubuntu questing/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 62s Get:91 http://ftpmaster.internal/ubuntu questing/main amd64 librdmacm1t64 amd64 56.0-4ubuntu1 [71.5 kB] 62s Get:92 http://ftpmaster.internal/ubuntu questing/universe amd64 libfabric1 amd64 1.17.0-3.1 [789 kB] 62s Get:93 http://ftpmaster.internal/ubuntu questing/universe amd64 libhwloc15 amd64 2.12.0-1 [194 kB] 62s Get:94 http://ftpmaster.internal/ubuntu questing/universe amd64 libmunge2 amd64 0.5.16-1 [16.5 kB] 62s Get:95 http://ftpmaster.internal/ubuntu questing/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 62s Get:96 http://ftpmaster.internal/ubuntu questing/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 62s Get:97 http://ftpmaster.internal/ubuntu questing/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1build1 [38.5 kB] 62s Get:98 http://ftpmaster.internal/ubuntu questing/universe amd64 libhwloc-plugins amd64 2.12.0-1 [16.0 kB] 62s Get:99 http://ftpmaster.internal/ubuntu questing/universe amd64 libpmix2t64 amd64 5.0.6-5 [714 kB] 62s Get:100 http://ftpmaster.internal/ubuntu questing/universe amd64 libllvm17t64 amd64 1:17.0.6-21 [26.0 MB] 63s Get:101 http://ftpmaster.internal/ubuntu questing/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build2 [14.4 MB] 63s Get:102 http://ftpmaster.internal/ubuntu questing/universe amd64 libhsakmt1 amd64 5.7.0-1build1 [62.9 kB] 63s Get:103 http://ftpmaster.internal/ubuntu questing/universe amd64 libhsa-runtime64-1 amd64 5.7.1-2build1 [491 kB] 63s Get:104 http://ftpmaster.internal/ubuntu questing/universe amd64 libamdhip64-5 amd64 5.7.1-5.1 [9695 kB] 63s Get:105 http://ftpmaster.internal/ubuntu questing/main amd64 libgomp1 amd64 15-20250404-0ubuntu1 [151 kB] 63s Get:106 http://ftpmaster.internal/ubuntu questing/main amd64 libibumad3 amd64 56.0-4ubuntu1 [31.2 kB] 63s Get:107 http://ftpmaster.internal/ubuntu questing/main amd64 libibmad5 amd64 56.0-4ubuntu1 [43.9 kB] 63s Get:108 http://ftpmaster.internal/ubuntu questing/universe amd64 libucx0 amd64 1.18.1+ds-2 [1293 kB] 63s Get:109 http://ftpmaster.internal/ubuntu questing/universe amd64 libopenmpi40 amd64 5.0.7-1 [2526 kB] 63s Get:110 http://ftpmaster.internal/ubuntu questing/universe amd64 sfftw2 amd64 2.1.5-7build1 [224 kB] 63s Get:111 http://ftpmaster.internal/ubuntu questing/universe amd64 libclipper2 amd64 2.1.20201109-2build1 [1188 kB] 63s Get:112 http://ftpmaster.internal/ubuntu questing/universe amd64 libgslcblas0 amd64 2.8+dfsg-5ubuntu1 [113 kB] 63s Get:113 http://ftpmaster.internal/ubuntu questing/universe amd64 libgsl28 amd64 2.8+dfsg-5ubuntu1 [1043 kB] 63s Get:114 http://ftpmaster.internal/ubuntu questing/universe amd64 libssm2 amd64 1.4.0-2build1 [87.7 kB] 64s Get:115 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 libcootapi1.1 amd64 1.1.15+dfsg-1 [3962 kB] 64s Get:116 http://ftpmaster.internal/ubuntu questing/main amd64 libogg0 amd64 1.3.5-3build1 [22.7 kB] 64s Get:117 http://ftpmaster.internal/ubuntu questing/main amd64 libvorbis0a amd64 1.3.7-2 [98.4 kB] 64s Get:118 http://ftpmaster.internal/ubuntu questing/main amd64 libvorbisfile3 amd64 1.3.7-2 [17.1 kB] 64s Get:119 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 coot amd64 1.1.15+dfsg-1 [8775 kB] 64s Get:120 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 coot-doc all 1.1.15+dfsg-1 [2049 kB] 64s Get:121 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 libcootapi-dev amd64 1.1.15+dfsg-1 [23.9 kB] 64s Fetched 172 MB in 4s (44.8 MB/s) 64s Selecting previously unselected package python3-numpy-dev:amd64. 64s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 80514 files and directories currently installed.) 64s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.3+ds-5_amd64.deb ... 64s Unpacking python3-numpy-dev:amd64 (1:2.2.3+ds-5) ... 64s Selecting previously unselected package libblas3:amd64. 64s Preparing to unpack .../001-libblas3_3.12.1-2_amd64.deb ... 64s Unpacking libblas3:amd64 (3.12.1-2) ... 64s Selecting previously unselected package libgfortran5:amd64. 64s Preparing to unpack .../002-libgfortran5_15-20250404-0ubuntu1_amd64.deb ... 64s Unpacking libgfortran5:amd64 (15-20250404-0ubuntu1) ... 64s Selecting previously unselected package liblapack3:amd64. 64s Preparing to unpack .../003-liblapack3_3.12.1-2_amd64.deb ... 64s Unpacking liblapack3:amd64 (3.12.1-2) ... 64s Selecting previously unselected package python3-numpy. 64s Preparing to unpack .../004-python3-numpy_1%3a2.2.3+ds-5_amd64.deb ... 64s Unpacking python3-numpy (1:2.2.3+ds-5) ... 66s Selecting previously unselected package libgdk-pixbuf2.0-common. 66s Preparing to unpack .../005-libgdk-pixbuf2.0-common_2.42.12+dfsg-2_all.deb ... 66s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... 66s Selecting previously unselected package libjpeg-turbo8:amd64. 66s Preparing to unpack .../006-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 66s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 66s Selecting previously unselected package libjpeg8:amd64. 66s Preparing to unpack .../007-libjpeg8_8c-2ubuntu11_amd64.deb ... 66s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 66s Selecting previously unselected package libdeflate0:amd64. 66s Preparing to unpack .../008-libdeflate0_1.23-2_amd64.deb ... 66s Unpacking libdeflate0:amd64 (1.23-2) ... 66s Selecting previously unselected package libjbig0:amd64. 66s Preparing to unpack .../009-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 66s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 66s Selecting previously unselected package liblerc4:amd64. 66s Preparing to unpack .../010-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 66s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 66s Selecting previously unselected package libsharpyuv0:amd64. 66s Preparing to unpack .../011-libsharpyuv0_1.5.0-0.1_amd64.deb ... 66s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 66s Selecting previously unselected package libwebp7:amd64. 66s Preparing to unpack .../012-libwebp7_1.5.0-0.1_amd64.deb ... 66s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 66s Selecting previously unselected package libtiff6:amd64. 66s Preparing to unpack .../013-libtiff6_4.7.0-3ubuntu1_amd64.deb ... 66s Unpacking libtiff6:amd64 (4.7.0-3ubuntu1) ... 66s Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. 66s Preparing to unpack .../014-libgdk-pixbuf-2.0-0_2.42.12+dfsg-2_amd64.deb ... 66s Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... 66s Selecting previously unselected package gtk-update-icon-cache. 66s Preparing to unpack .../015-gtk-update-icon-cache_4.18.4+ds-1_amd64.deb ... 66s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 66s 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. 66s Unpacking gtk-update-icon-cache (4.18.4+ds-1) ... 66s Selecting previously unselected package hicolor-icon-theme. 66s Preparing to unpack .../016-hicolor-icon-theme_0.18-2_all.deb ... 66s Unpacking hicolor-icon-theme (0.18-2) ... 66s Selecting previously unselected package adwaita-icon-theme. 66s Preparing to unpack .../017-adwaita-icon-theme_48.0-1_all.deb ... 66s Unpacking adwaita-icon-theme (48.0-1) ... 66s Selecting previously unselected package fonts-noto-mono. 66s Preparing to unpack .../018-fonts-noto-mono_20201225-2_all.deb ... 66s Unpacking fonts-noto-mono (20201225-2) ... 66s Selecting previously unselected package fonts-noto-core. 66s Preparing to unpack .../019-fonts-noto-core_20201225-2_all.deb ... 66s Unpacking fonts-noto-core (20201225-2) ... 66s Selecting previously unselected package ttf-bitstream-vera. 66s Preparing to unpack .../020-ttf-bitstream-vera_1.10-8.2_all.deb ... 66s Unpacking ttf-bitstream-vera (1.10-8.2) ... 66s Selecting previously unselected package coot-data. 66s Preparing to unpack .../021-coot-data_1.1.15+dfsg-1_all.deb ... 66s Unpacking coot-data (1.1.15+dfsg-1) ... 66s Selecting previously unselected package fonts-freefont-ttf. 66s Preparing to unpack .../022-fonts-freefont-ttf_20211204+svn4273-2_all.deb ... 66s Unpacking fonts-freefont-ttf (20211204+svn4273-2) ... 66s Selecting previously unselected package fontconfig-config. 66s Preparing to unpack .../023-fontconfig-config_2.15.0-2.2ubuntu1_amd64.deb ... 66s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 66s Selecting previously unselected package libfontconfig1:amd64. 66s Preparing to unpack .../024-libfontconfig1_2.15.0-2.2ubuntu1_amd64.deb ... 66s Unpacking libfontconfig1:amd64 (2.15.0-2.2ubuntu1) ... 66s Selecting previously unselected package libpixman-1-0:amd64. 66s Preparing to unpack .../025-libpixman-1-0_0.44.0-3_amd64.deb ... 66s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 66s Selecting previously unselected package libxcb-render0:amd64. 66s Preparing to unpack .../026-libxcb-render0_1.17.0-2_amd64.deb ... 66s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 66s Selecting previously unselected package libxcb-shm0:amd64. 66s Preparing to unpack .../027-libxcb-shm0_1.17.0-2_amd64.deb ... 66s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 66s Selecting previously unselected package libxrender1:amd64. 66s Preparing to unpack .../028-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 66s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 66s Selecting previously unselected package libcairo2:amd64. 66s Preparing to unpack .../029-libcairo2_1.18.4-1_amd64.deb ... 66s Unpacking libcairo2:amd64 (1.18.4-1) ... 66s Selecting previously unselected package libcairo-gobject2:amd64. 66s Preparing to unpack .../030-libcairo-gobject2_1.18.4-1_amd64.deb ... 66s Unpacking libcairo-gobject2:amd64 (1.18.4-1) ... 66s Selecting previously unselected package gir1.2-freedesktop:amd64. 66s Preparing to unpack .../031-gir1.2-freedesktop_1.84.0-1_amd64.deb ... 66s Unpacking gir1.2-freedesktop:amd64 (1.84.0-1) ... 66s Selecting previously unselected package gir1.2-gdkpixbuf-2.0:amd64. 66s Preparing to unpack .../032-gir1.2-gdkpixbuf-2.0_2.42.12+dfsg-2_amd64.deb ... 66s Unpacking gir1.2-gdkpixbuf-2.0:amd64 (2.42.12+dfsg-2) ... 66s Selecting previously unselected package libgraphene-1.0-0:amd64. 66s Preparing to unpack .../033-libgraphene-1.0-0_1.10.8-5_amd64.deb ... 66s Unpacking libgraphene-1.0-0:amd64 (1.10.8-5) ... 66s Selecting previously unselected package gir1.2-graphene-1.0:amd64. 66s Preparing to unpack .../034-gir1.2-graphene-1.0_1.10.8-5_amd64.deb ... 66s Unpacking gir1.2-graphene-1.0:amd64 (1.10.8-5) ... 66s Selecting previously unselected package libgraphite2-3:amd64. 66s Preparing to unpack .../035-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 66s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 66s Selecting previously unselected package libharfbuzz0b:amd64. 66s Preparing to unpack .../036-libharfbuzz0b_10.2.0-1_amd64.deb ... 66s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 66s Selecting previously unselected package libharfbuzz-gobject0:amd64. 66s Preparing to unpack .../037-libharfbuzz-gobject0_10.2.0-1_amd64.deb ... 66s Unpacking libharfbuzz-gobject0:amd64 (10.2.0-1) ... 66s Selecting previously unselected package gir1.2-harfbuzz-0.0:amd64. 66s Preparing to unpack .../038-gir1.2-harfbuzz-0.0_10.2.0-1_amd64.deb ... 66s Unpacking gir1.2-harfbuzz-0.0:amd64 (10.2.0-1) ... 66s Selecting previously unselected package fontconfig. 66s Preparing to unpack .../039-fontconfig_2.15.0-2.2ubuntu1_amd64.deb ... 66s Unpacking fontconfig (2.15.0-2.2ubuntu1) ... 66s Selecting previously unselected package libthai-data. 66s Preparing to unpack .../040-libthai-data_0.1.29-2build1_all.deb ... 66s Unpacking libthai-data (0.1.29-2build1) ... 66s Selecting previously unselected package libdatrie1:amd64. 66s Preparing to unpack .../041-libdatrie1_0.2.13-3build1_amd64.deb ... 66s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 66s Selecting previously unselected package libthai0:amd64. 66s Preparing to unpack .../042-libthai0_0.1.29-2build1_amd64.deb ... 66s Unpacking libthai0:amd64 (0.1.29-2build1) ... 66s Selecting previously unselected package libpango-1.0-0:amd64. 66s Preparing to unpack .../043-libpango-1.0-0_1.56.3-1_amd64.deb ... 66s Unpacking libpango-1.0-0:amd64 (1.56.3-1) ... 66s Selecting previously unselected package libpangoft2-1.0-0:amd64. 66s Preparing to unpack .../044-libpangoft2-1.0-0_1.56.3-1_amd64.deb ... 66s Unpacking libpangoft2-1.0-0:amd64 (1.56.3-1) ... 66s Selecting previously unselected package libpangocairo-1.0-0:amd64. 66s Preparing to unpack .../045-libpangocairo-1.0-0_1.56.3-1_amd64.deb ... 66s Unpacking libpangocairo-1.0-0:amd64 (1.56.3-1) ... 66s Selecting previously unselected package libxft2:amd64. 66s Preparing to unpack .../046-libxft2_2.3.6-1build1_amd64.deb ... 66s Unpacking libxft2:amd64 (2.3.6-1build1) ... 66s Selecting previously unselected package libpangoxft-1.0-0:amd64. 66s Preparing to unpack .../047-libpangoxft-1.0-0_1.56.3-1_amd64.deb ... 66s Unpacking libpangoxft-1.0-0:amd64 (1.56.3-1) ... 66s Selecting previously unselected package gir1.2-pango-1.0:amd64. 66s Preparing to unpack .../048-gir1.2-pango-1.0_1.56.3-1_amd64.deb ... 66s Unpacking gir1.2-pango-1.0:amd64 (1.56.3-1) ... 66s Selecting previously unselected package libcairo-script-interpreter2:amd64. 66s Preparing to unpack .../049-libcairo-script-interpreter2_1.18.4-1_amd64.deb ... 66s Unpacking libcairo-script-interpreter2:amd64 (1.18.4-1) ... 66s Selecting previously unselected package libcpdb2t64:amd64. 66s Preparing to unpack .../050-libcpdb2t64_2.0~b7-0ubuntu3_amd64.deb ... 66s Unpacking libcpdb2t64:amd64 (2.0~b7-0ubuntu3) ... 66s Selecting previously unselected package libcpdb-frontend2t64:amd64. 66s Preparing to unpack .../051-libcpdb-frontend2t64_2.0~b7-0ubuntu3_amd64.deb ... 66s Unpacking libcpdb-frontend2t64:amd64 (2.0~b7-0ubuntu3) ... 66s Selecting previously unselected package libepoxy0:amd64. 66s Preparing to unpack .../052-libepoxy0_1.5.10-2_amd64.deb ... 66s Unpacking libepoxy0:amd64 (1.5.10-2) ... 66s Selecting previously unselected package libharfbuzz-subset0:amd64. 66s Preparing to unpack .../053-libharfbuzz-subset0_10.2.0-1_amd64.deb ... 66s Unpacking libharfbuzz-subset0:amd64 (10.2.0-1) ... 66s Selecting previously unselected package libvulkan1:amd64. 66s Preparing to unpack .../054-libvulkan1_1.4.304.0-1_amd64.deb ... 66s Unpacking libvulkan1:amd64 (1.4.304.0-1) ... 66s Selecting previously unselected package libwayland-client0:amd64. 66s Preparing to unpack .../055-libwayland-client0_1.23.1-3_amd64.deb ... 66s Unpacking libwayland-client0:amd64 (1.23.1-3) ... 66s Selecting previously unselected package libwayland-egl1:amd64. 66s Preparing to unpack .../056-libwayland-egl1_1.23.1-3_amd64.deb ... 66s Unpacking libwayland-egl1:amd64 (1.23.1-3) ... 66s Selecting previously unselected package libxfixes3:amd64. 66s Preparing to unpack .../057-libxfixes3_1%3a6.0.0-2build1_amd64.deb ... 66s Unpacking libxfixes3:amd64 (1:6.0.0-2build1) ... 66s Selecting previously unselected package libxcursor1:amd64. 66s Preparing to unpack .../058-libxcursor1_1%3a1.2.3-1_amd64.deb ... 66s Unpacking libxcursor1:amd64 (1:1.2.3-1) ... 66s Selecting previously unselected package libxdamage1:amd64. 66s Preparing to unpack .../059-libxdamage1_1%3a1.1.6-1build1_amd64.deb ... 66s Unpacking libxdamage1:amd64 (1:1.1.6-1build1) ... 66s Selecting previously unselected package libxi6:amd64. 66s Preparing to unpack .../060-libxi6_2%3a1.8.2-1_amd64.deb ... 66s Unpacking libxi6:amd64 (2:1.8.2-1) ... 66s Selecting previously unselected package libxinerama1:amd64. 66s Preparing to unpack .../061-libxinerama1_2%3a1.1.4-3build1_amd64.deb ... 66s Unpacking libxinerama1:amd64 (2:1.1.4-3build1) ... 66s Selecting previously unselected package libxrandr2:amd64. 66s Preparing to unpack .../062-libxrandr2_2%3a1.5.4-1_amd64.deb ... 66s Unpacking libxrandr2:amd64 (2:1.5.4-1) ... 66s Selecting previously unselected package libglvnd0:amd64. 66s Preparing to unpack .../063-libglvnd0_1.7.0-1build1_amd64.deb ... 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previously unselected package librdkit1t64. 67s Preparing to unpack .../079-librdkit1t64_202409.6-2_amd64.deb ... 67s Unpacking librdkit1t64 (202409.6-2) ... 67s Selecting previously unselected package python3-rdkit. 67s Preparing to unpack .../080-python3-rdkit_202409.6-2_amd64.deb ... 67s Unpacking python3-rdkit (202409.6-2) ... 67s Selecting previously unselected package refmac-dictionary. 67s Preparing to unpack .../081-refmac-dictionary_5.41-3_all.deb ... 67s Unpacking refmac-dictionary (5.41-3) ... 68s Selecting previously unselected package libasound2-data. 68s Preparing to unpack .../082-libasound2-data_1.2.13-1build1_all.deb ... 68s Unpacking libasound2-data (1.2.13-1build1) ... 68s Selecting previously unselected package libasound2t64:amd64. 68s Preparing to unpack .../083-libasound2t64_1.2.13-1build1_amd64.deb ... 68s Unpacking libasound2t64:amd64 (1.2.13-1build1) ... 68s Selecting previously unselected package libccp4-data. 68s Preparing to unpack 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unpack .../100-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_amd64.deb ... 69s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 69s Selecting previously unselected package libhsakmt1:amd64. 69s Preparing to unpack .../101-libhsakmt1_5.7.0-1build1_amd64.deb ... 69s Unpacking libhsakmt1:amd64 (5.7.0-1build1) ... 69s Selecting previously unselected package libhsa-runtime64-1. 69s Preparing to unpack .../102-libhsa-runtime64-1_5.7.1-2build1_amd64.deb ... 69s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 69s Selecting previously unselected package libamdhip64-5. 69s Preparing to unpack .../103-libamdhip64-5_5.7.1-5.1_amd64.deb ... 69s Unpacking libamdhip64-5 (5.7.1-5.1) ... 70s Selecting previously unselected package libgomp1:amd64. 70s Preparing to unpack .../104-libgomp1_15-20250404-0ubuntu1_amd64.deb ... 70s Unpacking libgomp1:amd64 (15-20250404-0ubuntu1) ... 70s Selecting previously unselected package libibumad3:amd64. 70s Preparing to unpack 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up libsharpyuv0:amd64 (1.5.0-0.1) ... 70s Setting up libpciaccess0:amd64 (0.17-3build1) ... 70s Setting up ttf-bitstream-vera (1.10-8.2) ... 70s Setting up libxdamage1:amd64 (1:1.1.6-1build1) ... 70s Setting up libogg0:amd64 (1.3.5-3build1) ... 70s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 70s Setting up fonts-noto-mono (20201225-2) ... 70s Setting up hicolor-icon-theme (0.18-2) ... 70s Setting up libxi6:amd64 (2:1.8.2-1) ... 70s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 70s Setting up libdatrie1:amd64 (0.2.13-3build1) ... 70s Setting up libgslcblas0:amd64 (2.8+dfsg-5ubuntu1) ... 70s Setting up libmmdb2-0:amd64 (2.0.22-1) ... 70s Setting up libxcb-render0:amd64 (1.17.0-2) ... 70s Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 70s Setting up libglvnd0:amd64 (1.7.0-1build1) ... 70s Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... 70s Setting up libibumad3:amd64 (56.0-4ubuntu1) ... 70s Setting up libdeflate0:amd64 (1.23-2) ... 70s Setting up fonts-freefont-ttf (20211204+svn4273-2) ... 70s Setting up libcpdb2t64:amd64 (2.0~b7-0ubuntu3) ... 70s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 70s Setting up libibmad5:amd64 (56.0-4ubuntu1) ... 70s Setting up libcpdb-frontend2t64:amd64 (2.0~b7-0ubuntu3) ... 70s Setting up libccp4-data (8.0.0-4) ... 70s Setting up libgomp1:amd64 (15-20250404-0ubuntu1) ... 70s Setting up rdkit-data (202409.6-2) ... 70s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 70s Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 70s Setting up refmac-dictionary (5.41-3) ... 70s Setting up libdconf1:amd64 (0.40.0-5) ... 70s Setting up libasound2-data (1.2.13-1build1) ... 70s Setting up libboost-serialization1.83.0:amd64 (1.83.0-4.2ubuntu1) ... 70s Setting up libboost-numpy1.83.0 (1.83.0-4.2ubuntu1) ... 70s Setting up libblas3:amd64 (3.12.1-2) ... 70s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 70s Setting up libgles2:amd64 (1.7.0-1build1) ... 70s Setting up libasound2t64:amd64 (1.2.13-1build1) ... 70s Setting up libmunge2:amd64 (0.5.16-1) ... 70s Setting up libllvm17t64:amd64 (1:17.0.6-21) ... 70s Setting up libepoxy0:amd64 (1.5.10-2) ... 70s Setting up libxfixes3:amd64 (1:6.0.0-2build1) ... 70s Setting up libboost-iostreams1.83.0:amd64 (1.83.0-4.2ubuntu1) ... 70s Setting up libxinerama1:amd64 (2:1.1.4-3build1) ... 70s Setting up libhwloc15:amd64 (2.12.0-1) ... 70s Setting up python3-numpy-dev:amd64 (1:2.2.3+ds-5) ... 70s Setting up libvorbis0a:amd64 (1.3.7-2) ... 70s Setting up libxrandr2:amd64 (2:1.5.4-1) ... 70s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 70s Setting up libgfortran5:amd64 (15-20250404-0ubuntu1) ... 70s Setting up libvulkan1:amd64 (1.4.304.0-1) ... 70s Setting up libwebp7:amd64 (1.5.0-0.1) ... 70s Setting up ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 70s Setting up libccp4c0t64:amd64 (8.0.0-4) ... 70s Setting up libpsm2-2 (11.2.185-2.1) ... 70s Setting up librdmacm1t64:amd64 (56.0-4ubuntu1) ... 70s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 70s Setting up libthai-data (0.1.29-2build1) ... 70s Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 70s Setting up libwayland-egl1:amd64 (1.23.1-3) ... 70s Setting up libpsm-infinipath1 (3.3+20.604758e7-6.4) ... 70s update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode 70s Setting up libcoordgen3:amd64 (3.0.2-1) ... 70s Setting up libgsl28:amd64 (2.8+dfsg-5ubuntu1) ... 70s Setting up libinchi1.07 (1.07.3+dfsg-1) ... 70s Setting up fonts-noto-core (20201225-2) ... 70s Setting up libhsakmt1:amd64 (5.7.0-1build1) ... 70s Setting up libgraphene-1.0-0:amd64 (1.10.8-5) ... 70s Setting up libwayland-client0:amd64 (1.23.1-3) ... 70s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 70s Setting up gir1.2-graphene-1.0:amd64 (1.10.8-5) ... 70s Setting up libfabric1:amd64 (1.17.0-3.1) ... 70s Setting up liblapack3:amd64 (3.12.1-2) ... 70s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 70s Setting up libssm2:amd64 (1.4.0-2build1) ... 70s Setting up fontconfig-config (2.15.0-2.2ubuntu1) ... 70s Setting up libxcursor1:amd64 (1:1.2.3-1) ... 70s Setting up dconf-service (0.40.0-5) ... 70s Setting up libharfbuzz-gobject0:amd64 (10.2.0-1) ... 70s Setting up libhwloc-plugins:amd64 (2.12.0-1) ... 70s Setting up libmaeparser1:amd64 (1.3.1-1build1) ... 70s Setting up libthai0:amd64 (0.1.29-2build1) ... 70s Setting up libvorbisfile3:amd64 (1.3.7-2) ... 70s Setting up libpmix2t64:amd64 (5.0.6-5) ... 70s Setting up python3-numpy (1:2.2.3+ds-5) ... 71s Setting up libtiff6:amd64 (4.7.0-3ubuntu1) ... 71s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 71s Setting up libharfbuzz-subset0:amd64 (10.2.0-1) ... 71s Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... 71s Setting up libfontconfig1:amd64 (2.15.0-2.2ubuntu1) ... 71s Setting up coot-data (1.1.15+dfsg-1) ... 71s Setting up gtk-update-icon-cache (4.18.4+ds-1) ... 71s Setting up fontconfig (2.15.0-2.2ubuntu1) ... 73s Regenerating fonts cache... done. 73s Setting up libxft2:amd64 (2.3.6-1build1) ... 73s Setting up dconf-gsettings-backend:amd64 (0.40.0-5) ... 73s Setting up gir1.2-gdkpixbuf-2.0:amd64 (2.42.12+dfsg-2) ... 73s Setting up libpango-1.0-0:amd64 (1.56.3-1) ... 73s Setting up libcairo2:amd64 (1.18.4-1) ... 74s Setting up libamdhip64-5 (5.7.1-5.1) ... 74s Setting up adwaita-icon-theme (48.0-1) ... 74s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 74s Setting up libcairo-gobject2:amd64 (1.18.4-1) ... 74s Setting up libgtk-4-common (4.18.4+ds-1) ... 74s Setting up libpangoft2-1.0-0:amd64 (1.56.3-1) ... 74s Setting up libpangocairo-1.0-0:amd64 (1.56.3-1) ... 74s Setting up libcairo-script-interpreter2:amd64 (1.18.4-1) ... 74s Setting up libucx0:amd64 (1.18.1+ds-2) ... 74s Setting up gir1.2-freedesktop:amd64 (1.84.0-1) ... 74s Setting up libpangoxft-1.0-0:amd64 (1.56.3-1) ... 74s Setting up librdkit1t64 (202409.6-2) ... 74s Setting up gir1.2-harfbuzz-0.0:amd64 (10.2.0-1) ... 74s Setting up gir1.2-pango-1.0:amd64 (1.56.3-1) ... 74s Setting up python3-rdkit (202409.6-2) ... 74s Setting up libopenmpi40:amd64 (5.0.7-1) ... 74s Setting up sfftw2 (2.1.5-7build1) ... 74s Setting up libclipper2:amd64 (2.1.20201109-2build1) ... 74s Setting up libcootapi1.1 (1.1.15+dfsg-1) ... 74s Setting up libcootapi-dev (1.1.15+dfsg-1) ... 74s Processing triggers for libc-bin (2.41-6ubuntu1) ... 74s Processing triggers for man-db (2.13.0-1) ... 74s Processing triggers for libglib2.0-0t64:amd64 (2.84.1-1) ... 74s Setting up libgtk-4-1:amd64 (4.18.4+ds-1) ... 74s Setting up gir1.2-gtk-4.0:amd64 (4.18.4+ds-1) ... 74s Setting up coot (1.1.15+dfsg-1) ... 75s Processing triggers for libc-bin (2.41-6ubuntu1) ... 76s autopkgtest [13:19:22]: test command1: coot --self-test 76s autopkgtest [13:19:22]: test command1: [----------------------- 76s INFO:: Running internal self tests 79s INFO:: Test Clipper core : OK 79s INFO:: Test Clipper contrib: OK 79s run_internal_tests() --------- we have 8 internal test functionns 79s Entering test: kevin's torsion test 79s PASS: kevin's torsion test 79s Entering test: test_alt_conf_rotamers 79s DEBUG:: get_atom_selection() with file "/usr/share/coot/data/tutorial-modern.pdb" use_gemmi: 0 79s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 79s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 79s chis.size() 2 (should be 2) 79s DEBUG:: i_rot 0 chi: alt-conf: A chi-1: 65.911 79s DEBUG:: i_rot 1 chi: alt-conf: B chi-1: -144.68 79s For residue 80 chis size 1 79s residue 80 chis: -56.8781 -80.8484 79s PASS: test_alt_conf_rotamers 79s Entering test: test_fragmemt_atom_selection 79s DEBUG:: get_atom_selection() with file "/usr/share/coot/data/tutorial-modern.pdb" use_gemmi: 0 80s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 80s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 80s ----------------- create_mmdbmanager_from_inverted_atom_selection() 80s n_initial: 1465 n_1: 1401 n_2: 64 80s PASS: test_fragmemt_atom_selection 80s Entering test: test_add_atom 80s DEBUG:: get_atom_selection() with file "/usr/share/coot/data/tutorial-modern.pdb" use_gemmi: 0 80s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 80s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 80s PASS: test_add_atom 80s Entering test: test segid exchange 80s DEBUG:: get_atom_selection() with file "/usr/share/coot/data/tutorial-modern.pdb" use_gemmi: 0 80s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 80s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 80s Test with a rogue segid 80s INFO:: No consistent segids for residue 1 80s PASS: test segid exchange 80s Entering test: test peak search non-close 80s mtz_file_name /usr/share/coot/data/rnasa-1.8-all_refmac1.mtz 80s FFT Reso...0.444444 80s Sampling rate...1.5 80s Grid...Nuvw = ( 132, 160, 80) 80s Cell... Cell (64.897,78.323,38.792, 90, 90, 90) 80s Spacegroup...P 21 21 21 80s There are 2260 peaks and 0 problem peaks 80s PASS: test peak search non-close 80s Entering test: test symop card 80s 1 0 0 80s 0 1 0 80s 0 0 1 80s translations: -1 0 0 80s PASS: test symop card 80s Entering test: SSM sequence alignment output 80s 80s -- 80s Moving: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNR--ESVLPTQSYGYYHEYTVITP--GARTRG 80s Target: ---SGTVCLSALPPEATDTLNLIASDGPFPYSQDG 80s 80s Moving: TRRI.ICGEATQEDY..YTGDHYATFSLIDQTC 80s 80s -- 80s Moving: D 80s Target: --SGTVCLSALPPEATDTLNLIASDGPFPYSQDG 80s 80s -- 80s Moving: DVSGTVCLSALPPEATDTLNIASDGPFPYSQDGVVFQNR--ESVLPQSYG 80s Target: --SGTVCLSALPPEATDTLNIASDGPFPYSQDXXxxxxxxxxxxxxxxxG 80s 80s -- 80s PASS: SSM sequence alignment output 80s autopkgtest [13:19:26]: test command1: -----------------------] 80s autopkgtest [13:19:26]: test command1: - - - - - - - - - - results - - - - - - - - - - 80s command1 PASS 80s autopkgtest [13:19:26]: test command2: preparing testbed 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 81s Starting pkgProblemResolver with broken count: 0 81s Starting 2 pkgProblemResolver with broken count: 0 81s Done 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s autopkgtest [13:19:28]: test command2: pyrogen --help 82s autopkgtest [13:19:28]: test command2: [----------------------- 83s Usage: pyrogen [options] file-or-SMILES 83s if file-or-SMILES has extension ".smi" or ".smiles" then it is treated as a file 83s 83s Options: 83s -h, --help show this help message and exit 83s -c FILE, --mmcif=FILE 83s Make restraints from input mmcif FILE 83s -m FILE, --mol=FILE Make restraints from input sdf/mol FILE 83s -r COMP_ID, --residue-type=COMP_ID 83s Create restraints for this type. Default is LIG 83s -4, --quartet-planes Use 4-atom plane restraints, 83s forces --quartet-hydrogens 83s -H, --quartet-hydrogens 83s Use 4-atom hydrogen plane restraints 83s -b, --no-shift-hydrogen-atoms 83s Stop addition or deletion of Hydrogen atoms for 83s formally-charged atoms 83s -n, --no-mogul Don't run CSD Mogul to update bond and angle 83s restraints 83s -N COMPOUND_NAME, --name=COMPOUND_NAME 83s Compound name 83s -S, --smiles Write the SMILES for the input molecule 83s -t, --tautomers Show SMILES for tautomers, don't generate restraints 83s -T MOGUL_DIR, --tmp-directory=MOGUL_DIR 83s Directory into which the tmp files (e.g. for mogul) 83s are written 83s -d OUTPUT_DIR, --directory=OUTPUT_DIR 83s Directory into which the output files (e.g. mmCIF and 83s PDB) are written 83s -o OUTPUT_POSTFIX, --output-postfix=OUTPUT_POSTFIX 83s string to add to output file names, default is 83s "pyrogen" 83s -p, --picture Additionally output a chemical diagram PNG 83s -P, --preserve-input-coordinates 83s Preserve the inputput coordinates (if possible) 83s -v, --version Print version information 83s -a, --no-match-vs-reference-dictionaries 83s Don't match atom names vs. dictionary molecules 83s (default False) 83s -R DICT_FILES_FOR_NAMES_MATCH, --reference-dictionary-files=DICT_FILES_FOR_NAMES_MATCH 83s Try to match the atom names of the output molecule to 83s this dictionary in these files (comma-separated list) 83s -C COMP_ID_LIST_FOR_NAMES_MATCH, --reference-dictionary-comp-ids=COMP_ID_LIST_FOR_NAMES_MATCH 83s Try to match the atom names of the output molecule to 83s these comp-ids (comma-separated list) 83s -w, --wwPDB Fetch the wwPDB ligand definition and use that 83s -f FETCH (Just) fetch from the PDBe the CCD entry for the given 83s compound-id 83s -q, --quiet print less messages 83s autopkgtest [13:19:29]: test command2: -----------------------] 83s command2 PASS 83s autopkgtest [13:19:29]: test command2: - - - - - - - - - - results - - - - - - - - - - 84s autopkgtest [13:19:30]: @@@@@@@@@@@@@@@@@@@@ summary 84s command1 PASS 84s command2 PASS 123s nova [W] Skipping flock for amd64 123s Creating nova instance adt-questing-amd64-coot-20250503-131806-juju-7f2275-prod-proposed-migration-environment-20-aa1b250e-dc29-4e37-a66f-b5653cff6573 from image adt/ubuntu-questing-amd64-server-20250502.img (UUID 8201ee40-745e-4033-979b-719f9e8a69e6)... 123s nova [W] Timed out waiting for 1d1693a3-516c-4ff4-93ba-b728e3748ac8 to get deleted.