0s autopkgtest [09:34:43]: starting date and time: 2024-12-03 09:34:43+0000
  0s autopkgtest [09:34:43]: git checkout: be626eda Fix armhf LXD image generation for plucky
  0s autopkgtest [09:34:43]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.b_qhb24z/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:rdkit --apt-upgrade coot --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=rdkit/202409.2-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-9.secgroup --name adt-plucky-arm64-coot-20241203-093441-juju-7f2275-prod-proposed-migration-environment-20-b6533985-ce1f-4b9e-a86e-2f65e245dbb6 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
238s autopkgtest [09:38:41]: testbed dpkg architecture: arm64
238s autopkgtest [09:38:41]: testbed apt version: 2.9.14ubuntu1
238s autopkgtest [09:38:41]: @@@@@@@@@@@@@@@@@@@@ test bed setup
239s autopkgtest [09:38:42]: testbed release detected to be: None
239s autopkgtest [09:38:42]: updating testbed package index (apt update)
240s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
240s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
240s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
240s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
240s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B]
240s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.1 kB]
240s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [781 kB]
240s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [65.3 kB]
240s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [145 kB]
240s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [58.2 kB]
240s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [669 kB]
240s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [21.3 kB]
241s Fetched 1838 kB in 1s (1971 kB/s)
242s Reading package lists...
243s Reading package lists...
243s Building dependency tree...
243s Reading state information...
244s Calculating upgrade...
244s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
244s Reading package lists...
245s Building dependency tree...
245s Reading state information...
245s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
245s autopkgtest [09:38:48]: upgrading testbed (apt dist-upgrade and autopurge)
246s Reading package lists...
246s Building dependency tree...
246s Reading state information...
247s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
247s Starting 2 pkgProblemResolver with broken count: 0
247s Done
248s Entering ResolveByKeep
248s 
248s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
249s Reading package lists...
249s Building dependency tree...
249s Reading state information...
249s Starting pkgProblemResolver with broken count: 0
249s Starting 2 pkgProblemResolver with broken count: 0
249s Done
250s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
253s autopkgtest [09:38:56]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024
253s autopkgtest [09:38:56]: @@@@@@@@@@@@@@@@@@@@ apt-source coot
261s Get:1 http://ftpmaster.internal/ubuntu plucky/universe coot 1.1.09+dfsg-2build1 (dsc) [2941 B]
261s Get:2 http://ftpmaster.internal/ubuntu plucky/universe coot 1.1.09+dfsg-2build1 (tar) [88.5 MB]
261s Get:3 http://ftpmaster.internal/ubuntu plucky/universe coot 1.1.09+dfsg-2build1 (diff) [52.5 kB]
262s gpgv: Signature made Tue Jul 30 06:28:58 2024 UTC
262s gpgv:                using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9
262s gpgv: Can't check signature: No public key
262s dpkg-source: warning: cannot verify inline signature for ./coot_1.1.09+dfsg-2build1.dsc: no acceptable signature found
265s autopkgtest [09:39:08]: testing package coot version 1.1.09+dfsg-2build1
266s autopkgtest [09:39:09]: build not needed
273s autopkgtest [09:39:16]: test command1: preparing testbed
274s Reading package lists...
274s Building dependency tree...
274s Reading state information...
274s Starting pkgProblemResolver with broken count: 0
274s Starting 2 pkgProblemResolver with broken count: 0
274s Done
275s The following NEW packages will be installed:
275s   adwaita-icon-theme coot coot-data coot-doc dconf-gsettings-backend
275s   dconf-service fontconfig fontconfig-config fonts-freefont-ttf
275s   fonts-noto-core fonts-noto-mono gir1.2-freedesktop gir1.2-gdkpixbuf-2.0
275s   gir1.2-graphene-1.0 gir1.2-gtk-4.0 gir1.2-harfbuzz-0.0 gir1.2-pango-1.0
275s   gtk-update-icon-cache hicolor-icon-theme humanity-icon-theme libamd-comgr2
275s   libamdhip64-5 libasound2-data libasound2t64 libblas3
275s   libboost-iostreams1.83.0 libboost-numpy1.83.0 libboost-python1.83.0
275s   libboost-serialization1.83.0 libcairo-gobject2 libcairo-script-interpreter2
275s   libcairo2 libccp4-data libccp4c0t64 libclipper2 libcoordgen3 libcootapi-dev
275s   libcootapi1.1 libcpdb-frontend2t64 libcpdb2t64 libdatrie1 libdconf1
275s   libdeflate0 libepoxy0 libevent-pthreads-2.1-7t64 libfabric1 libfontconfig1
275s   libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgles2 libglvnd0
275s   libgomp1 libgraphene-1.0-0 libgraphite2-3 libgsl28 libgslcblas0 libgtk-4-1
275s   libgtk-4-common libharfbuzz-gobject0 libharfbuzz-subset0 libharfbuzz0b
275s   libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5
275s   libibumad3 libinchi1.07 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4
275s   libllvm17t64 libmaeparser1 libmmdb2-0 libmunge2 libogg0 libopenmpi3t64
275s   libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpangoxft-1.0-0
275s   libpciaccess0 libpixman-1-0 libpmix2t64 librdkit1t64 librdmacm1t64
275s   libsharpyuv0 libssm2 libthai-data libthai0 libtiff6 libucx0 libvorbis0a
275s   libvorbisfile3 libvulkan1 libwayland-client0 libwayland-egl1 libwebp7
275s   libxcb-render0 libxcb-shm0 libxcursor1 libxdamage1 libxfixes3 libxft2 libxi6
275s   libxinerama1 libxnvctrl0 libxrandr2 libxrender1 ocl-icd-libopencl1
275s   python3-numpy python3-rdkit rdkit-data refmac-dictionary sfftw2
275s   ttf-bitstream-vera ubuntu-mono
276s 0 upgraded, 120 newly installed, 0 to remove and 0 not upgraded.
276s Need to get 162 MB of archives.
276s After this operation, 847 MB of additional disk space will be used.
276s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [7888 B]
276s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB]
276s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
276s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB]
276s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB]
276s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB]
276s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB]
276s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB]
276s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB]
276s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-1 [145 kB]
276s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 gtk-update-icon-cache arm64 4.16.5+ds-2 [51.7 kB]
276s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 hicolor-icon-theme all 0.18-1 [13.5 kB]
276s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 humanity-icon-theme all 0.6.16 [1282 kB]
276s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 ubuntu-mono all 24.04-0ubuntu1 [151 kB]
276s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 adwaita-icon-theme all 47.0-2 [525 kB]
276s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-noto-mono all 20201225-2 [435 kB]
276s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-noto-core all 20201225-2 [13.3 MB]
277s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 ttf-bitstream-vera all 1.10-8.2 [244 kB]
277s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 coot-data all 1.1.09+dfsg-2build1 [11.8 MB]
277s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-freefont-ttf all 20211204+svn4273-2 [5641 kB]
277s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB]
277s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB]
277s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB]
277s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB]
277s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B]
277s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB]
277s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB]
277s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo-gobject2 arm64 1.18.2-2 [127 kB]
277s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 gir1.2-freedesktop arm64 1.82.0-2 [64.3 kB]
277s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 gir1.2-gdkpixbuf-2.0 arm64 2.42.12+dfsg-1 [9436 B]
277s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphene-1.0-0 arm64 1.10.8-4 [47.9 kB]
277s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 gir1.2-graphene-1.0 arm64 1.10.8-4 [11.0 kB]
277s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB]
277s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB]
277s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz-gobject0 arm64 10.0.1-1 [34.2 kB]
277s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 gir1.2-harfbuzz-0.0 arm64 10.0.1-1 [45.2 kB]
277s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-1.1ubuntu2 [190 kB]
277s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB]
277s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB]
277s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB]
277s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.54.0+ds-3 [234 kB]
277s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.54.0+ds-3 [48.9 kB]
277s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.54.0+ds-3 [27.5 kB]
277s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB]
277s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoxft-1.0-0 arm64 1.54.0+ds-3 [20.1 kB]
277s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 gir1.2-pango-1.0 arm64 1.54.0+ds-3 [34.5 kB]
277s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo-script-interpreter2 arm64 1.18.2-2 [61.5 kB]
278s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libcpdb2t64 arm64 2.0~b5-1.2build1 [25.8 kB]
278s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libcpdb-frontend2t64 arm64 2.0~b5-1.2build1 [19.8 kB]
278s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libepoxy0 arm64 1.5.10-2 [236 kB]
278s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz-subset0 arm64 10.0.1-1 [500 kB]
278s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libvulkan1 arm64 1.3.296.0-1 [153 kB]
278s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-client0 arm64 1.23.0-1 [26.7 kB]
278s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-egl1 arm64 1.23.0-1 [5636 B]
278s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libxfixes3 arm64 1:6.0.0-2build1 [11.2 kB]
278s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcursor1 arm64 1:1.2.2-1 [21.2 kB]
278s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libxdamage1 arm64 1:1.1.6-1build1 [6236 B]
278s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libxi6 arm64 2:1.8.2-1 [32.4 kB]
278s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libxinerama1 arm64 2:1.1.4-3build1 [6394 B]
278s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrandr2 arm64 2:1.5.4-1 [19.6 kB]
278s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 libglvnd0 arm64 1.7.0-1build1 [60.6 kB]
278s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 libgles2 arm64 1.7.0-1build1 [17.6 kB]
278s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 libdconf1 arm64 0.40.0-4build2 [39.8 kB]
278s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 dconf-service arm64 0.40.0-4build2 [26.9 kB]
278s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 dconf-gsettings-backend arm64 0.40.0-4build2 [22.0 kB]
278s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 libgtk-4-common all 4.16.5+ds-2 [1244 kB]
278s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 libgtk-4-1 arm64 4.16.5+ds-2 [3214 kB]
278s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 gir1.2-gtk-4.0 arm64 4.16.5+ds-2 [214 kB]
278s Get:69 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 rdkit-data all 202409.2-2 [12.6 MB]
278s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-4 [152 kB]
278s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-9ubuntu1 [437 kB]
278s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-4 [2305 kB]
278s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11ubuntu1 [4149 kB]
279s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-python1.83.0 arm64 1.83.0-3.2ubuntu2 [307 kB]
279s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 libboost-numpy1.83.0 arm64 1.83.0-3.2ubuntu2 [241 kB]
279s Get:76 http://ftpmaster.internal/ubuntu plucky/universe arm64 libboost-serialization1.83.0 arm64 1.83.0-3.2ubuntu2 [338 kB]
279s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcoordgen3 arm64 3.0.2-1 [207 kB]
279s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-3.2ubuntu2 [259 kB]
279s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 libinchi1.07 arm64 1.07.1+dfsg-5 [574 kB]
279s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmaeparser1 arm64 1.3.1-1build1 [84.5 kB]
279s Get:81 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 librdkit1t64 arm64 202409.2-2 [5218 kB]
279s Get:82 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-rdkit arm64 202409.2-2 [4513 kB]
279s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 refmac-dictionary all 5.41-3 [16.7 MB]
280s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 libasound2-data all 1.2.12-1 [21.0 kB]
280s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 libasound2t64 arm64 1.2.12-1 [384 kB]
280s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 libccp4-data all 8.0.0-4 [65.2 kB]
280s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 libccp4c0t64 arm64 8.0.0-4 [93.5 kB]
280s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmmdb2-0 arm64 2.0.22-1 [347 kB]
280s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10 [7922 B]
280s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 librdmacm1t64 arm64 52.0-2ubuntu1 [71.5 kB]
280s Get:91 http://ftpmaster.internal/ubuntu plucky/universe arm64 libfabric1 arm64 1.17.0-3ubuntu1 [542 kB]
280s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhwloc15 arm64 2.11.2-1 [162 kB]
280s Get:93 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmunge2 arm64 0.5.15-4build1 [14.9 kB]
280s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 libpciaccess0 arm64 0.17-3build1 [18.9 kB]
280s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu4 [12.4 kB]
280s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1build1 [37.6 kB]
280s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhwloc-plugins arm64 2.11.2-1 [15.8 kB]
280s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpmix2t64 arm64 5.0.4-1 [676 kB]
280s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 libllvm17t64 arm64 1:17.0.6-18 [24.9 MB]
281s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3build2 [14.1 MB]
282s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhsakmt1 arm64 5.7.0-1build1 [63.6 kB]
282s Get:102 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhsa-runtime64-1 arm64 5.7.1-2build1 [286 kB]
282s Get:103 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamdhip64-5 arm64 5.7.1-5 [9704 kB]
283s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-9ubuntu1 [145 kB]
283s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 libibumad3 arm64 52.0-2ubuntu1 [29.3 kB]
283s Get:106 http://ftpmaster.internal/ubuntu plucky/main arm64 libibmad5 arm64 52.0-2ubuntu1 [43.1 kB]
283s Get:107 http://ftpmaster.internal/ubuntu plucky/universe arm64 libucx0 arm64 1.17.0+ds-3build1 [1093 kB]
283s Get:108 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenmpi3t64 arm64 4.1.6-13.3ubuntu2 [2487 kB]
283s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 sfftw2 arm64 2.1.5-7 [184 kB]
283s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 libclipper2 arm64 2.1.20201109-2build1 [1150 kB]
283s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgslcblas0 arm64 2.8+dfsg-5 [87.3 kB]
283s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgsl28 arm64 2.8+dfsg-5 [983 kB]
283s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 libssm2 arm64 1.4.0-2build1 [83.8 kB]
283s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcootapi1.1 arm64 1.1.09+dfsg-2build1 [3196 kB]
283s Get:115 http://ftpmaster.internal/ubuntu plucky/main arm64 libogg0 arm64 1.3.5-3build1 [22.6 kB]
283s Get:116 http://ftpmaster.internal/ubuntu plucky/main arm64 libvorbis0a arm64 1.3.7-2 [95.0 kB]
283s Get:117 http://ftpmaster.internal/ubuntu plucky/main arm64 libvorbisfile3 arm64 1.3.7-2 [17.1 kB]
283s Get:118 http://ftpmaster.internal/ubuntu plucky/universe arm64 coot arm64 1.1.09+dfsg-2build1 [7893 kB]
284s Get:119 http://ftpmaster.internal/ubuntu plucky/universe arm64 coot-doc all 1.1.09+dfsg-2build1 [2048 kB]
284s Get:120 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcootapi-dev arm64 1.1.09+dfsg-2build1 [23.8 kB]
284s Fetched 162 MB in 8s (19.4 MB/s)
284s Selecting previously unselected package libgdk-pixbuf2.0-common.
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285s Preparing to unpack .../000-libgdk-pixbuf2.0-common_2.42.12+dfsg-1_all.deb ...
285s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ...
285s Selecting previously unselected package libjpeg-turbo8:arm64.
285s Preparing to unpack .../001-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ...
285s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ...
285s Selecting previously unselected package libjpeg8:arm64.
285s Preparing to unpack .../002-libjpeg8_8c-2ubuntu11_arm64.deb ...
285s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
285s Selecting previously unselected package libdeflate0:arm64.
285s Preparing to unpack .../003-libdeflate0_1.22-1_arm64.deb ...
285s Unpacking libdeflate0:arm64 (1.22-1) ...
285s Selecting previously unselected package libjbig0:arm64.
285s Preparing to unpack .../004-libjbig0_2.1-6.1ubuntu2_arm64.deb ...
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285s Selecting previously unselected package liblerc4:arm64.
285s Preparing to unpack .../005-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ...
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285s Selecting previously unselected package libsharpyuv0:arm64.
285s Preparing to unpack .../006-libsharpyuv0_1.4.0-0.1_arm64.deb ...
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285s Selecting previously unselected package libwebp7:arm64.
285s Preparing to unpack .../007-libwebp7_1.4.0-0.1_arm64.deb ...
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285s Selecting previously unselected package libtiff6:arm64.
285s Preparing to unpack .../008-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ...
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285s Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64.
285s Preparing to unpack .../009-libgdk-pixbuf-2.0-0_2.42.12+dfsg-1_arm64.deb ...
285s Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-1) ...
285s Selecting previously unselected package gtk-update-icon-cache.
285s Preparing to unpack .../010-gtk-update-icon-cache_4.16.5+ds-2_arm64.deb ...
285s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed.
285s 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.
285s Unpacking gtk-update-icon-cache (4.16.5+ds-2) ...
285s Selecting previously unselected package hicolor-icon-theme.
285s Preparing to unpack .../011-hicolor-icon-theme_0.18-1_all.deb ...
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285s Selecting previously unselected package humanity-icon-theme.
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286s Selecting previously unselected package ubuntu-mono.
286s Preparing to unpack .../013-ubuntu-mono_24.04-0ubuntu1_all.deb ...
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286s Selecting previously unselected package adwaita-icon-theme.
286s Preparing to unpack .../014-adwaita-icon-theme_47.0-2_all.deb ...
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286s Selecting previously unselected package fonts-noto-mono.
286s Preparing to unpack .../015-fonts-noto-mono_20201225-2_all.deb ...
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287s Selecting previously unselected package fonts-noto-core.
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287s Selecting previously unselected package ttf-bitstream-vera.
287s Preparing to unpack .../017-ttf-bitstream-vera_1.10-8.2_all.deb ...
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287s Selecting previously unselected package coot-data.
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287s Selecting previously unselected package fonts-freefont-ttf.
287s Preparing to unpack .../019-fonts-freefont-ttf_20211204+svn4273-2_all.deb ...
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287s Selecting previously unselected package fontconfig-config.
287s Preparing to unpack .../020-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ...
288s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
288s Selecting previously unselected package libfontconfig1:arm64.
288s Preparing to unpack .../021-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ...
288s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ...
288s Selecting previously unselected package libpixman-1-0:arm64.
288s Preparing to unpack .../022-libpixman-1-0_0.44.0-3_arm64.deb ...
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288s Selecting previously unselected package libxcb-render0:arm64.
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288s Selecting previously unselected package libxrender1:arm64.
288s Preparing to unpack .../025-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ...
288s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ...
288s Selecting previously unselected package libcairo2:arm64.
288s Preparing to unpack .../026-libcairo2_1.18.2-2_arm64.deb ...
288s Unpacking libcairo2:arm64 (1.18.2-2) ...
288s Selecting previously unselected package libcairo-gobject2:arm64.
288s Preparing to unpack .../027-libcairo-gobject2_1.18.2-2_arm64.deb ...
288s Unpacking libcairo-gobject2:arm64 (1.18.2-2) ...
288s Selecting previously unselected package gir1.2-freedesktop:arm64.
288s Preparing to unpack .../028-gir1.2-freedesktop_1.82.0-2_arm64.deb ...
288s Unpacking gir1.2-freedesktop:arm64 (1.82.0-2) ...
288s Selecting previously unselected package gir1.2-gdkpixbuf-2.0:arm64.
288s Preparing to unpack .../029-gir1.2-gdkpixbuf-2.0_2.42.12+dfsg-1_arm64.deb ...
288s Unpacking gir1.2-gdkpixbuf-2.0:arm64 (2.42.12+dfsg-1) ...
288s Selecting previously unselected package libgraphene-1.0-0:arm64.
288s Preparing to unpack .../030-libgraphene-1.0-0_1.10.8-4_arm64.deb ...
288s Unpacking libgraphene-1.0-0:arm64 (1.10.8-4) ...
288s Selecting previously unselected package gir1.2-graphene-1.0:arm64.
288s Preparing to unpack .../031-gir1.2-graphene-1.0_1.10.8-4_arm64.deb ...
288s Unpacking gir1.2-graphene-1.0:arm64 (1.10.8-4) ...
288s Selecting previously unselected package libgraphite2-3:arm64.
288s Preparing to unpack .../032-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ...
288s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
288s Selecting previously unselected package libharfbuzz0b:arm64.
288s Preparing to unpack .../033-libharfbuzz0b_10.0.1-1_arm64.deb ...
288s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ...
288s Selecting previously unselected package libharfbuzz-gobject0:arm64.
288s Preparing to unpack .../034-libharfbuzz-gobject0_10.0.1-1_arm64.deb ...
288s Unpacking libharfbuzz-gobject0:arm64 (10.0.1-1) ...
288s Selecting previously unselected package gir1.2-harfbuzz-0.0:arm64.
288s Preparing to unpack .../035-gir1.2-harfbuzz-0.0_10.0.1-1_arm64.deb ...
288s Unpacking gir1.2-harfbuzz-0.0:arm64 (10.0.1-1) ...
288s Selecting previously unselected package fontconfig.
288s Preparing to unpack .../036-fontconfig_2.15.0-1.1ubuntu2_arm64.deb ...
288s Unpacking fontconfig (2.15.0-1.1ubuntu2) ...
288s Selecting previously unselected package libthai-data.
288s Preparing to unpack .../037-libthai-data_0.1.29-2build1_all.deb ...
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288s Selecting previously unselected package libdatrie1:arm64.
288s Preparing to unpack .../038-libdatrie1_0.2.13-3build1_arm64.deb ...
288s Unpacking libdatrie1:arm64 (0.2.13-3build1) ...
289s Selecting previously unselected package libthai0:arm64.
289s Preparing to unpack .../039-libthai0_0.1.29-2build1_arm64.deb ...
289s Unpacking libthai0:arm64 (0.1.29-2build1) ...
289s Selecting previously unselected package libpango-1.0-0:arm64.
289s Preparing to unpack .../040-libpango-1.0-0_1.54.0+ds-3_arm64.deb ...
289s Unpacking libpango-1.0-0:arm64 (1.54.0+ds-3) ...
289s Selecting previously unselected package libpangoft2-1.0-0:arm64.
289s Preparing to unpack .../041-libpangoft2-1.0-0_1.54.0+ds-3_arm64.deb ...
289s Unpacking libpangoft2-1.0-0:arm64 (1.54.0+ds-3) ...
289s Selecting previously unselected package libpangocairo-1.0-0:arm64.
289s Preparing to unpack .../042-libpangocairo-1.0-0_1.54.0+ds-3_arm64.deb ...
289s Unpacking libpangocairo-1.0-0:arm64 (1.54.0+ds-3) ...
289s Selecting previously unselected package libxft2:arm64.
289s Preparing to unpack .../043-libxft2_2.3.6-1build1_arm64.deb ...
289s Unpacking libxft2:arm64 (2.3.6-1build1) ...
289s Selecting previously unselected package libpangoxft-1.0-0:arm64.
289s Preparing to unpack .../044-libpangoxft-1.0-0_1.54.0+ds-3_arm64.deb ...
289s Unpacking libpangoxft-1.0-0:arm64 (1.54.0+ds-3) ...
289s Selecting previously unselected package gir1.2-pango-1.0:arm64.
289s Preparing to unpack .../045-gir1.2-pango-1.0_1.54.0+ds-3_arm64.deb ...
289s Unpacking gir1.2-pango-1.0:arm64 (1.54.0+ds-3) ...
289s Selecting previously unselected package libcairo-script-interpreter2:arm64.
289s Preparing to unpack .../046-libcairo-script-interpreter2_1.18.2-2_arm64.deb ...
289s Unpacking libcairo-script-interpreter2:arm64 (1.18.2-2) ...
289s Selecting previously unselected package libcpdb2t64:arm64.
289s Preparing to unpack .../047-libcpdb2t64_2.0~b5-1.2build1_arm64.deb ...
289s Unpacking libcpdb2t64:arm64 (2.0~b5-1.2build1) ...
289s Selecting previously unselected package libcpdb-frontend2t64:arm64.
289s Preparing to unpack .../048-libcpdb-frontend2t64_2.0~b5-1.2build1_arm64.deb ...
289s Unpacking libcpdb-frontend2t64:arm64 (2.0~b5-1.2build1) ...
289s Selecting previously unselected package libepoxy0:arm64.
289s Preparing to unpack .../049-libepoxy0_1.5.10-2_arm64.deb ...
289s Unpacking libepoxy0:arm64 (1.5.10-2) ...
289s Selecting previously unselected package libharfbuzz-subset0:arm64.
289s Preparing to unpack .../050-libharfbuzz-subset0_10.0.1-1_arm64.deb ...
289s Unpacking libharfbuzz-subset0:arm64 (10.0.1-1) ...
289s Selecting previously unselected package libvulkan1:arm64.
289s Preparing to unpack .../051-libvulkan1_1.3.296.0-1_arm64.deb ...
289s Unpacking libvulkan1:arm64 (1.3.296.0-1) ...
289s Selecting previously unselected package libwayland-client0:arm64.
289s Preparing to unpack .../052-libwayland-client0_1.23.0-1_arm64.deb ...
289s Unpacking libwayland-client0:arm64 (1.23.0-1) ...
289s Selecting previously unselected package libwayland-egl1:arm64.
289s Preparing to unpack .../053-libwayland-egl1_1.23.0-1_arm64.deb ...
289s Unpacking libwayland-egl1:arm64 (1.23.0-1) ...
289s Selecting previously unselected package libxfixes3:arm64.
289s Preparing to unpack .../054-libxfixes3_1%3a6.0.0-2build1_arm64.deb ...
289s Unpacking libxfixes3:arm64 (1:6.0.0-2build1) ...
289s Selecting previously unselected package libxcursor1:arm64.
289s Preparing to unpack .../055-libxcursor1_1%3a1.2.2-1_arm64.deb ...
289s Unpacking libxcursor1:arm64 (1:1.2.2-1) ...
289s Selecting previously unselected package libxdamage1:arm64.
289s Preparing to unpack .../056-libxdamage1_1%3a1.1.6-1build1_arm64.deb ...
289s Unpacking libxdamage1:arm64 (1:1.1.6-1build1) ...
289s Selecting previously unselected package libxi6:arm64.
289s Preparing to unpack .../057-libxi6_2%3a1.8.2-1_arm64.deb ...
289s Unpacking libxi6:arm64 (2:1.8.2-1) ...
289s Selecting previously unselected package libxinerama1:arm64.
289s Preparing to unpack .../058-libxinerama1_2%3a1.1.4-3build1_arm64.deb ...
289s Unpacking libxinerama1:arm64 (2:1.1.4-3build1) ...
289s Selecting previously unselected package libxrandr2:arm64.
289s Preparing to unpack .../059-libxrandr2_2%3a1.5.4-1_arm64.deb ...
289s Unpacking libxrandr2:arm64 (2:1.5.4-1) ...
289s Selecting previously unselected package libglvnd0:arm64.
289s Preparing to unpack .../060-libglvnd0_1.7.0-1build1_arm64.deb ...
289s Unpacking libglvnd0:arm64 (1.7.0-1build1) ...
289s Selecting previously unselected package libgles2:arm64.
289s Preparing to unpack .../061-libgles2_1.7.0-1build1_arm64.deb ...
289s Unpacking libgles2:arm64 (1.7.0-1build1) ...
289s Selecting previously unselected package libdconf1:arm64.
289s Preparing to unpack .../062-libdconf1_0.40.0-4build2_arm64.deb ...
289s Unpacking libdconf1:arm64 (0.40.0-4build2) ...
290s Selecting previously unselected package dconf-service.
290s Preparing to unpack .../063-dconf-service_0.40.0-4build2_arm64.deb ...
290s Unpacking dconf-service (0.40.0-4build2) ...
290s Selecting previously unselected package dconf-gsettings-backend:arm64.
290s Preparing to unpack .../064-dconf-gsettings-backend_0.40.0-4build2_arm64.deb ...
290s Unpacking dconf-gsettings-backend:arm64 (0.40.0-4build2) ...
290s Selecting previously unselected package libgtk-4-common.
290s Preparing to unpack .../065-libgtk-4-common_4.16.5+ds-2_all.deb ...
290s Unpacking libgtk-4-common (4.16.5+ds-2) ...
290s Selecting previously unselected package libgtk-4-1:arm64.
290s Preparing to unpack .../066-libgtk-4-1_4.16.5+ds-2_arm64.deb ...
290s Unpacking libgtk-4-1:arm64 (4.16.5+ds-2) ...
290s Selecting previously unselected package gir1.2-gtk-4.0:arm64.
290s Preparing to unpack .../067-gir1.2-gtk-4.0_4.16.5+ds-2_arm64.deb ...
290s Unpacking gir1.2-gtk-4.0:arm64 (4.16.5+ds-2) ...
290s Selecting previously unselected package rdkit-data.
290s Preparing to unpack .../068-rdkit-data_202409.2-2_all.deb ...
290s Unpacking rdkit-data (202409.2-2) ...
290s Selecting previously unselected package libblas3:arm64.
290s Preparing to unpack .../069-libblas3_3.12.0-4_arm64.deb ...
290s Unpacking libblas3:arm64 (3.12.0-4) ...
290s Selecting previously unselected package libgfortran5:arm64.
290s Preparing to unpack .../070-libgfortran5_14.2.0-9ubuntu1_arm64.deb ...
290s Unpacking libgfortran5:arm64 (14.2.0-9ubuntu1) ...
290s Selecting previously unselected package liblapack3:arm64.
290s Preparing to unpack .../071-liblapack3_3.12.0-4_arm64.deb ...
290s Unpacking liblapack3:arm64 (3.12.0-4) ...
291s Selecting previously unselected package python3-numpy.
291s Preparing to unpack .../072-python3-numpy_1%3a1.26.4+ds-11ubuntu1_arm64.deb ...
291s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ...
291s Selecting previously unselected package libboost-python1.83.0.
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291s Selecting previously unselected package libboost-numpy1.83.0.
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291s Unpacking libboost-numpy1.83.0 (1.83.0-3.2ubuntu2) ...
291s Selecting previously unselected package libboost-serialization1.83.0:arm64.
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291s Unpacking libboost-serialization1.83.0:arm64 (1.83.0-3.2ubuntu2) ...
291s Selecting previously unselected package libcoordgen3:arm64.
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291s Unpacking libcoordgen3:arm64 (3.0.2-1) ...
291s Selecting previously unselected package libboost-iostreams1.83.0:arm64.
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291s Unpacking libboost-iostreams1.83.0:arm64 (1.83.0-3.2ubuntu2) ...
291s Selecting previously unselected package libinchi1.07.
291s Preparing to unpack .../078-libinchi1.07_1.07.1+dfsg-5_arm64.deb ...
291s Unpacking libinchi1.07 (1.07.1+dfsg-5) ...
291s Selecting previously unselected package libmaeparser1:arm64.
291s Preparing to unpack .../079-libmaeparser1_1.3.1-1build1_arm64.deb ...
291s Unpacking libmaeparser1:arm64 (1.3.1-1build1) ...
291s Selecting previously unselected package librdkit1t64.
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291s Unpacking librdkit1t64 (202409.2-2) ...
291s Selecting previously unselected package python3-rdkit.
291s Preparing to unpack .../081-python3-rdkit_202409.2-2_arm64.deb ...
291s Unpacking python3-rdkit (202409.2-2) ...
292s Selecting previously unselected package refmac-dictionary.
292s Preparing to unpack .../082-refmac-dictionary_5.41-3_all.deb ...
292s Unpacking refmac-dictionary (5.41-3) ...
293s Selecting previously unselected package libasound2-data.
293s Preparing to unpack .../083-libasound2-data_1.2.12-1_all.deb ...
293s Unpacking libasound2-data (1.2.12-1) ...
293s Selecting previously unselected package libasound2t64:arm64.
293s Preparing to unpack .../084-libasound2t64_1.2.12-1_arm64.deb ...
293s Unpacking libasound2t64:arm64 (1.2.12-1) ...
293s Selecting previously unselected package libccp4-data.
293s Preparing to unpack .../085-libccp4-data_8.0.0-4_all.deb ...
293s Unpacking libccp4-data (8.0.0-4) ...
293s Selecting previously unselected package libccp4c0t64:arm64.
293s Preparing to unpack .../086-libccp4c0t64_8.0.0-4_arm64.deb ...
293s Unpacking libccp4c0t64:arm64 (8.0.0-4) ...
293s Selecting previously unselected package libmmdb2-0:arm64.
293s Preparing to unpack .../087-libmmdb2-0_2.0.22-1_arm64.deb ...
293s Unpacking libmmdb2-0:arm64 (2.0.22-1) ...
293s Selecting previously unselected package libevent-pthreads-2.1-7t64:arm64.
294s Preparing to unpack .../088-libevent-pthreads-2.1-7t64_2.1.12-stable-10_arm64.deb ...
294s Unpacking libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ...
294s Selecting previously unselected package librdmacm1t64:arm64.
294s Preparing to unpack .../089-librdmacm1t64_52.0-2ubuntu1_arm64.deb ...
294s Unpacking librdmacm1t64:arm64 (52.0-2ubuntu1) ...
294s Selecting previously unselected package libfabric1:arm64.
294s Preparing to unpack .../090-libfabric1_1.17.0-3ubuntu1_arm64.deb ...
294s Unpacking libfabric1:arm64 (1.17.0-3ubuntu1) ...
294s Selecting previously unselected package libhwloc15:arm64.
294s Preparing to unpack .../091-libhwloc15_2.11.2-1_arm64.deb ...
294s Unpacking libhwloc15:arm64 (2.11.2-1) ...
294s Selecting previously unselected package libmunge2:arm64.
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294s Unpacking libmunge2:arm64 (0.5.15-4build1) ...
294s Selecting previously unselected package libpciaccess0:arm64.
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294s Unpacking libpciaccess0:arm64 (0.17-3build1) ...
294s Selecting previously unselected package libxnvctrl0:arm64.
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294s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu4) ...
294s Selecting previously unselected package ocl-icd-libopencl1:arm64.
294s Preparing to unpack .../095-ocl-icd-libopencl1_2.3.2-1build1_arm64.deb ...
294s Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1build1) ...
294s Selecting previously unselected package libhwloc-plugins:arm64.
294s Preparing to unpack .../096-libhwloc-plugins_2.11.2-1_arm64.deb ...
294s Unpacking libhwloc-plugins:arm64 (2.11.2-1) ...
294s Selecting previously unselected package libpmix2t64:arm64.
294s Preparing to unpack .../097-libpmix2t64_5.0.4-1_arm64.deb ...
294s Unpacking libpmix2t64:arm64 (5.0.4-1) ...
294s Selecting previously unselected package libllvm17t64:arm64.
294s Preparing to unpack .../098-libllvm17t64_1%3a17.0.6-18_arm64.deb ...
294s Unpacking libllvm17t64:arm64 (1:17.0.6-18) ...
295s Selecting previously unselected package libamd-comgr2:arm64.
295s Preparing to unpack .../099-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_arm64.deb ...
295s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ...
295s Selecting previously unselected package libhsakmt1:arm64.
295s Preparing to unpack .../100-libhsakmt1_5.7.0-1build1_arm64.deb ...
295s Unpacking libhsakmt1:arm64 (5.7.0-1build1) ...
295s Selecting previously unselected package libhsa-runtime64-1.
295s Preparing to unpack .../101-libhsa-runtime64-1_5.7.1-2build1_arm64.deb ...
295s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ...
295s Selecting previously unselected package libamdhip64-5.
295s Preparing to unpack .../102-libamdhip64-5_5.7.1-5_arm64.deb ...
295s Unpacking libamdhip64-5 (5.7.1-5) ...
295s Selecting previously unselected package libgomp1:arm64.
295s Preparing to unpack .../103-libgomp1_14.2.0-9ubuntu1_arm64.deb ...
295s Unpacking libgomp1:arm64 (14.2.0-9ubuntu1) ...
295s Selecting previously unselected package libibumad3:arm64.
295s Preparing to unpack .../104-libibumad3_52.0-2ubuntu1_arm64.deb ...
295s Unpacking libibumad3:arm64 (52.0-2ubuntu1) ...
295s Selecting previously unselected package libibmad5:arm64.
295s Preparing to unpack .../105-libibmad5_52.0-2ubuntu1_arm64.deb ...
295s Unpacking libibmad5:arm64 (52.0-2ubuntu1) ...
296s Selecting previously unselected package libucx0:arm64.
296s Preparing to unpack .../106-libucx0_1.17.0+ds-3build1_arm64.deb ...
296s Unpacking libucx0:arm64 (1.17.0+ds-3build1) ...
296s Selecting previously unselected package libopenmpi3t64:arm64.
296s Preparing to unpack .../107-libopenmpi3t64_4.1.6-13.3ubuntu2_arm64.deb ...
296s Unpacking libopenmpi3t64:arm64 (4.1.6-13.3ubuntu2) ...
296s Selecting previously unselected package sfftw2.
296s Preparing to unpack .../108-sfftw2_2.1.5-7_arm64.deb ...
296s Unpacking sfftw2 (2.1.5-7) ...
296s Selecting previously unselected package libclipper2:arm64.
296s Preparing to unpack .../109-libclipper2_2.1.20201109-2build1_arm64.deb ...
296s Unpacking libclipper2:arm64 (2.1.20201109-2build1) ...
296s Selecting previously unselected package libgslcblas0:arm64.
296s Preparing to unpack .../110-libgslcblas0_2.8+dfsg-5_arm64.deb ...
296s Unpacking libgslcblas0:arm64 (2.8+dfsg-5) ...
296s Selecting previously unselected package libgsl28:arm64.
296s Preparing to unpack .../111-libgsl28_2.8+dfsg-5_arm64.deb ...
296s Unpacking libgsl28:arm64 (2.8+dfsg-5) ...
296s Selecting previously unselected package libssm2:arm64.
296s Preparing to unpack .../112-libssm2_1.4.0-2build1_arm64.deb ...
296s Unpacking libssm2:arm64 (1.4.0-2build1) ...
296s Selecting previously unselected package libcootapi1.1.
296s Preparing to unpack .../113-libcootapi1.1_1.1.09+dfsg-2build1_arm64.deb ...
296s Unpacking libcootapi1.1 (1.1.09+dfsg-2build1) ...
296s Selecting previously unselected package libogg0:arm64.
296s Preparing to unpack .../114-libogg0_1.3.5-3build1_arm64.deb ...
296s Unpacking libogg0:arm64 (1.3.5-3build1) ...
296s Selecting previously unselected package libvorbis0a:arm64.
296s Preparing to unpack .../115-libvorbis0a_1.3.7-2_arm64.deb ...
296s Unpacking libvorbis0a:arm64 (1.3.7-2) ...
296s Selecting previously unselected package libvorbisfile3:arm64.
296s Preparing to unpack .../116-libvorbisfile3_1.3.7-2_arm64.deb ...
296s Unpacking libvorbisfile3:arm64 (1.3.7-2) ...
296s Selecting previously unselected package coot.
296s Preparing to unpack .../117-coot_1.1.09+dfsg-2build1_arm64.deb ...
296s Unpacking coot (1.1.09+dfsg-2build1) ...
296s Selecting previously unselected package coot-doc.
297s Preparing to unpack .../118-coot-doc_1.1.09+dfsg-2build1_all.deb ...
297s Unpacking coot-doc (1.1.09+dfsg-2build1) ...
297s Selecting previously unselected package libcootapi-dev.
297s Preparing to unpack .../119-libcootapi-dev_1.1.09+dfsg-2build1_arm64.deb ...
297s Unpacking libcootapi-dev (1.1.09+dfsg-2build1) ...
297s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
297s Setting up libboost-python1.83.0 (1.83.0-3.2ubuntu2) ...
297s Setting up libpixman-1-0:arm64 (0.44.0-3) ...
297s Setting up coot-doc (1.1.09+dfsg-2build1) ...
297s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ...
297s Setting up libpciaccess0:arm64 (0.17-3build1) ...
297s Setting up ttf-bitstream-vera (1.10-8.2) ...
297s Setting up libxdamage1:arm64 (1:1.1.6-1build1) ...
297s Setting up libogg0:arm64 (1.3.5-3build1) ...
297s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ...
297s Setting up fonts-noto-mono (20201225-2) ...
297s Setting up hicolor-icon-theme (0.18-1) ...
297s Setting up libxi6:arm64 (2:1.8.2-1) ...
297s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ...
297s Setting up libdatrie1:arm64 (0.2.13-3build1) ...
297s Setting up libgslcblas0:arm64 (2.8+dfsg-5) ...
297s Setting up libmmdb2-0:arm64 (2.0.22-1) ...
297s Setting up libxcb-render0:arm64 (1.17.0-2) ...
297s Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ...
297s Setting up libglvnd0:arm64 (1.7.0-1build1) ...
297s Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ...
297s Setting up libibumad3:arm64 (52.0-2ubuntu1) ...
297s Setting up libdeflate0:arm64 (1.22-1) ...
297s Setting up fonts-freefont-ttf (20211204+svn4273-2) ...
297s Setting up libcpdb2t64:arm64 (2.0~b5-1.2build1) ...
297s Setting up libxcb-shm0:arm64 (1.17.0-2) ...
297s Setting up libibmad5:arm64 (52.0-2ubuntu1) ...
297s Setting up libcpdb-frontend2t64:arm64 (2.0~b5-1.2build1) ...
297s Setting up libccp4-data (8.0.0-4) ...
297s Setting up libgomp1:arm64 (14.2.0-9ubuntu1) ...
297s Setting up rdkit-data (202409.2-2) ...
297s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ...
297s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu4) ...
297s Setting up refmac-dictionary (5.41-3) ...
297s Setting up libdconf1:arm64 (0.40.0-4build2) ...
297s Setting up libasound2-data (1.2.12-1) ...
297s Setting up libboost-serialization1.83.0:arm64 (1.83.0-3.2ubuntu2) ...
297s Setting up libboost-numpy1.83.0 (1.83.0-3.2ubuntu2) ...
297s Setting up libblas3:arm64 (3.12.0-4) ...
297s 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
297s Setting up libgles2:arm64 (1.7.0-1build1) ...
297s Setting up libasound2t64:arm64 (1.2.12-1) ...
297s Setting up libmunge2:arm64 (0.5.15-4build1) ...
297s Setting up libllvm17t64:arm64 (1:17.0.6-18) ...
297s Setting up libepoxy0:arm64 (1.5.10-2) ...
297s Setting up libxfixes3:arm64 (1:6.0.0-2build1) ...
297s Setting up libboost-iostreams1.83.0:arm64 (1.83.0-3.2ubuntu2) ...
297s Setting up libxinerama1:arm64 (2:1.1.4-3build1) ...
297s Setting up libhwloc15:arm64 (2.11.2-1) ...
297s Setting up libvorbis0a:arm64 (1.3.7-2) ...
297s Setting up libxrandr2:arm64 (2:1.5.4-1) ...
297s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ...
297s Setting up libgfortran5:arm64 (14.2.0-9ubuntu1) ...
297s Setting up libvulkan1:arm64 (1.3.296.0-1) ...
297s Setting up libwebp7:arm64 (1.4.0-0.1) ...
297s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1build1) ...
297s Setting up libccp4c0t64:arm64 (8.0.0-4) ...
297s Setting up librdmacm1t64:arm64 (52.0-2ubuntu1) ...
297s Setting up libharfbuzz0b:arm64 (10.0.1-1) ...
297s Setting up libthai-data (0.1.29-2build1) ...
297s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ...
297s Setting up libwayland-egl1:arm64 (1.23.0-1) ...
297s Setting up libcoordgen3:arm64 (3.0.2-1) ...
297s Setting up libgsl28:arm64 (2.8+dfsg-5) ...
297s Setting up libinchi1.07 (1.07.1+dfsg-5) ...
297s Setting up fonts-noto-core (20201225-2) ...
297s Setting up libhsakmt1:arm64 (5.7.0-1build1) ...
297s Setting up libgraphene-1.0-0:arm64 (1.10.8-4) ...
297s Setting up libwayland-client0:arm64 (1.23.0-1) ...
297s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
297s Setting up gir1.2-graphene-1.0:arm64 (1.10.8-4) ...
297s Setting up libfabric1:arm64 (1.17.0-3ubuntu1) ...
297s Setting up liblapack3:arm64 (3.12.0-4) ...
297s 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
297s Setting up libssm2:arm64 (1.4.0-2build1) ...
297s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
297s Setting up libxcursor1:arm64 (1:1.2.2-1) ...
297s Setting up dconf-service (0.40.0-4build2) ...
297s Setting up libharfbuzz-gobject0:arm64 (10.0.1-1) ...
297s Setting up libhwloc-plugins:arm64 (2.11.2-1) ...
297s Setting up libmaeparser1:arm64 (1.3.1-1build1) ...
297s Setting up libthai0:arm64 (0.1.29-2build1) ...
297s Setting up libvorbisfile3:arm64 (1.3.7-2) ...
297s Setting up libpmix2t64:arm64 (5.0.4-1) ...
297s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ...
299s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ...
299s Setting up libhsa-runtime64-1 (5.7.1-2build1) ...
299s Setting up libharfbuzz-subset0:arm64 (10.0.1-1) ...
299s Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-1) ...
299s Setting up coot-data (1.1.09+dfsg-2build1) ...
299s Setting up gtk-update-icon-cache (4.16.5+ds-2) ...
299s Setting up dconf-gsettings-backend:arm64 (0.40.0-4build2) ...
299s Setting up gir1.2-gdkpixbuf-2.0:arm64 (2.42.12+dfsg-1) ...
299s Setting up libamdhip64-5 (5.7.1-5) ...
299s Setting up libgtk-4-common (4.16.5+ds-2) ...
299s Setting up libucx0:arm64 (1.17.0+ds-3build1) ...
299s Setting up libopenmpi3t64:arm64 (4.1.6-13.3ubuntu2) ...
299s Setting up sfftw2 (2.1.5-7) ...
299s Setting up libclipper2:arm64 (2.1.20201109-2build1) ...
299s Setting up libcootapi1.1 (1.1.09+dfsg-2build1) ...
299s Setting up libcootapi-dev (1.1.09+dfsg-2build1) ...
299s Setting up adwaita-icon-theme (47.0-2) ...
299s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
299s Setting up humanity-icon-theme (0.6.16) ...
299s Setting up ubuntu-mono (24.04-0ubuntu1) ...
299s Processing triggers for man-db (2.13.0-1) ...
301s Processing triggers for libglib2.0-0t64:arm64 (2.82.2-3) ...
301s Processing triggers for sgml-base (1.31) ...
301s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ...
301s Setting up fontconfig (2.15.0-1.1ubuntu2) ...
304s Regenerating fonts cache... done.
304s Setting up libxft2:arm64 (2.3.6-1build1) ...
304s Processing triggers for libc-bin (2.40-1ubuntu3) ...
304s Setting up libpango-1.0-0:arm64 (1.54.0+ds-3) ...
304s Setting up libcairo2:arm64 (1.18.2-2) ...
304s Setting up libcairo-gobject2:arm64 (1.18.2-2) ...
304s Setting up libpangoft2-1.0-0:arm64 (1.54.0+ds-3) ...
304s Setting up libpangocairo-1.0-0:arm64 (1.54.0+ds-3) ...
304s Setting up libcairo-script-interpreter2:arm64 (1.18.2-2) ...
304s Setting up gir1.2-freedesktop:arm64 (1.82.0-2) ...
304s Setting up libpangoxft-1.0-0:arm64 (1.54.0+ds-3) ...
304s Setting up librdkit1t64 (202409.2-2) ...
304s Setting up gir1.2-harfbuzz-0.0:arm64 (10.0.1-1) ...
304s Setting up gir1.2-pango-1.0:arm64 (1.54.0+ds-3) ...
304s Setting up python3-rdkit (202409.2-2) ...
304s Setting up libgtk-4-1:arm64 (4.16.5+ds-2) ...
304s Setting up gir1.2-gtk-4.0:arm64 (4.16.5+ds-2) ...
304s Setting up coot (1.1.09+dfsg-2build1) ...
305s /usr/lib/python3/dist-packages/coot/tautomer.py:289: SyntaxWarning: invalid escape sequence '\C'
305s   ('Remove stereochemistry from mobile double bonds', 'C/C=C\C(C)=O', {'C=C(O)C=CC', 'C=CCC(=C)O', 'CC=CC(C)=O', 'C=CCC(C)=O', 'C=CC=C(C)O'}),
305s Processing triggers for libc-bin (2.40-1ubuntu3) ...
307s autopkgtest [09:39:50]: test command1: coot --self-test
307s autopkgtest [09:39:50]: test command1: [-----------------------
307s INFO:: Running internal self tests
312s  INFO:: Test Clipper core   : OK
312s  INFO:: Test Clipper contrib: OK
312s run_internal_tests() --------- we have 8 internal test functionns 
312s Entering test: kevin's torsion test
312s PASS: kevin's torsion test
312s Entering test: test_alt_conf_rotamers
312s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb
312s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read.
312s chis.size() 2 (should be 2)
312s DEBUG:: i_rot 0 chi: alt-conf: A chi-1: 65.911
312s DEBUG:: i_rot 1 chi: alt-conf: B chi-1: -144.68
312s For residue 80 chis size 1
312s   residue 80 chis: -56.8781 -80.8484
312s PASS: test_alt_conf_rotamers
312s Entering test: test_fragmemt_atom_selection
312s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb
312s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read.
312s ----------------- create_mmdbmanager_from_inverted_atom_selection() 
312s    n_initial: 1465   n_1: 1401   n_2: 64
312s PASS: test_fragmemt_atom_selection
312s Entering test: test_add_atom
312s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb
312s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read.
312s PASS: test_add_atom
312s Entering test: test segid exchange
312s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb
312s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read.
312s    Test with a rogue segid 
312s    INFO:: No consistent segids for residue 1
312s PASS: test segid exchange
312s Entering test: test peak search non-close
312s mtz_file_name /usr/share/coot/data/rnasa-1.8-all_refmac1.mtz
312s FFT Reso...0.444444
312s Sampling rate...1.5
312s Grid...Nuvw = ( 132, 160,  80)
312s Cell... Cell (64.897,78.323,38.792,    90,    90,    90)
312s Spacegroup...P 21 21 21
312s    There are 2260 peaks and 0 problem peaks
312s PASS: test peak search non-close
312s Entering test: test symop card
312s 1 0 0
312s 0 1 0
312s 0 0 1
312s translations: -1 0 0
312s PASS: test symop card
312s Entering test: SSM sequence alignment output
312s 
312s --
312s  Moving: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNR--ESVLPTQSYGYYHEYTVITP--GARTRG
312s  Target: ---SGTVCLSALPPEATDTLNLIASDGPFPYSQDG
312s 
312s  Moving: TRRI.ICGEATQEDY..YTGDHYATFSLIDQTC
312s 
312s --
312s  Moving: D
312s  Target: --SGTVCLSALPPEATDTLNLIASDGPFPYSQDG
312s 
312s --
312s  Moving: DVSGTVCLSALPPEATDTLNIASDGPFPYSQDGVVFQNR--ESVLPQSYG
312s  Target: --SGTVCLSALPPEATDTLNIASDGPFPYSQDXXxxxxxxxxxxxxxxxG
312s 
312s --
312s PASS: SSM sequence alignment output
312s autopkgtest [09:39:55]: test command1: -----------------------]
313s command1             PASS
313s autopkgtest [09:39:56]: test command1:  - - - - - - - - - - results - - - - - - - - - -
313s autopkgtest [09:39:56]: test command2: preparing testbed
313s Reading package lists...
314s Building dependency tree...
314s Reading state information...
314s Starting pkgProblemResolver with broken count: 0
314s Starting 2 pkgProblemResolver with broken count: 0
314s Done
315s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
316s autopkgtest [09:39:59]: test command2: pyrogen --help
316s autopkgtest [09:39:59]: test command2: [-----------------------
317s Traceback (most recent call last):
317s   File "<frozen runpy>", line 198, in _run_module_as_main
317s   File "<frozen runpy>", line 88, in _run_code
317s   File "/usr/lib/python3/dist-packages/coot/pyrogen.py", line 38, in <module>
317s     import pyrogen_swig as pysw # relies on above rdkit.Chem import AllChem (but ideally should not)
317s     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
317s   File "/usr/lib/python3/dist-packages/coot/pyrogen_swig.py", line 12, in <module>
317s     import _pyrogen_swig
317s ImportError: /usr/lib/aarch64-linux-gnu/coot/libcoot-lidia-core.so.0: undefined symbol: _ZN5RDKit9ConformerC1ERKS0_
318s autopkgtest [09:40:01]: test command2: -----------------------]
318s autopkgtest [09:40:01]: test command2:  - - - - - - - - - - results - - - - - - - - - -
318s command2             FAIL non-zero exit status 1
318s autopkgtest [09:40:01]: test command2:  - - - - - - - - - - stderr - - - - - - - - - -
318s Traceback (most recent call last):
318s   File "<frozen runpy>", line 198, in _run_module_as_main
318s   File "<frozen runpy>", line 88, in _run_code
318s   File "/usr/lib/python3/dist-packages/coot/pyrogen.py", line 38, in <module>
318s     import pyrogen_swig as pysw # relies on above rdkit.Chem import AllChem (but ideally should not)
318s     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
318s   File "/usr/lib/python3/dist-packages/coot/pyrogen_swig.py", line 12, in <module>
318s     import _pyrogen_swig
318s ImportError: /usr/lib/aarch64-linux-gnu/coot/libcoot-lidia-core.so.0: undefined symbol: _ZN5RDKit9ConformerC1ERKS0_
319s autopkgtest [09:40:02]: @@@@@@@@@@@@@@@@@@@@ summary
319s command1             PASS
319s command2             FAIL non-zero exit status 1
333s nova [W] Using flock in prodstack6-arm64
333s flock: timeout while waiting to get lock
333s Creating nova instance adt-plucky-arm64-coot-20241203-093441-juju-7f2275-prod-proposed-migration-environment-20-b6533985-ce1f-4b9e-a86e-2f65e245dbb6 from image adt/ubuntu-plucky-arm64-server-20241203.img (UUID b9293590-1195-42ea-ba16-5ab4b1e94eab)...