0s autopkgtest [13:10:28]: starting date and time: 2025-05-03 13:10:28+0000 0s autopkgtest [13:10:28]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [13:10:28]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ddp8vfla/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-55.secgroup --name adt-questing-arm64-coot-20250503-131028-juju-7f2275-prod-proposed-migration-environment-2-29aaab0c-b804-46e0-b3e3-82b75963c3bf --image adt/ubuntu-questing-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 103s autopkgtest [13:12:11]: testbed dpkg architecture: arm64 104s autopkgtest [13:12:12]: testbed apt version: 3.0.0 104s autopkgtest [13:12:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup 104s autopkgtest [13:12:12]: testbed release detected to be: None 105s autopkgtest [13:12:13]: updating testbed package index (apt update) 105s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 106s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 106s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 106s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 106s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [38.8 kB] 106s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [150 kB] 106s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1597 kB] 106s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 Packages [186 kB] 106s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 Packages [1466 kB] 106s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse arm64 Packages [33.0 kB] 107s Fetched 3580 kB in 1s (3165 kB/s) 108s Reading package lists... 108s autopkgtest [13:12:16]: upgrading testbed (apt dist-upgrade and autopurge) 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 110s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 110s Starting 2 pkgProblemResolver with broken count: 0 110s Done 111s Entering ResolveByKeep 111s 111s Calculating upgrade... 112s The following packages will be upgraded: 112s libmbim-glib4 libmbim-proxy libpython3.12-minimal libpython3.12-stdlib 112s libpython3.12t64 libqmi-glib5 libqmi-proxy 112s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s Need to get 6306 kB of archives. 112s After this operation, 217 kB disk space will be freed. 112s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 libmbim-proxy arm64 1.32.0-1 [6218 B] 112s Get:2 http://ftpmaster.internal/ubuntu questing/main arm64 libmbim-glib4 arm64 1.32.0-1 [225 kB] 112s Get:3 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 libpython3.12t64 arm64 3.12.10-1 [2314 kB] 112s Get:4 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 libpython3.12-stdlib arm64 3.12.10-1 [2029 kB] 113s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 libpython3.12-minimal arm64 3.12.10-1 [836 kB] 113s Get:6 http://ftpmaster.internal/ubuntu questing/main arm64 libqmi-proxy arm64 1.36.0-1 [6190 B] 113s Get:7 http://ftpmaster.internal/ubuntu questing/main arm64 libqmi-glib5 arm64 1.36.0-1 [889 kB] 113s Fetched 6306 kB in 1s (7282 kB/s) 114s (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 ... 117821 files and directories currently installed.) 114s Preparing to unpack .../0-libmbim-proxy_1.32.0-1_arm64.deb ... 114s Unpacking libmbim-proxy (1.32.0-1) over (1.31.2-0ubuntu4) ... 114s Preparing to unpack .../1-libmbim-glib4_1.32.0-1_arm64.deb ... 114s Unpacking libmbim-glib4:arm64 (1.32.0-1) over (1.31.2-0ubuntu4) ... 114s Preparing to unpack .../2-libpython3.12t64_3.12.10-1_arm64.deb ... 114s Unpacking libpython3.12t64:arm64 (3.12.10-1) over (3.12.8-3) ... 114s Preparing to unpack .../3-libpython3.12-stdlib_3.12.10-1_arm64.deb ... 114s Unpacking libpython3.12-stdlib:arm64 (3.12.10-1) over (3.12.8-3) ... 114s Preparing to unpack .../4-libpython3.12-minimal_3.12.10-1_arm64.deb ... 114s Unpacking libpython3.12-minimal:arm64 (3.12.10-1) over (3.12.8-3) ... 114s Preparing to unpack .../5-libqmi-proxy_1.36.0-1_arm64.deb ... 114s Unpacking libqmi-proxy (1.36.0-1) over (1.35.6-1) ... 114s Preparing to unpack .../6-libqmi-glib5_1.36.0-1_arm64.deb ... 114s Unpacking libqmi-glib5:arm64 (1.36.0-1) over (1.35.6-1) ... 115s Setting up libpython3.12-minimal:arm64 (3.12.10-1) ... 115s Setting up libmbim-glib4:arm64 (1.32.0-1) ... 115s Setting up libpython3.12-stdlib:arm64 (3.12.10-1) ... 115s Setting up libmbim-proxy (1.32.0-1) ... 115s Setting up libpython3.12t64:arm64 (3.12.10-1) ... 115s Setting up libqmi-glib5:arm64 (1.36.0-1) ... 115s Setting up libqmi-proxy (1.36.0-1) ... 115s Processing triggers for libc-bin (2.41-6ubuntu1) ... 115s Reading package lists... 116s Building dependency tree... 116s Reading state information... 117s Starting pkgProblemResolver with broken count: 0 117s Starting 2 pkgProblemResolver with broken count: 0 117s Done 118s Solving dependencies... 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s autopkgtest [13:12:30]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Sun Apr 6 14:37:51 UTC 2025 122s autopkgtest [13:12:30]: @@@@@@@@@@@@@@@@@@@@ apt-source coot 132s Get:1 http://ftpmaster.internal/ubuntu questing-proposed/universe coot 1.1.15+dfsg-1 (dsc) [2998 B] 132s Get:2 http://ftpmaster.internal/ubuntu questing-proposed/universe coot 1.1.15+dfsg-1 (tar) [89.2 MB] 132s Get:3 http://ftpmaster.internal/ubuntu questing-proposed/universe coot 1.1.15+dfsg-1 (diff) [53.6 kB] 132s gpgv: Signature made Wed Apr 2 13:41:35 2025 UTC 132s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 132s gpgv: issuer "merkys@debian.org" 132s gpgv: Can't check signature: No public key 132s dpkg-source: warning: cannot verify inline signature for ./coot_1.1.15+dfsg-1.dsc: no acceptable signature found 135s autopkgtest [13:12:43]: testing package coot version 1.1.15+dfsg-1 136s autopkgtest [13:12:44]: build not needed 144s autopkgtest [13:12:52]: test command1: preparing testbed 144s Reading package lists... 145s Building dependency tree... 145s Reading state information... 145s Starting pkgProblemResolver with broken count: 0 146s Starting 2 pkgProblemResolver with broken count: 0 146s Done 147s The following NEW packages will be installed: 147s adwaita-icon-theme coot coot-data coot-doc dconf-gsettings-backend 147s dconf-service fontconfig fontconfig-config fonts-freefont-ttf 147s fonts-noto-core fonts-noto-mono gir1.2-freedesktop gir1.2-gdkpixbuf-2.0 147s gir1.2-graphene-1.0 gir1.2-gtk-4.0 gir1.2-harfbuzz-0.0 gir1.2-pango-1.0 147s gtk-update-icon-cache hicolor-icon-theme libamd-comgr2 libamdhip64-5 147s libasound2-data libasound2t64 libblas3 libboost-iostreams1.83.0 147s libboost-numpy1.83.0 libboost-python1.83.0 libboost-serialization1.83.0 147s libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libccp4-data 147s libccp4c0t64 libclipper2 libcoordgen3 libcootapi-dev libcootapi1.1 147s libcpdb-frontend2t64 libcpdb2t64 libdatrie1 libdconf1 libdeflate0 libepoxy0 147s libevent-pthreads-2.1-7t64 libfabric1 libfontconfig1 libgdk-pixbuf-2.0-0 147s libgdk-pixbuf2.0-common libgfortran5 libgles2 libglvnd0 libgomp1 147s libgraphene-1.0-0 libgraphite2-3 libgsl28 libgslcblas0 libgtk-4-1 147s libgtk-4-common libharfbuzz-gobject0 libharfbuzz-subset0 libharfbuzz0b 147s libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 147s libibumad3 libinchi1.07 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 147s libllvm17t64 libmaeparser1 libmmdb2-0 libmunge2 libogg0 libopenmpi40 147s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpangoxft-1.0-0 147s libpciaccess0 libpixman-1-0 libpmix2t64 librdkit1t64 librdmacm1t64 147s libsharpyuv0 libssm2 libthai-data libthai0 libtiff6 libucx0 libvorbis0a 147s libvorbisfile3 libvulkan1 libwayland-client0 libwayland-egl1 libwebp7 147s libxcb-render0 libxcb-shm0 libxcursor1 libxdamage1 libxfixes3 libxft2 libxi6 147s libxinerama1 libxnvctrl0 libxrandr2 libxrender1 ocl-icd-libopencl1 147s python3-numpy python3-numpy-dev python3-rdkit rdkit-data refmac-dictionary 147s sfftw2 ttf-bitstream-vera 147s 0 upgraded, 119 newly installed, 0 to remove and 0 not upgraded. 147s Need to get 162 MB of archives. 147s After this operation, 818 MB of additional disk space will be used. 147s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 148s Get:2 http://ftpmaster.internal/ubuntu questing/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 148s Get:3 http://ftpmaster.internal/ubuntu questing/main arm64 libgfortran5 arm64 15-20250404-0ubuntu1 [444 kB] 148s Get:4 http://ftpmaster.internal/ubuntu questing/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 148s Get:5 http://ftpmaster.internal/ubuntu questing/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 149s Get:6 http://ftpmaster.internal/ubuntu questing/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [8004 B] 149s Get:7 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 149s Get:8 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 149s Get:9 http://ftpmaster.internal/ubuntu questing/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 149s Get:10 http://ftpmaster.internal/ubuntu questing/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 149s Get:11 http://ftpmaster.internal/ubuntu questing/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 149s Get:12 http://ftpmaster.internal/ubuntu questing/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 149s Get:13 http://ftpmaster.internal/ubuntu questing/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 149s Get:14 http://ftpmaster.internal/ubuntu questing/main arm64 libtiff6 arm64 4.7.0-3ubuntu1 [197 kB] 149s Get:15 http://ftpmaster.internal/ubuntu questing/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-2 [147 kB] 149s Get:16 http://ftpmaster.internal/ubuntu questing/main arm64 gtk-update-icon-cache arm64 4.18.4+ds-1 [53.0 kB] 149s Get:17 http://ftpmaster.internal/ubuntu questing/main arm64 hicolor-icon-theme all 0.18-2 [13.3 kB] 149s Get:18 http://ftpmaster.internal/ubuntu questing/main arm64 adwaita-icon-theme all 48.0-1 [578 kB] 149s Get:19 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-noto-mono all 20201225-2 [435 kB] 149s Get:20 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-noto-core all 20201225-2 [13.3 MB] 150s Get:21 http://ftpmaster.internal/ubuntu questing/universe arm64 ttf-bitstream-vera all 1.10-8.2 [244 kB] 150s Get:22 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 coot-data all 1.1.15+dfsg-1 [11.8 MB] 151s Get:23 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-freefont-ttf all 20211204+svn4273-2 [5641 kB] 151s Get:24 http://ftpmaster.internal/ubuntu questing/main arm64 fontconfig-config arm64 2.15.0-2.2ubuntu1 [37.9 kB] 151s Get:25 http://ftpmaster.internal/ubuntu questing/main arm64 libfontconfig1 arm64 2.15.0-2.2ubuntu1 [144 kB] 151s Get:26 http://ftpmaster.internal/ubuntu questing/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 151s Get:27 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 151s Get:28 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 151s Get:29 http://ftpmaster.internal/ubuntu questing/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 151s Get:30 http://ftpmaster.internal/ubuntu questing/main arm64 libcairo2 arm64 1.18.4-1 [560 kB] 151s Get:31 http://ftpmaster.internal/ubuntu questing/main arm64 libcairo-gobject2 arm64 1.18.4-1 [127 kB] 151s Get:32 http://ftpmaster.internal/ubuntu questing/main arm64 gir1.2-freedesktop arm64 1.84.0-1 [65.0 kB] 151s Get:33 http://ftpmaster.internal/ubuntu questing/main arm64 gir1.2-gdkpixbuf-2.0 arm64 2.42.12+dfsg-2 [9382 B] 151s Get:34 http://ftpmaster.internal/ubuntu questing/main arm64 libgraphene-1.0-0 arm64 1.10.8-5 [48.0 kB] 151s Get:35 http://ftpmaster.internal/ubuntu questing/main arm64 gir1.2-graphene-1.0 arm64 1.10.8-5 [11.1 kB] 151s Get:36 http://ftpmaster.internal/ubuntu questing/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 151s Get:37 http://ftpmaster.internal/ubuntu questing/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 151s Get:38 http://ftpmaster.internal/ubuntu questing/main arm64 libharfbuzz-gobject0 arm64 10.2.0-1 [34.2 kB] 151s Get:39 http://ftpmaster.internal/ubuntu questing/main arm64 gir1.2-harfbuzz-0.0 arm64 10.2.0-1 [45.0 kB] 151s Get:40 http://ftpmaster.internal/ubuntu questing/main arm64 fontconfig arm64 2.15.0-2.2ubuntu1 [191 kB] 151s Get:41 http://ftpmaster.internal/ubuntu questing/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 151s Get:42 http://ftpmaster.internal/ubuntu questing/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 151s Get:43 http://ftpmaster.internal/ubuntu questing/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 151s Get:44 http://ftpmaster.internal/ubuntu questing/main arm64 libpango-1.0-0 arm64 1.56.3-1 [238 kB] 151s Get:45 http://ftpmaster.internal/ubuntu questing/main arm64 libpangoft2-1.0-0 arm64 1.56.3-1 [49.8 kB] 151s Get:46 http://ftpmaster.internal/ubuntu questing/main arm64 libpangocairo-1.0-0 arm64 1.56.3-1 [27.6 kB] 151s Get:47 http://ftpmaster.internal/ubuntu questing/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 151s Get:48 http://ftpmaster.internal/ubuntu questing/main arm64 libpangoxft-1.0-0 arm64 1.56.3-1 [20.1 kB] 151s Get:49 http://ftpmaster.internal/ubuntu questing/main arm64 gir1.2-pango-1.0 arm64 1.56.3-1 [34.6 kB] 151s Get:50 http://ftpmaster.internal/ubuntu questing/main arm64 libcairo-script-interpreter2 arm64 1.18.4-1 [61.5 kB] 151s Get:51 http://ftpmaster.internal/ubuntu questing/main arm64 libcpdb2t64 arm64 2.0~b7-0ubuntu3 [31.1 kB] 151s Get:52 http://ftpmaster.internal/ubuntu questing/main arm64 libcpdb-frontend2t64 arm64 2.0~b7-0ubuntu3 [22.1 kB] 151s Get:53 http://ftpmaster.internal/ubuntu questing/main arm64 libepoxy0 arm64 1.5.10-2 [236 kB] 151s Get:54 http://ftpmaster.internal/ubuntu questing/main arm64 libharfbuzz-subset0 arm64 10.2.0-1 [502 kB] 151s Get:55 http://ftpmaster.internal/ubuntu questing/main arm64 libvulkan1 arm64 1.4.304.0-1 [158 kB] 151s Get:56 http://ftpmaster.internal/ubuntu questing/main arm64 libwayland-client0 arm64 1.23.1-3 [27.0 kB] 151s Get:57 http://ftpmaster.internal/ubuntu questing/main arm64 libwayland-egl1 arm64 1.23.1-3 [6180 B] 151s Get:58 http://ftpmaster.internal/ubuntu questing/main arm64 libxfixes3 arm64 1:6.0.0-2build1 [11.2 kB] 151s Get:59 http://ftpmaster.internal/ubuntu questing/main arm64 libxcursor1 arm64 1:1.2.3-1 [22.2 kB] 151s Get:60 http://ftpmaster.internal/ubuntu questing/main arm64 libxdamage1 arm64 1:1.1.6-1build1 [6236 B] 151s Get:61 http://ftpmaster.internal/ubuntu questing/main arm64 libxi6 arm64 2:1.8.2-1 [32.4 kB] 151s Get:62 http://ftpmaster.internal/ubuntu questing/main arm64 libxinerama1 arm64 2:1.1.4-3build1 [6394 B] 151s Get:63 http://ftpmaster.internal/ubuntu questing/main arm64 libxrandr2 arm64 2:1.5.4-1 [19.6 kB] 151s Get:64 http://ftpmaster.internal/ubuntu questing/main arm64 libglvnd0 arm64 1.7.0-1build1 [60.6 kB] 151s Get:65 http://ftpmaster.internal/ubuntu questing/main arm64 libgles2 arm64 1.7.0-1build1 [17.6 kB] 151s Get:66 http://ftpmaster.internal/ubuntu questing/main arm64 libdconf1 arm64 0.40.0-5 [40.0 kB] 151s Get:67 http://ftpmaster.internal/ubuntu questing/main arm64 dconf-service arm64 0.40.0-5 [27.1 kB] 151s Get:68 http://ftpmaster.internal/ubuntu questing/main arm64 dconf-gsettings-backend arm64 0.40.0-5 [22.3 kB] 151s Get:69 http://ftpmaster.internal/ubuntu questing/main arm64 libgtk-4-common all 4.18.4+ds-1 [1514 kB] 151s Get:70 http://ftpmaster.internal/ubuntu questing/main arm64 libgtk-4-1 arm64 4.18.4+ds-1 [3194 kB] 152s Get:71 http://ftpmaster.internal/ubuntu questing/main arm64 gir1.2-gtk-4.0 arm64 4.18.4+ds-1 [218 kB] 152s Get:72 http://ftpmaster.internal/ubuntu questing/universe arm64 rdkit-data all 202409.6-2 [12.6 MB] 152s Get:73 http://ftpmaster.internal/ubuntu questing/main arm64 libboost-python1.83.0 arm64 1.83.0-4.2ubuntu1 [309 kB] 152s Get:74 http://ftpmaster.internal/ubuntu questing/universe arm64 libboost-numpy1.83.0 arm64 1.83.0-4.2ubuntu1 [242 kB] 152s Get:75 http://ftpmaster.internal/ubuntu questing/universe arm64 libboost-serialization1.83.0 arm64 1.83.0-4.2ubuntu1 [338 kB] 152s Get:76 http://ftpmaster.internal/ubuntu questing/universe arm64 libcoordgen3 arm64 3.0.2-1 [207 kB] 152s Get:77 http://ftpmaster.internal/ubuntu questing/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-4.2ubuntu1 [259 kB] 153s Get:78 http://ftpmaster.internal/ubuntu questing/universe arm64 libinchi1.07 arm64 1.07.3+dfsg-1 [573 kB] 153s Get:79 http://ftpmaster.internal/ubuntu questing/universe arm64 libmaeparser1 arm64 1.3.1-1build1 [84.5 kB] 153s Get:80 http://ftpmaster.internal/ubuntu questing/universe arm64 librdkit1t64 arm64 202409.6-2 [5378 kB] 153s Get:81 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-rdkit arm64 202409.6-2 [4679 kB] 153s Get:82 http://ftpmaster.internal/ubuntu questing/universe arm64 refmac-dictionary all 5.41-3 [16.7 MB] 154s Get:83 http://ftpmaster.internal/ubuntu questing/main arm64 libasound2-data all 1.2.13-1build1 [21.1 kB] 154s Get:84 http://ftpmaster.internal/ubuntu questing/main arm64 libasound2t64 arm64 1.2.13-1build1 [390 kB] 154s Get:85 http://ftpmaster.internal/ubuntu questing/universe arm64 libccp4-data all 8.0.0-4 [65.2 kB] 154s Get:86 http://ftpmaster.internal/ubuntu questing/universe arm64 libccp4c0t64 arm64 8.0.0-4 [93.5 kB] 154s Get:87 http://ftpmaster.internal/ubuntu questing/universe arm64 libmmdb2-0 arm64 2.0.22-1 [347 kB] 154s Get:88 http://ftpmaster.internal/ubuntu questing/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10 [7922 B] 154s Get:89 http://ftpmaster.internal/ubuntu questing/main arm64 librdmacm1t64 arm64 56.0-4ubuntu1 [71.4 kB] 154s Get:90 http://ftpmaster.internal/ubuntu questing/universe arm64 libfabric1 arm64 1.17.0-3.1 [542 kB] 154s Get:91 http://ftpmaster.internal/ubuntu questing/universe arm64 libhwloc15 arm64 2.12.0-1 [162 kB] 154s Get:92 http://ftpmaster.internal/ubuntu questing/universe arm64 libmunge2 arm64 0.5.16-1 [15.2 kB] 154s Get:93 http://ftpmaster.internal/ubuntu questing/main arm64 libpciaccess0 arm64 0.17-3build1 [18.9 kB] 154s Get:94 http://ftpmaster.internal/ubuntu questing/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu4 [12.4 kB] 154s Get:95 http://ftpmaster.internal/ubuntu questing/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1build1 [37.6 kB] 154s Get:96 http://ftpmaster.internal/ubuntu questing/universe arm64 libhwloc-plugins arm64 2.12.0-1 [15.9 kB] 154s Get:97 http://ftpmaster.internal/ubuntu questing/universe arm64 libpmix2t64 arm64 5.0.6-5 [666 kB] 154s Get:98 http://ftpmaster.internal/ubuntu questing/universe arm64 libllvm17t64 arm64 1:17.0.6-21 [24.9 MB] 156s Get:99 http://ftpmaster.internal/ubuntu questing/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3build2 [14.1 MB] 156s Get:100 http://ftpmaster.internal/ubuntu questing/universe arm64 libhsakmt1 arm64 5.7.0-1build1 [63.6 kB] 156s Get:101 http://ftpmaster.internal/ubuntu questing/universe arm64 libhsa-runtime64-1 arm64 5.7.1-2build1 [286 kB] 157s Get:102 http://ftpmaster.internal/ubuntu questing/universe arm64 libamdhip64-5 arm64 5.7.1-5.1 [9707 kB] 157s Get:103 http://ftpmaster.internal/ubuntu questing/main arm64 libgomp1 arm64 15-20250404-0ubuntu1 [147 kB] 157s Get:104 http://ftpmaster.internal/ubuntu questing/main arm64 libibumad3 arm64 56.0-4ubuntu1 [31.3 kB] 157s Get:105 http://ftpmaster.internal/ubuntu questing/main arm64 libibmad5 arm64 56.0-4ubuntu1 [44.1 kB] 157s Get:106 http://ftpmaster.internal/ubuntu questing/universe arm64 libucx0 arm64 1.18.1+ds-2 [1161 kB] 158s Get:107 http://ftpmaster.internal/ubuntu questing/universe arm64 libopenmpi40 arm64 5.0.7-1 [2419 kB] 158s Get:108 http://ftpmaster.internal/ubuntu questing/universe arm64 sfftw2 arm64 2.1.5-7build1 [184 kB] 158s Get:109 http://ftpmaster.internal/ubuntu questing/universe arm64 libclipper2 arm64 2.1.20201109-2build1 [1150 kB] 158s Get:110 http://ftpmaster.internal/ubuntu questing/universe arm64 libgslcblas0 arm64 2.8+dfsg-5ubuntu1 [87.4 kB] 158s Get:111 http://ftpmaster.internal/ubuntu questing/universe arm64 libgsl28 arm64 2.8+dfsg-5ubuntu1 [982 kB] 158s Get:112 http://ftpmaster.internal/ubuntu questing/universe arm64 libssm2 arm64 1.4.0-2build1 [83.8 kB] 158s Get:113 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 libcootapi1.1 arm64 1.1.15+dfsg-1 [3669 kB] 158s Get:114 http://ftpmaster.internal/ubuntu questing/main arm64 libogg0 arm64 1.3.5-3build1 [22.6 kB] 158s Get:115 http://ftpmaster.internal/ubuntu questing/main arm64 libvorbis0a arm64 1.3.7-2 [95.0 kB] 158s Get:116 http://ftpmaster.internal/ubuntu questing/main arm64 libvorbisfile3 arm64 1.3.7-2 [17.1 kB] 158s Get:117 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 coot arm64 1.1.15+dfsg-1 [8249 kB] 158s Get:118 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 coot-doc all 1.1.15+dfsg-1 [2049 kB] 158s Get:119 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 libcootapi-dev arm64 1.1.15+dfsg-1 [23.9 kB] 159s Fetched 162 MB in 11s (14.6 MB/s) 159s Selecting previously unselected package python3-numpy-dev:arm64. 159s (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 ... 117821 files and directories currently installed.) 159s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 159s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 159s Selecting previously unselected package libblas3:arm64. 159s Preparing to unpack .../001-libblas3_3.12.1-2_arm64.deb ... 159s Unpacking libblas3:arm64 (3.12.1-2) ... 159s Selecting previously unselected package libgfortran5:arm64. 159s Preparing to unpack .../002-libgfortran5_15-20250404-0ubuntu1_arm64.deb ... 159s Unpacking libgfortran5:arm64 (15-20250404-0ubuntu1) ... 159s Selecting previously unselected package liblapack3:arm64. 159s Preparing to unpack .../003-liblapack3_3.12.1-2_arm64.deb ... 159s Unpacking liblapack3:arm64 (3.12.1-2) ... 159s Selecting previously unselected package python3-numpy. 159s Preparing to unpack .../004-python3-numpy_1%3a2.2.3+ds-5_arm64.deb ... 159s Unpacking python3-numpy (1:2.2.3+ds-5) ... 160s Selecting previously unselected package libgdk-pixbuf2.0-common. 160s Preparing to unpack .../005-libgdk-pixbuf2.0-common_2.42.12+dfsg-2_all.deb ... 160s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... 160s Selecting previously unselected package libjpeg-turbo8:arm64. 160s Preparing to unpack .../006-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 160s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 160s Selecting previously unselected package libjpeg8:arm64. 160s Preparing to unpack .../007-libjpeg8_8c-2ubuntu11_arm64.deb ... 160s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 160s Selecting previously unselected package libdeflate0:arm64. 160s Preparing to unpack .../008-libdeflate0_1.23-2_arm64.deb ... 160s Unpacking libdeflate0:arm64 (1.23-2) ... 160s Selecting previously unselected package libjbig0:arm64. 160s Preparing to unpack .../009-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 160s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 160s Selecting previously unselected package liblerc4:arm64. 160s Preparing to unpack .../010-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 160s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 160s Selecting previously unselected package libsharpyuv0:arm64. 160s Preparing to unpack .../011-libsharpyuv0_1.5.0-0.1_arm64.deb ... 160s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 160s Selecting previously unselected package libwebp7:arm64. 160s Preparing to unpack .../012-libwebp7_1.5.0-0.1_arm64.deb ... 160s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 160s Selecting previously unselected package libtiff6:arm64. 160s Preparing to unpack .../013-libtiff6_4.7.0-3ubuntu1_arm64.deb ... 160s Unpacking libtiff6:arm64 (4.7.0-3ubuntu1) ... 160s Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64. 160s Preparing to unpack .../014-libgdk-pixbuf-2.0-0_2.42.12+dfsg-2_arm64.deb ... 160s Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-2) ... 160s Selecting previously unselected package gtk-update-icon-cache. 160s Preparing to unpack .../015-gtk-update-icon-cache_4.18.4+ds-1_arm64.deb ... 160s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 160s 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. 160s Unpacking gtk-update-icon-cache (4.18.4+ds-1) ... 160s Selecting previously unselected package hicolor-icon-theme. 160s Preparing to unpack .../016-hicolor-icon-theme_0.18-2_all.deb ... 160s Unpacking hicolor-icon-theme (0.18-2) ... 160s Selecting previously unselected package adwaita-icon-theme. 160s Preparing to unpack .../017-adwaita-icon-theme_48.0-1_all.deb ... 160s Unpacking adwaita-icon-theme (48.0-1) ... 161s Selecting previously unselected package fonts-noto-mono. 161s Preparing to unpack .../018-fonts-noto-mono_20201225-2_all.deb ... 161s Unpacking fonts-noto-mono (20201225-2) ... 161s Selecting previously unselected package fonts-noto-core. 161s Preparing to unpack .../019-fonts-noto-core_20201225-2_all.deb ... 161s Unpacking fonts-noto-core (20201225-2) ... 161s Selecting previously unselected package ttf-bitstream-vera. 161s Preparing to unpack .../020-ttf-bitstream-vera_1.10-8.2_all.deb ... 161s Unpacking ttf-bitstream-vera (1.10-8.2) ... 161s Selecting previously unselected package coot-data. 161s Preparing to unpack .../021-coot-data_1.1.15+dfsg-1_all.deb ... 161s Unpacking coot-data (1.1.15+dfsg-1) ... 162s Selecting previously unselected package fonts-freefont-ttf. 162s Preparing to unpack .../022-fonts-freefont-ttf_20211204+svn4273-2_all.deb ... 162s Unpacking fonts-freefont-ttf (20211204+svn4273-2) ... 162s Selecting previously unselected package fontconfig-config. 162s Preparing to unpack .../023-fontconfig-config_2.15.0-2.2ubuntu1_arm64.deb ... 162s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 162s Selecting previously unselected package libfontconfig1:arm64. 162s Preparing to unpack .../024-libfontconfig1_2.15.0-2.2ubuntu1_arm64.deb ... 162s Unpacking libfontconfig1:arm64 (2.15.0-2.2ubuntu1) ... 162s Selecting previously unselected package libpixman-1-0:arm64. 162s Preparing to unpack .../025-libpixman-1-0_0.44.0-3_arm64.deb ... 162s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 162s Selecting previously unselected package libxcb-render0:arm64. 162s Preparing to unpack .../026-libxcb-render0_1.17.0-2_arm64.deb ... 162s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 162s Selecting previously unselected package libxcb-shm0:arm64. 162s Preparing to unpack .../027-libxcb-shm0_1.17.0-2_arm64.deb ... 162s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 162s Selecting previously unselected package libxrender1:arm64. 162s Preparing to unpack .../028-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 162s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 163s Selecting previously unselected package libcairo2:arm64. 163s Preparing to unpack .../029-libcairo2_1.18.4-1_arm64.deb ... 163s Unpacking libcairo2:arm64 (1.18.4-1) ... 163s Selecting previously unselected package libcairo-gobject2:arm64. 163s Preparing to unpack .../030-libcairo-gobject2_1.18.4-1_arm64.deb ... 163s Unpacking libcairo-gobject2:arm64 (1.18.4-1) ... 163s Selecting previously unselected package gir1.2-freedesktop:arm64. 163s Preparing to unpack .../031-gir1.2-freedesktop_1.84.0-1_arm64.deb ... 163s Unpacking gir1.2-freedesktop:arm64 (1.84.0-1) ... 163s Selecting previously unselected package gir1.2-gdkpixbuf-2.0:arm64. 163s Preparing to unpack .../032-gir1.2-gdkpixbuf-2.0_2.42.12+dfsg-2_arm64.deb ... 163s Unpacking gir1.2-gdkpixbuf-2.0:arm64 (2.42.12+dfsg-2) ... 163s Selecting previously unselected package libgraphene-1.0-0:arm64. 163s Preparing to unpack .../033-libgraphene-1.0-0_1.10.8-5_arm64.deb ... 163s Unpacking libgraphene-1.0-0:arm64 (1.10.8-5) ... 163s Selecting previously unselected package gir1.2-graphene-1.0:arm64. 163s Preparing to unpack .../034-gir1.2-graphene-1.0_1.10.8-5_arm64.deb ... 163s Unpacking gir1.2-graphene-1.0:arm64 (1.10.8-5) ... 163s Selecting previously unselected package libgraphite2-3:arm64. 163s Preparing to unpack .../035-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 163s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 163s Selecting previously unselected package libharfbuzz0b:arm64. 163s Preparing to unpack .../036-libharfbuzz0b_10.2.0-1_arm64.deb ... 163s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 163s Selecting previously unselected package libharfbuzz-gobject0:arm64. 163s Preparing to unpack .../037-libharfbuzz-gobject0_10.2.0-1_arm64.deb ... 163s Unpacking libharfbuzz-gobject0:arm64 (10.2.0-1) ... 163s Selecting previously unselected package gir1.2-harfbuzz-0.0:arm64. 163s Preparing to unpack .../038-gir1.2-harfbuzz-0.0_10.2.0-1_arm64.deb ... 163s Unpacking gir1.2-harfbuzz-0.0:arm64 (10.2.0-1) ... 163s Selecting previously unselected package fontconfig. 163s Preparing to unpack .../039-fontconfig_2.15.0-2.2ubuntu1_arm64.deb ... 163s Unpacking fontconfig (2.15.0-2.2ubuntu1) ... 163s Selecting previously unselected package libthai-data. 163s Preparing to unpack .../040-libthai-data_0.1.29-2build1_all.deb ... 163s Unpacking libthai-data (0.1.29-2build1) ... 163s Selecting previously unselected package libdatrie1:arm64. 163s Preparing to unpack .../041-libdatrie1_0.2.13-3build1_arm64.deb ... 163s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 163s Selecting previously unselected package libthai0:arm64. 163s Preparing to unpack .../042-libthai0_0.1.29-2build1_arm64.deb ... 163s Unpacking libthai0:arm64 (0.1.29-2build1) ... 164s Selecting previously unselected package libpango-1.0-0:arm64. 164s Preparing to unpack .../043-libpango-1.0-0_1.56.3-1_arm64.deb ... 164s Unpacking libpango-1.0-0:arm64 (1.56.3-1) ... 164s Selecting previously unselected package libpangoft2-1.0-0:arm64. 164s Preparing to unpack .../044-libpangoft2-1.0-0_1.56.3-1_arm64.deb ... 164s Unpacking libpangoft2-1.0-0:arm64 (1.56.3-1) ... 164s Selecting previously unselected package libpangocairo-1.0-0:arm64. 164s Preparing to unpack .../045-libpangocairo-1.0-0_1.56.3-1_arm64.deb ... 164s Unpacking libpangocairo-1.0-0:arm64 (1.56.3-1) ... 164s Selecting previously unselected package libxft2:arm64. 164s Preparing to unpack .../046-libxft2_2.3.6-1build1_arm64.deb ... 164s Unpacking libxft2:arm64 (2.3.6-1build1) ... 164s Selecting previously unselected package libpangoxft-1.0-0:arm64. 164s Preparing to unpack .../047-libpangoxft-1.0-0_1.56.3-1_arm64.deb ... 164s Unpacking libpangoxft-1.0-0:arm64 (1.56.3-1) ... 164s Selecting previously unselected package gir1.2-pango-1.0:arm64. 164s Preparing to unpack .../048-gir1.2-pango-1.0_1.56.3-1_arm64.deb ... 164s Unpacking gir1.2-pango-1.0:arm64 (1.56.3-1) ... 164s Selecting previously unselected package libcairo-script-interpreter2:arm64. 164s Preparing to unpack .../049-libcairo-script-interpreter2_1.18.4-1_arm64.deb ... 164s Unpacking libcairo-script-interpreter2:arm64 (1.18.4-1) ... 164s Selecting previously unselected package libcpdb2t64:arm64. 164s Preparing to unpack .../050-libcpdb2t64_2.0~b7-0ubuntu3_arm64.deb ... 164s Unpacking libcpdb2t64:arm64 (2.0~b7-0ubuntu3) ... 164s Selecting previously unselected package libcpdb-frontend2t64:arm64. 164s Preparing to unpack .../051-libcpdb-frontend2t64_2.0~b7-0ubuntu3_arm64.deb ... 164s Unpacking libcpdb-frontend2t64:arm64 (2.0~b7-0ubuntu3) ... 164s Selecting previously unselected package libepoxy0:arm64. 164s Preparing to unpack .../052-libepoxy0_1.5.10-2_arm64.deb ... 164s Unpacking libepoxy0:arm64 (1.5.10-2) ... 164s Selecting previously unselected package libharfbuzz-subset0:arm64. 164s Preparing to unpack .../053-libharfbuzz-subset0_10.2.0-1_arm64.deb ... 164s Unpacking libharfbuzz-subset0:arm64 (10.2.0-1) ... 164s Selecting previously unselected package libvulkan1:arm64. 164s Preparing to unpack .../054-libvulkan1_1.4.304.0-1_arm64.deb ... 164s Unpacking libvulkan1:arm64 (1.4.304.0-1) ... 164s Selecting previously unselected package libwayland-client0:arm64. 164s Preparing to unpack .../055-libwayland-client0_1.23.1-3_arm64.deb ... 164s Unpacking libwayland-client0:arm64 (1.23.1-3) ... 164s Selecting previously unselected package libwayland-egl1:arm64. 164s Preparing to unpack .../056-libwayland-egl1_1.23.1-3_arm64.deb ... 164s Unpacking libwayland-egl1:arm64 (1.23.1-3) ... 164s Selecting previously unselected package libxfixes3:arm64. 164s Preparing to unpack .../057-libxfixes3_1%3a6.0.0-2build1_arm64.deb ... 164s Unpacking libxfixes3:arm64 (1:6.0.0-2build1) ... 164s Selecting previously unselected package libxcursor1:arm64. 164s Preparing to unpack .../058-libxcursor1_1%3a1.2.3-1_arm64.deb ... 164s Unpacking libxcursor1:arm64 (1:1.2.3-1) ... 164s Selecting previously unselected package libxdamage1:arm64. 165s Preparing to unpack .../059-libxdamage1_1%3a1.1.6-1build1_arm64.deb ... 165s Unpacking libxdamage1:arm64 (1:1.1.6-1build1) ... 165s Selecting previously unselected package libxi6:arm64. 165s Preparing to unpack .../060-libxi6_2%3a1.8.2-1_arm64.deb ... 165s Unpacking libxi6:arm64 (2:1.8.2-1) ... 165s Selecting previously unselected package libxinerama1:arm64. 165s Preparing to unpack .../061-libxinerama1_2%3a1.1.4-3build1_arm64.deb ... 165s Unpacking libxinerama1:arm64 (2:1.1.4-3build1) ... 165s Selecting previously unselected package libxrandr2:arm64. 165s Preparing to unpack .../062-libxrandr2_2%3a1.5.4-1_arm64.deb ... 165s Unpacking libxrandr2:arm64 (2:1.5.4-1) ... 165s Selecting previously unselected package libglvnd0:arm64. 165s Preparing to unpack .../063-libglvnd0_1.7.0-1build1_arm64.deb ... 165s Unpacking libglvnd0:arm64 (1.7.0-1build1) ... 165s Selecting previously unselected package libgles2:arm64. 165s Preparing to unpack .../064-libgles2_1.7.0-1build1_arm64.deb ... 165s Unpacking libgles2:arm64 (1.7.0-1build1) ... 165s Selecting previously unselected package libdconf1:arm64. 165s Preparing to unpack .../065-libdconf1_0.40.0-5_arm64.deb ... 165s Unpacking libdconf1:arm64 (0.40.0-5) ... 165s Selecting previously unselected package dconf-service. 165s Preparing to unpack .../066-dconf-service_0.40.0-5_arm64.deb ... 165s Unpacking dconf-service (0.40.0-5) ... 165s Selecting previously unselected package dconf-gsettings-backend:arm64. 165s Preparing to unpack .../067-dconf-gsettings-backend_0.40.0-5_arm64.deb ... 165s Unpacking dconf-gsettings-backend:arm64 (0.40.0-5) ... 165s Selecting previously unselected package libgtk-4-common. 165s Preparing to unpack .../068-libgtk-4-common_4.18.4+ds-1_all.deb ... 165s Unpacking libgtk-4-common (4.18.4+ds-1) ... 165s Selecting previously unselected package libgtk-4-1:arm64. 165s Preparing to unpack .../069-libgtk-4-1_4.18.4+ds-1_arm64.deb ... 165s Unpacking libgtk-4-1:arm64 (4.18.4+ds-1) ... 165s Selecting previously unselected package gir1.2-gtk-4.0:arm64. 165s Preparing to unpack .../070-gir1.2-gtk-4.0_4.18.4+ds-1_arm64.deb ... 165s Unpacking gir1.2-gtk-4.0:arm64 (4.18.4+ds-1) ... 165s Selecting previously unselected package rdkit-data. 165s Preparing to unpack .../071-rdkit-data_202409.6-2_all.deb ... 165s Unpacking rdkit-data (202409.6-2) ... 166s Selecting previously unselected package libboost-python1.83.0. 166s Preparing to unpack .../072-libboost-python1.83.0_1.83.0-4.2ubuntu1_arm64.deb ... 166s Unpacking libboost-python1.83.0 (1.83.0-4.2ubuntu1) ... 166s Selecting previously unselected package libboost-numpy1.83.0. 166s Preparing to unpack .../073-libboost-numpy1.83.0_1.83.0-4.2ubuntu1_arm64.deb ... 166s Unpacking libboost-numpy1.83.0 (1.83.0-4.2ubuntu1) ... 166s Selecting previously unselected package libboost-serialization1.83.0:arm64. 166s Preparing to unpack .../074-libboost-serialization1.83.0_1.83.0-4.2ubuntu1_arm64.deb ... 166s Unpacking libboost-serialization1.83.0:arm64 (1.83.0-4.2ubuntu1) ... 166s Selecting previously unselected package libcoordgen3:arm64. 166s Preparing to unpack .../075-libcoordgen3_3.0.2-1_arm64.deb ... 166s Unpacking libcoordgen3:arm64 (3.0.2-1) ... 166s Selecting previously unselected package libboost-iostreams1.83.0:arm64. 166s Preparing to unpack .../076-libboost-iostreams1.83.0_1.83.0-4.2ubuntu1_arm64.deb ... 166s Unpacking libboost-iostreams1.83.0:arm64 (1.83.0-4.2ubuntu1) ... 166s Selecting previously unselected package libinchi1.07. 166s Preparing to unpack .../077-libinchi1.07_1.07.3+dfsg-1_arm64.deb ... 166s Unpacking libinchi1.07 (1.07.3+dfsg-1) ... 166s Selecting previously unselected package libmaeparser1:arm64. 166s Preparing to unpack .../078-libmaeparser1_1.3.1-1build1_arm64.deb ... 166s Unpacking libmaeparser1:arm64 (1.3.1-1build1) ... 166s Selecting previously unselected package librdkit1t64. 166s Preparing to unpack .../079-librdkit1t64_202409.6-2_arm64.deb ... 166s Unpacking librdkit1t64 (202409.6-2) ... 167s Selecting previously unselected package python3-rdkit. 167s Preparing to unpack .../080-python3-rdkit_202409.6-2_arm64.deb ... 167s Unpacking python3-rdkit (202409.6-2) ... 167s Selecting previously unselected package refmac-dictionary. 167s Preparing to unpack .../081-refmac-dictionary_5.41-3_all.deb ... 167s Unpacking refmac-dictionary (5.41-3) ... 169s Selecting previously unselected package libasound2-data. 169s Preparing to unpack .../082-libasound2-data_1.2.13-1build1_all.deb ... 169s Unpacking libasound2-data (1.2.13-1build1) ... 169s Selecting previously unselected package libasound2t64:arm64. 169s Preparing to unpack .../083-libasound2t64_1.2.13-1build1_arm64.deb ... 169s Unpacking libasound2t64:arm64 (1.2.13-1build1) ... 169s Selecting previously unselected package libccp4-data. 169s Preparing to unpack .../084-libccp4-data_8.0.0-4_all.deb ... 169s Unpacking libccp4-data (8.0.0-4) ... 169s Selecting previously unselected package libccp4c0t64:arm64. 169s Preparing to unpack .../085-libccp4c0t64_8.0.0-4_arm64.deb ... 169s Unpacking libccp4c0t64:arm64 (8.0.0-4) ... 169s Selecting previously unselected package libmmdb2-0:arm64. 169s Preparing to unpack .../086-libmmdb2-0_2.0.22-1_arm64.deb ... 169s Unpacking libmmdb2-0:arm64 (2.0.22-1) ... 169s Selecting previously unselected package libevent-pthreads-2.1-7t64:arm64. 169s Preparing to unpack .../087-libevent-pthreads-2.1-7t64_2.1.12-stable-10_arm64.deb ... 169s Unpacking libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ... 169s Selecting previously unselected package librdmacm1t64:arm64. 169s Preparing to unpack .../088-librdmacm1t64_56.0-4ubuntu1_arm64.deb ... 169s Unpacking librdmacm1t64:arm64 (56.0-4ubuntu1) ... 169s Selecting previously unselected package libfabric1:arm64. 169s Preparing to unpack .../089-libfabric1_1.17.0-3.1_arm64.deb ... 169s Unpacking libfabric1:arm64 (1.17.0-3.1) ... 169s Selecting previously unselected package libhwloc15:arm64. 170s Preparing to unpack .../090-libhwloc15_2.12.0-1_arm64.deb ... 170s Unpacking libhwloc15:arm64 (2.12.0-1) ... 170s Selecting previously unselected package libmunge2:arm64. 170s Preparing to unpack .../091-libmunge2_0.5.16-1_arm64.deb ... 170s Unpacking libmunge2:arm64 (0.5.16-1) ... 170s Selecting previously unselected package libpciaccess0:arm64. 170s Preparing to unpack .../092-libpciaccess0_0.17-3build1_arm64.deb ... 170s Unpacking libpciaccess0:arm64 (0.17-3build1) ... 170s Selecting previously unselected package libxnvctrl0:arm64. 170s Preparing to unpack .../093-libxnvctrl0_510.47.03-0ubuntu4_arm64.deb ... 170s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 170s Selecting previously unselected package ocl-icd-libopencl1:arm64. 170s Preparing to unpack .../094-ocl-icd-libopencl1_2.3.2-1build1_arm64.deb ... 170s Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1build1) ... 170s Selecting previously unselected package libhwloc-plugins:arm64. 170s Preparing to unpack .../095-libhwloc-plugins_2.12.0-1_arm64.deb ... 170s Unpacking libhwloc-plugins:arm64 (2.12.0-1) ... 170s Selecting previously unselected package libpmix2t64:arm64. 170s Preparing to unpack .../096-libpmix2t64_5.0.6-5_arm64.deb ... 170s Unpacking libpmix2t64:arm64 (5.0.6-5) ... 170s Selecting previously unselected package libllvm17t64:arm64. 170s Preparing to unpack .../097-libllvm17t64_1%3a17.0.6-21_arm64.deb ... 170s Unpacking libllvm17t64:arm64 (1:17.0.6-21) ... 171s Selecting previously unselected package libamd-comgr2:arm64. 171s Preparing to unpack .../098-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_arm64.deb ... 171s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ... 172s Selecting previously unselected package libhsakmt1:arm64. 172s Preparing to unpack .../099-libhsakmt1_5.7.0-1build1_arm64.deb ... 172s Unpacking libhsakmt1:arm64 (5.7.0-1build1) ... 172s Selecting previously unselected package libhsa-runtime64-1. 172s Preparing to unpack .../100-libhsa-runtime64-1_5.7.1-2build1_arm64.deb ... 172s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 172s Selecting previously unselected package libamdhip64-5. 172s Preparing to unpack .../101-libamdhip64-5_5.7.1-5.1_arm64.deb ... 172s Unpacking libamdhip64-5 (5.7.1-5.1) ... 172s Selecting previously unselected package libgomp1:arm64. 172s Preparing to unpack .../102-libgomp1_15-20250404-0ubuntu1_arm64.deb ... 172s Unpacking libgomp1:arm64 (15-20250404-0ubuntu1) ... 172s Selecting previously unselected package libibumad3:arm64. 172s Preparing to unpack .../103-libibumad3_56.0-4ubuntu1_arm64.deb ... 172s Unpacking libibumad3:arm64 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fonts-freefont-ttf (20211204+svn4273-2) ... 174s Setting up libcpdb2t64:arm64 (2.0~b7-0ubuntu3) ... 174s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 174s Setting up libibmad5:arm64 (56.0-4ubuntu1) ... 174s Setting up libcpdb-frontend2t64:arm64 (2.0~b7-0ubuntu3) ... 174s Setting up libccp4-data (8.0.0-4) ... 174s Setting up libgomp1:arm64 (15-20250404-0ubuntu1) ... 174s Setting up rdkit-data (202409.6-2) ... 174s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 174s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 174s Setting up refmac-dictionary (5.41-3) ... 174s Setting up libdconf1:arm64 (0.40.0-5) ... 174s Setting up libasound2-data (1.2.13-1build1) ... 174s Setting up libboost-serialization1.83.0:arm64 (1.83.0-4.2ubuntu1) ... 174s Setting up libboost-numpy1.83.0 (1.83.0-4.2ubuntu1) ... 174s Setting up libblas3:arm64 (3.12.1-2) ... 174s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 174s Setting up libgles2:arm64 (1.7.0-1build1) ... 174s Setting up libasound2t64:arm64 (1.2.13-1build1) ... 174s Setting up libmunge2:arm64 (0.5.16-1) ... 174s Setting up libllvm17t64:arm64 (1:17.0.6-21) ... 174s Setting up libepoxy0:arm64 (1.5.10-2) ... 174s Setting up libxfixes3:arm64 (1:6.0.0-2build1) ... 174s Setting up libboost-iostreams1.83.0:arm64 (1.83.0-4.2ubuntu1) ... 174s Setting up libxinerama1:arm64 (2:1.1.4-3build1) ... 174s Setting up libhwloc15:arm64 (2.12.0-1) ... 174s Setting up python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 174s Setting up libvorbis0a:arm64 (1.3.7-2) ... 174s Setting up libxrandr2:arm64 (2:1.5.4-1) ... 174s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 174s Setting up libgfortran5:arm64 (15-20250404-0ubuntu1) ... 174s Setting up libvulkan1:arm64 (1.4.304.0-1) ... 174s Setting up libwebp7:arm64 (1.5.0-0.1) ... 174s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1build1) ... 174s Setting up libccp4c0t64:arm64 (8.0.0-4) ... 174s Setting up librdmacm1t64:arm64 (56.0-4ubuntu1) ... 174s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 174s Setting up libthai-data (0.1.29-2build1) ... 174s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ... 174s Setting up libwayland-egl1:arm64 (1.23.1-3) ... 174s Setting up libcoordgen3:arm64 (3.0.2-1) ... 174s Setting up libgsl28:arm64 (2.8+dfsg-5ubuntu1) ... 174s Setting up libinchi1.07 (1.07.3+dfsg-1) ... 174s Setting up fonts-noto-core (20201225-2) ... 174s Setting up libhsakmt1:arm64 (5.7.0-1build1) ... 174s Setting up libgraphene-1.0-0:arm64 (1.10.8-5) ... 174s Setting up libwayland-client0:arm64 (1.23.1-3) ... 174s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 174s Setting up gir1.2-graphene-1.0:arm64 (1.10.8-5) ... 174s Setting up libfabric1:arm64 (1.17.0-3.1) ... 174s Setting up liblapack3:arm64 (3.12.1-2) ... 174s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 174s Setting up libssm2:arm64 (1.4.0-2build1) ... 174s Setting up fontconfig-config (2.15.0-2.2ubuntu1) ... 174s Setting up libxcursor1:arm64 (1:1.2.3-1) ... 174s Setting up dconf-service (0.40.0-5) ... 174s Setting up libharfbuzz-gobject0:arm64 (10.2.0-1) ... 174s Setting up libhwloc-plugins:arm64 (2.12.0-1) ... 174s Setting up libmaeparser1:arm64 (1.3.1-1build1) ... 174s Setting up libthai0:arm64 (0.1.29-2build1) ... 174s Setting up libvorbisfile3:arm64 (1.3.7-2) ... 174s Setting up libpmix2t64:arm64 (5.0.6-5) ... 174s Setting up python3-numpy (1:2.2.3+ds-5) ... 177s Setting up libtiff6:arm64 (4.7.0-3ubuntu1) ... 177s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 177s Setting up libharfbuzz-subset0:arm64 (10.2.0-1) ... 177s Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-2) ... 177s Setting up libfontconfig1:arm64 (2.15.0-2.2ubuntu1) ... 177s Setting up coot-data (1.1.15+dfsg-1) ... 177s Setting up gtk-update-icon-cache (4.18.4+ds-1) ... 177s Setting up fontconfig (2.15.0-2.2ubuntu1) ... 179s Regenerating fonts cache... done. 179s Setting up libxft2:arm64 (2.3.6-1build1) ... 179s Setting up dconf-gsettings-backend:arm64 (0.40.0-5) ... 179s Setting up gir1.2-gdkpixbuf-2.0:arm64 (2.42.12+dfsg-2) ... 179s Setting up libpango-1.0-0:arm64 (1.56.3-1) ... 179s Setting up libcairo2:arm64 (1.18.4-1) ... 179s Setting up libamdhip64-5 (5.7.1-5.1) ... 179s Setting up adwaita-icon-theme (48.0-1) ... 179s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 179s Setting up libcairo-gobject2:arm64 (1.18.4-1) ... 179s Setting up libgtk-4-common (4.18.4+ds-1) ... 179s Setting up libpangoft2-1.0-0:arm64 (1.56.3-1) ... 179s Setting up libpangocairo-1.0-0:arm64 (1.56.3-1) ... 179s Setting up libcairo-script-interpreter2:arm64 (1.18.4-1) ... 179s Setting up libucx0:arm64 (1.18.1+ds-2) ... 179s Setting up gir1.2-freedesktop:arm64 (1.84.0-1) ... 179s Setting up libpangoxft-1.0-0:arm64 (1.56.3-1) ... 179s Setting up librdkit1t64 (202409.6-2) ... 179s Setting up gir1.2-harfbuzz-0.0:arm64 (10.2.0-1) ... 179s Setting up gir1.2-pango-1.0:arm64 (1.56.3-1) ... 179s Setting up python3-rdkit (202409.6-2) ... 180s Setting up libopenmpi40:arm64 (5.0.7-1) ... 180s Setting up sfftw2 (2.1.5-7build1) ... 180s Setting up libclipper2:arm64 (2.1.20201109-2build1) ... 180s Setting up libcootapi1.1 (1.1.15+dfsg-1) ... 180s Setting up libcootapi-dev (1.1.15+dfsg-1) ... 180s Processing triggers for libc-bin (2.41-6ubuntu1) ... 180s Processing triggers for man-db (2.13.0-1) ... 181s Processing triggers for libglib2.0-0t64:arm64 (2.84.1-1) ... 182s Setting up libgtk-4-1:arm64 (4.18.4+ds-1) ... 182s Setting up gir1.2-gtk-4.0:arm64 (4.18.4+ds-1) ... 182s Setting up coot (1.1.15+dfsg-1) ... 182s Processing triggers for libc-bin (2.41-6ubuntu1) ... 184s autopkgtest [13:13:32]: test command1: coot --self-test 184s autopkgtest [13:13:32]: test command1: [----------------------- 185s INFO:: Running internal self tests 189s INFO:: Test Clipper core : OK 189s INFO:: Test Clipper contrib: OK 189s run_internal_tests() --------- we have 8 internal test functionns 189s Entering test: kevin's torsion test 189s PASS: kevin's torsion test 189s Entering test: test_alt_conf_rotamers 189s DEBUG:: get_atom_selection() with file "/usr/share/coot/data/tutorial-modern.pdb" use_gemmi: 0 189s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 189s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 189s chis.size() 2 (should be 2) 189s DEBUG:: i_rot 0 chi: alt-conf: A chi-1: 65.911 189s DEBUG:: i_rot 1 chi: alt-conf: B chi-1: -144.68 189s For residue 80 chis size 1 189s residue 80 chis: -56.8781 -80.8484 189s PASS: test_alt_conf_rotamers 189s Entering test: test_fragmemt_atom_selection 189s DEBUG:: get_atom_selection() with file "/usr/share/coot/data/tutorial-modern.pdb" use_gemmi: 0 189s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 189s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 189s ----------------- create_mmdbmanager_from_inverted_atom_selection() 189s n_initial: 1465 n_1: 1401 n_2: 64 189s PASS: test_fragmemt_atom_selection 189s Entering test: test_add_atom 189s DEBUG:: get_atom_selection() with file "/usr/share/coot/data/tutorial-modern.pdb" use_gemmi: 0 189s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 189s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 189s PASS: test_add_atom 189s Entering test: test segid exchange 189s DEBUG:: get_atom_selection() with file "/usr/share/coot/data/tutorial-modern.pdb" use_gemmi: 0 189s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 189s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 189s Test with a rogue segid 189s INFO:: No consistent segids for residue 1 189s PASS: test segid exchange 189s Entering test: test peak search non-close 189s mtz_file_name /usr/share/coot/data/rnasa-1.8-all_refmac1.mtz 190s FFT Reso...0.444444 190s Sampling rate...1.5 190s Grid...Nuvw = ( 132, 160, 80) 190s Cell... Cell (64.897,78.323,38.792, 90, 90, 90) 190s Spacegroup...P 21 21 21 190s There are 2260 peaks and 0 problem peaks 190s PASS: test peak search non-close 190s Entering test: test symop card 190s 1 0 0 190s 0 1 0 190s 0 0 1 190s translations: -1 0 0 190s PASS: test symop card 190s Entering test: SSM sequence alignment output 190s 190s -- 190s Moving: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNR--ESVLPTQSYGYYHEYTVITP--GARTRG 190s Target: ---SGTVCLSALPPEATDTLNLIASDGPFPYSQDG 190s 190s Moving: TRRI.ICGEATQEDY..YTGDHYATFSLIDQTC 190s 190s -- 190s Moving: D 190s Target: --SGTVCLSALPPEATDTLNLIASDGPFPYSQDG 190s 190s -- 190s Moving: DVSGTVCLSALPPEATDTLNIASDGPFPYSQDGVVFQNR--ESVLPQSYG 190s Target: --SGTVCLSALPPEATDTLNIASDGPFPYSQDXXxxxxxxxxxxxxxxxG 190s 190s -- 190s PASS: SSM sequence alignment output 190s autopkgtest [13:13:38]: test command1: -----------------------] 190s command1 PASS 190s autopkgtest [13:13:38]: test command1: - - - - - - - - - - results - - - - - - - - - - 191s autopkgtest [13:13:39]: test command2: preparing testbed 191s Reading package lists... 192s Building dependency tree... 192s Reading state information... 193s Starting pkgProblemResolver with broken count: 0 193s Starting 2 pkgProblemResolver with broken count: 0 193s Done 194s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 196s autopkgtest [13:13:44]: test command2: pyrogen --help 196s autopkgtest [13:13:44]: test command2: [----------------------- 197s Usage: pyrogen [options] file-or-SMILES 197s if file-or-SMILES has extension ".smi" or ".smiles" then it is treated as a file 197s 197s Options: 197s -h, --help show this help message and exit 197s -c FILE, --mmcif=FILE 197s Make restraints from input mmcif FILE 197s -m FILE, --mol=FILE Make restraints from input sdf/mol FILE 197s -r COMP_ID, --residue-type=COMP_ID 197s Create restraints for this type. Default is LIG 197s -4, --quartet-planes Use 4-atom plane restraints, 197s forces --quartet-hydrogens 197s -H, --quartet-hydrogens 197s Use 4-atom hydrogen plane restraints 197s -b, --no-shift-hydrogen-atoms 197s Stop addition or deletion of Hydrogen atoms for 197s formally-charged atoms 197s -n, --no-mogul Don't run CSD Mogul to update bond and angle 197s restraints 197s -N COMPOUND_NAME, --name=COMPOUND_NAME 197s Compound name 197s -S, --smiles Write the SMILES for the input molecule 197s -t, --tautomers Show SMILES for tautomers, don't generate restraints 197s -T MOGUL_DIR, --tmp-directory=MOGUL_DIR 197s Directory into which the tmp files (e.g. for mogul) 197s are written 197s -d OUTPUT_DIR, --directory=OUTPUT_DIR 197s Directory into which the output files (e.g. mmCIF and 197s PDB) are written 197s -o OUTPUT_POSTFIX, --output-postfix=OUTPUT_POSTFIX 197s string to add to output file names, default is 197s "pyrogen" 197s -p, --picture Additionally output a chemical diagram PNG 197s -P, --preserve-input-coordinates 197s Preserve the inputput coordinates (if possible) 197s -v, --version Print version information 197s -a, --no-match-vs-reference-dictionaries 197s Don't match atom names vs. dictionary molecules 197s (default False) 197s -R DICT_FILES_FOR_NAMES_MATCH, --reference-dictionary-files=DICT_FILES_FOR_NAMES_MATCH 197s Try to match the atom names of the output molecule to 197s this dictionary in these files (comma-separated list) 197s -C COMP_ID_LIST_FOR_NAMES_MATCH, --reference-dictionary-comp-ids=COMP_ID_LIST_FOR_NAMES_MATCH 197s Try to match the atom names of the output molecule to 197s these comp-ids (comma-separated list) 197s -w, --wwPDB Fetch the wwPDB ligand definition and use that 197s -f FETCH (Just) fetch from the PDBe the CCD entry for the given 197s compound-id 197s -q, --quiet print less messages 197s autopkgtest [13:13:45]: test command2: -----------------------] 198s autopkgtest [13:13:46]: test command2: - - - - - - - - - - results - - - - - - - - - - 198s command2 PASS 198s autopkgtest [13:13:46]: @@@@@@@@@@@@@@@@@@@@ summary 198s command1 PASS 198s command2 PASS 217s nova [W] Using flock in prodstack6-arm64 217s Creating nova instance adt-questing-arm64-coot-20250503-131028-juju-7f2275-prod-proposed-migration-environment-2-29aaab0c-b804-46e0-b3e3-82b75963c3bf from image adt/ubuntu-questing-arm64-server-20250503.img (UUID ddf52c76-fc5c-4398-9b9f-46f48d819d2e)... 217s nova [W] Timed out waiting for 26c3676d-5a43-4422-8531-440a3db21b59 to get deleted.