0s autopkgtest [09:54:04]: starting date and time: 2024-12-03 09:54:04+0000
  0s autopkgtest [09:54:04]: git checkout: be626eda Fix armhf LXD image generation for plucky
  0s autopkgtest [09:54:04]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.xoxh_gha/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-14.secgroup --name adt-plucky-ppc64el-coot-20241203-093440-juju-7f2275-prod-proposed-migration-environment-15-e4d34576-cccb-4dde-a445-8f370574704d --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -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/
101s autopkgtest [09:55:45]: testbed dpkg architecture: ppc64el
101s autopkgtest [09:55:45]: testbed apt version: 2.9.14ubuntu1
102s autopkgtest [09:55:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup
102s autopkgtest [09:55:46]: testbed release detected to be: None
103s autopkgtest [09:55:47]: updating testbed package index (apt update)
104s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
104s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
104s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
104s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
104s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B]
104s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [65.3 kB]
104s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [781 kB]
104s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.1 kB]
104s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [127 kB]
104s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted ppc64el Packages [928 B]
104s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [655 kB]
104s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [11.0 kB]
104s Fetched 1739 kB in 1s (1595 kB/s)
105s Reading package lists...
106s Reading package lists...
106s Building dependency tree...
106s Reading state information...
107s Calculating upgrade...
107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
107s Reading package lists...
107s Building dependency tree...
107s Reading state information...
108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
108s autopkgtest [09:55:52]: upgrading testbed (apt dist-upgrade and autopurge)
108s Reading package lists...
108s Building dependency tree...
108s Reading state information...
109s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
109s Starting 2 pkgProblemResolver with broken count: 0
109s Done
109s Entering ResolveByKeep
109s 
110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
110s Reading package lists...
110s Building dependency tree...
110s Reading state information...
110s Starting pkgProblemResolver with broken count: 0
110s Starting 2 pkgProblemResolver with broken count: 0
110s Done
111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
114s autopkgtest [09:55:57]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024
114s autopkgtest [09:55:58]: @@@@@@@@@@@@@@@@@@@@ apt-source coot
123s Get:1 http://ftpmaster.internal/ubuntu plucky/universe coot 1.1.09+dfsg-2build1 (dsc) [2941 B]
123s Get:2 http://ftpmaster.internal/ubuntu plucky/universe coot 1.1.09+dfsg-2build1 (tar) [88.5 MB]
123s Get:3 http://ftpmaster.internal/ubuntu plucky/universe coot 1.1.09+dfsg-2build1 (diff) [52.5 kB]
123s gpgv: Signature made Tue Jul 30 06:28:58 2024 UTC
123s gpgv:                using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9
123s gpgv: Can't check signature: No public key
123s dpkg-source: warning: cannot verify inline signature for ./coot_1.1.09+dfsg-2build1.dsc: no acceptable signature found
127s autopkgtest [09:56:11]: testing package coot version 1.1.09+dfsg-2build1
127s autopkgtest [09:56:11]: build not needed
158s autopkgtest [09:56:42]: test command1: preparing testbed
159s Reading package lists...
159s Building dependency tree...
159s Reading state information...
159s Starting pkgProblemResolver with broken count: 0
159s Starting 2 pkgProblemResolver with broken count: 0
159s Done
160s The following NEW packages will be installed:
160s   adwaita-icon-theme coot coot-data coot-doc dconf-gsettings-backend
160s   dconf-service fontconfig fontconfig-config fonts-freefont-ttf
160s   fonts-noto-core fonts-noto-mono gir1.2-freedesktop gir1.2-gdkpixbuf-2.0
160s   gir1.2-graphene-1.0 gir1.2-gtk-4.0 gir1.2-harfbuzz-0.0 gir1.2-pango-1.0
160s   gtk-update-icon-cache hicolor-icon-theme humanity-icon-theme libamd-comgr2
160s   libamdhip64-5 libasound2-data libasound2t64 libblas3
160s   libboost-iostreams1.83.0 libboost-numpy1.83.0 libboost-python1.83.0
160s   libboost-serialization1.83.0 libcairo-gobject2 libcairo-script-interpreter2
160s   libcairo2 libccp4-data libccp4c0t64 libclipper2 libcoordgen3 libcootapi-dev
160s   libcootapi1.1 libcpdb-frontend2t64 libcpdb2t64 libdatrie1 libdconf1
160s   libdeflate0 libepoxy0 libevent-pthreads-2.1-7t64 libfabric1 libfontconfig1
160s   libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgles2 libglvnd0
160s   libgomp1 libgraphene-1.0-0 libgraphite2-3 libgsl28 libgslcblas0 libgtk-4-1
160s   libgtk-4-common libharfbuzz-gobject0 libharfbuzz-subset0 libharfbuzz0b
160s   libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5
160s   libibumad3 libinchi1.07 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4
160s   libllvm17t64 libmaeparser1 libmmdb2-0 libmunge2 libogg0 libopenmpi3t64
160s   libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpangoxft-1.0-0
160s   libpciaccess0 libpixman-1-0 libpmix2t64 librdkit1t64 librdmacm1t64
160s   libsharpyuv0 libssm2 libthai-data libthai0 libtiff6 libucx0 libvorbis0a
160s   libvorbisfile3 libvulkan1 libwayland-client0 libwayland-egl1 libwebp7
160s   libxcb-render0 libxcb-shm0 libxcursor1 libxdamage1 libxfixes3 libxft2 libxi6
160s   libxinerama1 libxnvctrl0 libxrandr2 libxrender1 ocl-icd-libopencl1
160s   python3-numpy python3-rdkit rdkit-data refmac-dictionary sfftw2
160s   ttf-bitstream-vera ubuntu-mono
160s 0 upgraded, 120 newly installed, 0 to remove and 0 not upgraded.
160s Need to get 174 MB of archives.
160s After this operation, 914 MB of additional disk space will be used.
160s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [7888 B]
160s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-3ubuntu2 [215 kB]
160s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B]
160s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.22-1 [63.3 kB]
160s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB]
160s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblerc4 ppc64el 4.0.0+ds-5ubuntu1 [298 kB]
160s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsharpyuv0 ppc64el 1.4.0-0.1 [22.0 kB]
160s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebp7 ppc64el 1.4.0-0.1 [309 kB]
160s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu4 [272 kB]
160s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgdk-pixbuf-2.0-0 ppc64el 2.42.12+dfsg-1 [186 kB]
160s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el gtk-update-icon-cache ppc64el 4.16.5+ds-2 [53.7 kB]
160s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el hicolor-icon-theme all 0.18-1 [13.5 kB]
160s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el humanity-icon-theme all 0.6.16 [1282 kB]
160s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el ubuntu-mono all 24.04-0ubuntu1 [151 kB]
160s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el adwaita-icon-theme all 47.0-2 [525 kB]
160s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-noto-mono all 20201225-2 [435 kB]
160s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-noto-core all 20201225-2 [13.3 MB]
161s Get:18 http://ftpmaster.internal/ubuntu plucky/universe ppc64el ttf-bitstream-vera all 1.10-8.2 [244 kB]
161s Get:19 http://ftpmaster.internal/ubuntu plucky/universe ppc64el coot-data all 1.1.09+dfsg-2build1 [11.8 MB]
161s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-freefont-ttf all 20211204+svn4273-2 [5641 kB]
162s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig-config ppc64el 2.15.0-1.1ubuntu2 [37.4 kB]
162s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontconfig1 ppc64el 2.15.0-1.1ubuntu2 [190 kB]
162s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpixman-1-0 ppc64el 0.44.0-3 [334 kB]
162s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-render0 ppc64el 1.17.0-2 [17.2 kB]
162s Get:25 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-shm0 ppc64el 1.17.0-2 [5980 B]
162s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB]
162s Get:27 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcairo2 ppc64el 1.18.2-2 [747 kB]
162s Get:28 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcairo-gobject2 ppc64el 1.18.2-2 [127 kB]
162s Get:29 http://ftpmaster.internal/ubuntu plucky/main ppc64el gir1.2-freedesktop ppc64el 1.82.0-2 [64.3 kB]
162s Get:30 http://ftpmaster.internal/ubuntu plucky/main ppc64el gir1.2-gdkpixbuf-2.0 ppc64el 2.42.12+dfsg-1 [9432 B]
162s Get:31 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgraphene-1.0-0 ppc64el 1.10.8-4 [53.7 kB]
162s Get:32 http://ftpmaster.internal/ubuntu plucky/main ppc64el gir1.2-graphene-1.0 ppc64el 1.10.8-4 [11.1 kB]
162s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB]
162s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el libharfbuzz0b ppc64el 10.0.1-1 [596 kB]
162s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el libharfbuzz-gobject0 ppc64el 10.0.1-1 [34.5 kB]
162s Get:36 http://ftpmaster.internal/ubuntu plucky/main ppc64el gir1.2-harfbuzz-0.0 ppc64el 10.0.1-1 [45.2 kB]
162s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig ppc64el 2.15.0-1.1ubuntu2 [192 kB]
162s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el libthai-data all 0.1.29-2build1 [158 kB]
162s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdatrie1 ppc64el 0.2.13-3build1 [22.7 kB]
162s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el libthai0 ppc64el 0.1.29-2build1 [21.8 kB]
162s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpango-1.0-0 ppc64el 1.54.0+ds-3 [272 kB]
162s Get:42 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpangoft2-1.0-0 ppc64el 1.54.0+ds-3 [57.5 kB]
162s Get:43 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpangocairo-1.0-0 ppc64el 1.54.0+ds-3 [30.6 kB]
162s Get:44 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxft2 ppc64el 2.3.6-1build1 [61.5 kB]
162s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpangoxft-1.0-0 ppc64el 1.54.0+ds-3 [22.7 kB]
162s Get:46 http://ftpmaster.internal/ubuntu plucky/main ppc64el gir1.2-pango-1.0 ppc64el 1.54.0+ds-3 [34.5 kB]
162s Get:47 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcairo-script-interpreter2 ppc64el 1.18.2-2 [78.9 kB]
162s Get:48 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcpdb2t64 ppc64el 2.0~b5-1.2build1 [27.4 kB]
162s Get:49 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcpdb-frontend2t64 ppc64el 2.0~b5-1.2build1 [22.2 kB]
162s Get:50 http://ftpmaster.internal/ubuntu plucky/main ppc64el libepoxy0 ppc64el 1.5.10-2 [234 kB]
162s Get:51 http://ftpmaster.internal/ubuntu plucky/main ppc64el libharfbuzz-subset0 ppc64el 10.0.1-1 [598 kB]
162s Get:52 http://ftpmaster.internal/ubuntu plucky/main ppc64el libvulkan1 ppc64el 1.3.296.0-1 [163 kB]
162s Get:53 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwayland-client0 ppc64el 1.23.0-1 [31.4 kB]
162s Get:54 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwayland-egl1 ppc64el 1.23.0-1 [5730 B]
162s Get:55 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxfixes3 ppc64el 1:6.0.0-2build1 [11.8 kB]
162s Get:56 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcursor1 ppc64el 1:1.2.2-1 [26.3 kB]
162s Get:57 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxdamage1 ppc64el 1:1.1.6-1build1 [6550 B]
162s Get:58 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxi6 ppc64el 2:1.8.2-1 [37.9 kB]
162s Get:59 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxinerama1 ppc64el 2:1.1.4-3build1 [6908 B]
162s Get:60 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxrandr2 ppc64el 2:1.5.4-1 [21.7 kB]
162s Get:61 http://ftpmaster.internal/ubuntu plucky/main ppc64el libglvnd0 ppc64el 1.7.0-1build1 [72.4 kB]
162s Get:62 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgles2 ppc64el 1.7.0-1build1 [18.8 kB]
162s Get:63 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdconf1 ppc64el 0.40.0-4build2 [44.0 kB]
162s Get:64 http://ftpmaster.internal/ubuntu plucky/main ppc64el dconf-service ppc64el 0.40.0-4build2 [31.1 kB]
162s Get:65 http://ftpmaster.internal/ubuntu plucky/main ppc64el dconf-gsettings-backend ppc64el 0.40.0-4build2 [26.5 kB]
162s Get:66 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgtk-4-common all 4.16.5+ds-2 [1244 kB]
162s Get:67 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgtk-4-1 ppc64el 4.16.5+ds-2 [3816 kB]
162s Get:68 http://ftpmaster.internal/ubuntu plucky/main ppc64el gir1.2-gtk-4.0 ppc64el 4.16.5+ds-2 [214 kB]
162s Get:69 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el rdkit-data all 202409.2-2 [12.6 MB]
163s Get:70 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-4 [222 kB]
163s Get:71 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-9ubuntu1 [571 kB]
163s Get:72 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-4 [2814 kB]
163s Get:73 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11ubuntu1 [5148 kB]
163s Get:74 http://ftpmaster.internal/ubuntu plucky/main ppc64el libboost-python1.83.0 ppc64el 1.83.0-3.2ubuntu2 [316 kB]
163s Get:75 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libboost-numpy1.83.0 ppc64el 1.83.0-3.2ubuntu2 [242 kB]
163s Get:76 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libboost-serialization1.83.0 ppc64el 1.83.0-3.2ubuntu2 [348 kB]
163s Get:77 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcoordgen3 ppc64el 3.0.2-1 [263 kB]
163s Get:78 http://ftpmaster.internal/ubuntu plucky/main ppc64el libboost-iostreams1.83.0 ppc64el 1.83.0-3.2ubuntu2 [260 kB]
163s Get:79 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libinchi1.07 ppc64el 1.07.1+dfsg-5 [775 kB]
163s Get:80 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libmaeparser1 ppc64el 1.3.1-1build1 [96.1 kB]
163s Get:81 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el librdkit1t64 ppc64el 202409.2-2 [6147 kB]
163s Get:82 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el python3-rdkit ppc64el 202409.2-2 [4726 kB]
163s Get:83 http://ftpmaster.internal/ubuntu plucky/universe ppc64el refmac-dictionary all 5.41-3 [16.7 MB]
164s Get:84 http://ftpmaster.internal/ubuntu plucky/main ppc64el libasound2-data all 1.2.12-1 [21.0 kB]
164s Get:85 http://ftpmaster.internal/ubuntu plucky/main ppc64el libasound2t64 ppc64el 1.2.12-1 [493 kB]
164s Get:86 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libccp4-data all 8.0.0-4 [65.2 kB]
164s Get:87 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libccp4c0t64 ppc64el 8.0.0-4 [118 kB]
164s Get:88 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libmmdb2-0 ppc64el 2.0.22-1 [441 kB]
164s Get:89 http://ftpmaster.internal/ubuntu plucky/main ppc64el libevent-pthreads-2.1-7t64 ppc64el 2.1.12-stable-10 [8026 B]
164s Get:90 http://ftpmaster.internal/ubuntu plucky/main ppc64el librdmacm1t64 ppc64el 52.0-2ubuntu1 [80.6 kB]
164s Get:91 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libfabric1 ppc64el 1.17.0-3ubuntu1 [692 kB]
164s Get:92 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhwloc15 ppc64el 2.11.2-1 [220 kB]
164s Get:93 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libmunge2 ppc64el 0.5.15-4build1 [17.7 kB]
164s Get:94 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpciaccess0 ppc64el 0.17-3build1 [21.4 kB]
164s Get:95 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxnvctrl0 ppc64el 510.47.03-0ubuntu4 [12.6 kB]
164s Get:96 http://ftpmaster.internal/ubuntu plucky/universe ppc64el ocl-icd-libopencl1 ppc64el 2.3.2-1build1 [42.9 kB]
164s Get:97 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhwloc-plugins ppc64el 2.11.2-1 [17.5 kB]
164s Get:98 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libpmix2t64 ppc64el 5.0.4-1 [774 kB]
164s Get:99 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libllvm17t64 ppc64el 1:17.0.6-18 [27.0 MB]
165s Get:100 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libamd-comgr2 ppc64el 6.0+git20231212.4510c28+dfsg-3build2 [15.3 MB]
165s Get:101 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhsakmt1 ppc64el 5.7.0-1build1 [76.4 kB]
166s Get:102 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhsa-runtime64-1 ppc64el 5.7.1-2build1 [330 kB]
166s Get:103 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libamdhip64-5 ppc64el 5.7.1-5 [9354 kB]
168s Get:104 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-9ubuntu1 [161 kB]
168s Get:105 http://ftpmaster.internal/ubuntu plucky/main ppc64el libibumad3 ppc64el 52.0-2ubuntu1 [31.1 kB]
168s Get:106 http://ftpmaster.internal/ubuntu plucky/main ppc64el libibmad5 ppc64el 52.0-2ubuntu1 [45.5 kB]
168s Get:107 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libucx0 ppc64el 1.17.0+ds-3build1 [1224 kB]
168s Get:108 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libopenmpi3t64 ppc64el 4.1.6-13.3ubuntu2 [2696 kB]
168s Get:109 http://ftpmaster.internal/ubuntu plucky/universe ppc64el sfftw2 ppc64el 2.1.5-7 [206 kB]
168s Get:110 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libclipper2 ppc64el 2.1.20201109-2build1 [1278 kB]
168s Get:111 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libgslcblas0 ppc64el 2.8+dfsg-5 [276 kB]
169s Get:112 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libgsl28 ppc64el 2.8+dfsg-5 [1394 kB]
169s Get:113 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libssm2 ppc64el 1.4.0-2build1 [107 kB]
169s Get:114 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcootapi1.1 ppc64el 1.1.09+dfsg-2build1 [3783 kB]
169s Get:115 http://ftpmaster.internal/ubuntu plucky/main ppc64el libogg0 ppc64el 1.3.5-3build1 [27.6 kB]
169s Get:116 http://ftpmaster.internal/ubuntu plucky/main ppc64el libvorbis0a ppc64el 1.3.7-2 [142 kB]
169s Get:117 http://ftpmaster.internal/ubuntu plucky/main ppc64el libvorbisfile3 ppc64el 1.3.7-2 [22.5 kB]
169s Get:118 http://ftpmaster.internal/ubuntu plucky/universe ppc64el coot ppc64el 1.1.09+dfsg-2build1 [9064 kB]
169s Get:119 http://ftpmaster.internal/ubuntu plucky/universe ppc64el coot-doc all 1.1.09+dfsg-2build1 [2048 kB]
170s Get:120 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcootapi-dev ppc64el 1.1.09+dfsg-2build1 [23.8 kB]
170s Fetched 174 MB in 10s (17.3 MB/s)
170s Selecting previously unselected package libgdk-pixbuf2.0-common.
171s (Reading database ... 
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171s Preparing to unpack .../000-libgdk-pixbuf2.0-common_2.42.12+dfsg-1_all.deb ...
171s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ...
171s Selecting previously unselected package libjpeg-turbo8:ppc64el.
171s Preparing to unpack .../001-libjpeg-turbo8_2.1.5-3ubuntu2_ppc64el.deb ...
171s Unpacking libjpeg-turbo8:ppc64el (2.1.5-3ubuntu2) ...
171s Selecting previously unselected package libjpeg8:ppc64el.
171s Preparing to unpack .../002-libjpeg8_8c-2ubuntu11_ppc64el.deb ...
171s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ...
171s Selecting previously unselected package libdeflate0:ppc64el.
171s Preparing to unpack .../003-libdeflate0_1.22-1_ppc64el.deb ...
171s Unpacking libdeflate0:ppc64el (1.22-1) ...
171s Selecting previously unselected package libjbig0:ppc64el.
171s Preparing to unpack .../004-libjbig0_2.1-6.1ubuntu2_ppc64el.deb ...
171s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu2) ...
171s Selecting previously unselected package liblerc4:ppc64el.
171s Preparing to unpack .../005-liblerc4_4.0.0+ds-5ubuntu1_ppc64el.deb ...
171s Unpacking liblerc4:ppc64el (4.0.0+ds-5ubuntu1) ...
171s Selecting previously unselected package libsharpyuv0:ppc64el.
171s Preparing to unpack .../006-libsharpyuv0_1.4.0-0.1_ppc64el.deb ...
171s Unpacking libsharpyuv0:ppc64el (1.4.0-0.1) ...
171s Selecting previously unselected package libwebp7:ppc64el.
171s Preparing to unpack .../007-libwebp7_1.4.0-0.1_ppc64el.deb ...
171s Unpacking libwebp7:ppc64el (1.4.0-0.1) ...
171s Selecting previously unselected package libtiff6:ppc64el.
171s Preparing to unpack .../008-libtiff6_4.5.1+git230720-4ubuntu4_ppc64el.deb ...
171s Unpacking libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ...
171s Selecting previously unselected package libgdk-pixbuf-2.0-0:ppc64el.
171s Preparing to unpack .../009-libgdk-pixbuf-2.0-0_2.42.12+dfsg-1_ppc64el.deb ...
171s Unpacking libgdk-pixbuf-2.0-0:ppc64el (2.42.12+dfsg-1) ...
171s Selecting previously unselected package gtk-update-icon-cache.
171s Preparing to unpack .../010-gtk-update-icon-cache_4.16.5+ds-2_ppc64el.deb ...
171s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed.
171s 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.
171s Unpacking gtk-update-icon-cache (4.16.5+ds-2) ...
171s Selecting previously unselected package hicolor-icon-theme.
171s Preparing to unpack .../011-hicolor-icon-theme_0.18-1_all.deb ...
171s Unpacking hicolor-icon-theme (0.18-1) ...
171s Selecting previously unselected package humanity-icon-theme.
171s Preparing to unpack .../012-humanity-icon-theme_0.6.16_all.deb ...
171s Unpacking humanity-icon-theme (0.6.16) ...
172s Selecting previously unselected package ubuntu-mono.
172s Preparing to unpack .../013-ubuntu-mono_24.04-0ubuntu1_all.deb ...
172s Unpacking ubuntu-mono (24.04-0ubuntu1) ...
172s Selecting previously unselected package adwaita-icon-theme.
172s Preparing to unpack .../014-adwaita-icon-theme_47.0-2_all.deb ...
172s Unpacking adwaita-icon-theme (47.0-2) ...
173s Selecting previously unselected package fonts-noto-mono.
173s Preparing to unpack .../015-fonts-noto-mono_20201225-2_all.deb ...
173s Unpacking fonts-noto-mono (20201225-2) ...
173s Selecting previously unselected package fonts-noto-core.
173s Preparing to unpack .../016-fonts-noto-core_20201225-2_all.deb ...
173s Unpacking fonts-noto-core (20201225-2) ...
173s Selecting previously unselected package ttf-bitstream-vera.
173s Preparing to unpack .../017-ttf-bitstream-vera_1.10-8.2_all.deb ...
173s Unpacking ttf-bitstream-vera (1.10-8.2) ...
173s Selecting previously unselected package coot-data.
173s Preparing to unpack .../018-coot-data_1.1.09+dfsg-2build1_all.deb ...
173s Unpacking coot-data (1.1.09+dfsg-2build1) ...
174s Selecting previously unselected package fonts-freefont-ttf.
174s Preparing to unpack .../019-fonts-freefont-ttf_20211204+svn4273-2_all.deb ...
174s Unpacking fonts-freefont-ttf (20211204+svn4273-2) ...
174s Selecting previously unselected package fontconfig-config.
174s Preparing to unpack .../020-fontconfig-config_2.15.0-1.1ubuntu2_ppc64el.deb ...
174s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
174s Selecting previously unselected package libfontconfig1:ppc64el.
174s Preparing to unpack .../021-libfontconfig1_2.15.0-1.1ubuntu2_ppc64el.deb ...
174s Unpacking libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ...
174s Selecting previously unselected package libpixman-1-0:ppc64el.
174s Preparing to unpack .../022-libpixman-1-0_0.44.0-3_ppc64el.deb ...
174s Unpacking libpixman-1-0:ppc64el (0.44.0-3) ...
174s Selecting previously unselected package libxcb-render0:ppc64el.
174s Preparing to unpack .../023-libxcb-render0_1.17.0-2_ppc64el.deb ...
174s Unpacking libxcb-render0:ppc64el (1.17.0-2) ...
174s Selecting previously unselected package libxcb-shm0:ppc64el.
174s Preparing to unpack .../024-libxcb-shm0_1.17.0-2_ppc64el.deb ...
174s Unpacking libxcb-shm0:ppc64el (1.17.0-2) ...
174s Selecting previously unselected package libxrender1:ppc64el.
174s Preparing to unpack .../025-libxrender1_1%3a0.9.10-1.1build1_ppc64el.deb ...
174s Unpacking libxrender1:ppc64el (1:0.9.10-1.1build1) ...
174s Selecting previously unselected package libcairo2:ppc64el.
174s Preparing to unpack .../026-libcairo2_1.18.2-2_ppc64el.deb ...
174s Unpacking libcairo2:ppc64el (1.18.2-2) ...
174s Selecting previously unselected package libcairo-gobject2:ppc64el.
174s Preparing to unpack .../027-libcairo-gobject2_1.18.2-2_ppc64el.deb ...
174s Unpacking libcairo-gobject2:ppc64el (1.18.2-2) ...
174s Selecting previously unselected package gir1.2-freedesktop:ppc64el.
174s Preparing to unpack .../028-gir1.2-freedesktop_1.82.0-2_ppc64el.deb ...
174s Unpacking gir1.2-freedesktop:ppc64el (1.82.0-2) ...
174s Selecting previously unselected package gir1.2-gdkpixbuf-2.0:ppc64el.
174s Preparing to unpack .../029-gir1.2-gdkpixbuf-2.0_2.42.12+dfsg-1_ppc64el.deb ...
174s Unpacking gir1.2-gdkpixbuf-2.0:ppc64el (2.42.12+dfsg-1) ...
174s Selecting previously unselected package libgraphene-1.0-0:ppc64el.
174s Preparing to unpack .../030-libgraphene-1.0-0_1.10.8-4_ppc64el.deb ...
174s Unpacking libgraphene-1.0-0:ppc64el (1.10.8-4) ...
174s Selecting previously unselected package gir1.2-graphene-1.0:ppc64el.
174s Preparing to unpack .../031-gir1.2-graphene-1.0_1.10.8-4_ppc64el.deb ...
174s Unpacking gir1.2-graphene-1.0:ppc64el (1.10.8-4) ...
174s Selecting previously unselected package libgraphite2-3:ppc64el.
174s Preparing to unpack .../032-libgraphite2-3_1.3.14-2ubuntu1_ppc64el.deb ...
174s Unpacking libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ...
174s Selecting previously unselected package libharfbuzz0b:ppc64el.
174s Preparing to unpack .../033-libharfbuzz0b_10.0.1-1_ppc64el.deb ...
174s Unpacking libharfbuzz0b:ppc64el (10.0.1-1) ...
175s Selecting previously unselected package libharfbuzz-gobject0:ppc64el.
175s Preparing to unpack .../034-libharfbuzz-gobject0_10.0.1-1_ppc64el.deb ...
175s Unpacking libharfbuzz-gobject0:ppc64el (10.0.1-1) ...
175s Selecting previously unselected package gir1.2-harfbuzz-0.0:ppc64el.
175s Preparing to unpack .../035-gir1.2-harfbuzz-0.0_10.0.1-1_ppc64el.deb ...
175s Unpacking gir1.2-harfbuzz-0.0:ppc64el (10.0.1-1) ...
175s Selecting previously unselected package fontconfig.
175s Preparing to unpack .../036-fontconfig_2.15.0-1.1ubuntu2_ppc64el.deb ...
175s Unpacking fontconfig (2.15.0-1.1ubuntu2) ...
175s Selecting previously unselected package libthai-data.
175s Preparing to unpack .../037-libthai-data_0.1.29-2build1_all.deb ...
175s Unpacking libthai-data (0.1.29-2build1) ...
175s Selecting previously unselected package libdatrie1:ppc64el.
175s Preparing to unpack .../038-libdatrie1_0.2.13-3build1_ppc64el.deb ...
175s Unpacking libdatrie1:ppc64el (0.2.13-3build1) ...
175s Selecting previously unselected package libthai0:ppc64el.
175s Preparing to unpack .../039-libthai0_0.1.29-2build1_ppc64el.deb ...
175s Unpacking libthai0:ppc64el (0.1.29-2build1) ...
175s Selecting previously unselected package libpango-1.0-0:ppc64el.
175s Preparing to unpack .../040-libpango-1.0-0_1.54.0+ds-3_ppc64el.deb ...
175s Unpacking libpango-1.0-0:ppc64el (1.54.0+ds-3) ...
175s Selecting previously unselected package libpangoft2-1.0-0:ppc64el.
175s Preparing to unpack .../041-libpangoft2-1.0-0_1.54.0+ds-3_ppc64el.deb ...
175s Unpacking libpangoft2-1.0-0:ppc64el (1.54.0+ds-3) ...
175s Selecting previously unselected package libpangocairo-1.0-0:ppc64el.
175s Preparing to unpack .../042-libpangocairo-1.0-0_1.54.0+ds-3_ppc64el.deb ...
175s Unpacking libpangocairo-1.0-0:ppc64el (1.54.0+ds-3) ...
175s Selecting previously unselected package libxft2:ppc64el.
175s Preparing to unpack .../043-libxft2_2.3.6-1build1_ppc64el.deb ...
175s Unpacking libxft2:ppc64el (2.3.6-1build1) ...
175s Selecting previously unselected package libpangoxft-1.0-0:ppc64el.
175s Preparing to unpack .../044-libpangoxft-1.0-0_1.54.0+ds-3_ppc64el.deb ...
175s Unpacking libpangoxft-1.0-0:ppc64el (1.54.0+ds-3) ...
175s Selecting previously unselected package gir1.2-pango-1.0:ppc64el.
175s Preparing to unpack .../045-gir1.2-pango-1.0_1.54.0+ds-3_ppc64el.deb ...
175s Unpacking gir1.2-pango-1.0:ppc64el (1.54.0+ds-3) ...
175s Selecting previously unselected package libcairo-script-interpreter2:ppc64el.
175s Preparing to unpack .../046-libcairo-script-interpreter2_1.18.2-2_ppc64el.deb ...
175s Unpacking libcairo-script-interpreter2:ppc64el (1.18.2-2) ...
175s Selecting previously unselected package libcpdb2t64:ppc64el.
175s Preparing to unpack .../047-libcpdb2t64_2.0~b5-1.2build1_ppc64el.deb ...
175s Unpacking libcpdb2t64:ppc64el (2.0~b5-1.2build1) ...
175s Selecting previously unselected package libcpdb-frontend2t64:ppc64el.
175s Preparing to unpack .../048-libcpdb-frontend2t64_2.0~b5-1.2build1_ppc64el.deb ...
175s Unpacking libcpdb-frontend2t64:ppc64el (2.0~b5-1.2build1) ...
175s Selecting previously unselected package libepoxy0:ppc64el.
175s Preparing to unpack .../049-libepoxy0_1.5.10-2_ppc64el.deb ...
175s Unpacking libepoxy0:ppc64el (1.5.10-2) ...
175s Selecting previously unselected package libharfbuzz-subset0:ppc64el.
175s Preparing to unpack .../050-libharfbuzz-subset0_10.0.1-1_ppc64el.deb ...
175s Unpacking libharfbuzz-subset0:ppc64el (10.0.1-1) ...
175s Selecting previously unselected package libvulkan1:ppc64el.
175s Preparing to unpack .../051-libvulkan1_1.3.296.0-1_ppc64el.deb ...
175s Unpacking libvulkan1:ppc64el (1.3.296.0-1) ...
175s Selecting previously unselected package libwayland-client0:ppc64el.
175s Preparing to unpack .../052-libwayland-client0_1.23.0-1_ppc64el.deb ...
175s Unpacking libwayland-client0:ppc64el (1.23.0-1) ...
175s Selecting previously unselected package libwayland-egl1:ppc64el.
175s Preparing to unpack .../053-libwayland-egl1_1.23.0-1_ppc64el.deb ...
175s Unpacking libwayland-egl1:ppc64el (1.23.0-1) ...
175s Selecting previously unselected package libxfixes3:ppc64el.
175s Preparing to unpack .../054-libxfixes3_1%3a6.0.0-2build1_ppc64el.deb ...
175s Unpacking libxfixes3:ppc64el (1:6.0.0-2build1) ...
175s Selecting previously unselected package libxcursor1:ppc64el.
175s Preparing to unpack .../055-libxcursor1_1%3a1.2.2-1_ppc64el.deb ...
175s Unpacking libxcursor1:ppc64el (1:1.2.2-1) ...
175s Selecting previously unselected package libxdamage1:ppc64el.
175s Preparing to unpack .../056-libxdamage1_1%3a1.1.6-1build1_ppc64el.deb ...
175s Unpacking libxdamage1:ppc64el (1:1.1.6-1build1) ...
175s Selecting previously unselected package libxi6:ppc64el.
175s Preparing to unpack .../057-libxi6_2%3a1.8.2-1_ppc64el.deb ...
175s Unpacking libxi6:ppc64el (2:1.8.2-1) ...
175s Selecting previously unselected package libxinerama1:ppc64el.
175s Preparing to unpack .../058-libxinerama1_2%3a1.1.4-3build1_ppc64el.deb ...
175s Unpacking libxinerama1:ppc64el (2:1.1.4-3build1) ...
175s Selecting previously unselected package libxrandr2:ppc64el.
175s Preparing to unpack .../059-libxrandr2_2%3a1.5.4-1_ppc64el.deb ...
175s Unpacking libxrandr2:ppc64el (2:1.5.4-1) ...
175s Selecting previously unselected package libglvnd0:ppc64el.
175s Preparing to unpack .../060-libglvnd0_1.7.0-1build1_ppc64el.deb ...
175s Unpacking libglvnd0:ppc64el (1.7.0-1build1) ...
175s Selecting previously unselected package libgles2:ppc64el.
175s Preparing to unpack .../061-libgles2_1.7.0-1build1_ppc64el.deb ...
175s Unpacking libgles2:ppc64el (1.7.0-1build1) ...
175s Selecting previously unselected package libdconf1:ppc64el.
175s Preparing to unpack .../062-libdconf1_0.40.0-4build2_ppc64el.deb ...
175s Unpacking libdconf1:ppc64el (0.40.0-4build2) ...
175s Selecting previously unselected package dconf-service.
175s Preparing to unpack .../063-dconf-service_0.40.0-4build2_ppc64el.deb ...
175s Unpacking dconf-service (0.40.0-4build2) ...
175s Selecting previously unselected package dconf-gsettings-backend:ppc64el.
175s Preparing to unpack .../064-dconf-gsettings-backend_0.40.0-4build2_ppc64el.deb ...
175s Unpacking dconf-gsettings-backend:ppc64el (0.40.0-4build2) ...
175s Selecting previously unselected package libgtk-4-common.
175s Preparing to unpack .../065-libgtk-4-common_4.16.5+ds-2_all.deb ...
175s Unpacking libgtk-4-common (4.16.5+ds-2) ...
175s Selecting previously unselected package libgtk-4-1:ppc64el.
175s Preparing to unpack .../066-libgtk-4-1_4.16.5+ds-2_ppc64el.deb ...
175s Unpacking libgtk-4-1:ppc64el (4.16.5+ds-2) ...
176s Selecting previously unselected package gir1.2-gtk-4.0:ppc64el.
176s Preparing to unpack .../067-gir1.2-gtk-4.0_4.16.5+ds-2_ppc64el.deb ...
176s Unpacking gir1.2-gtk-4.0:ppc64el (4.16.5+ds-2) ...
176s Selecting previously unselected package rdkit-data.
176s Preparing to unpack .../068-rdkit-data_202409.2-2_all.deb ...
176s Unpacking rdkit-data (202409.2-2) ...
176s Selecting previously unselected package libblas3:ppc64el.
176s Preparing to unpack .../069-libblas3_3.12.0-4_ppc64el.deb ...
176s Unpacking libblas3:ppc64el (3.12.0-4) ...
176s Selecting previously unselected package libgfortran5:ppc64el.
176s Preparing to unpack .../070-libgfortran5_14.2.0-9ubuntu1_ppc64el.deb ...
176s Unpacking libgfortran5:ppc64el (14.2.0-9ubuntu1) ...
176s Selecting previously unselected package liblapack3:ppc64el.
176s Preparing to unpack .../071-liblapack3_3.12.0-4_ppc64el.deb ...
176s Unpacking liblapack3:ppc64el (3.12.0-4) ...
176s Selecting previously unselected package python3-numpy.
176s Preparing to unpack .../072-python3-numpy_1%3a1.26.4+ds-11ubuntu1_ppc64el.deb ...
176s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ...
177s Selecting previously unselected package libboost-python1.83.0.
177s Preparing to unpack .../073-libboost-python1.83.0_1.83.0-3.2ubuntu2_ppc64el.deb ...
177s Unpacking libboost-python1.83.0 (1.83.0-3.2ubuntu2) ...
177s Selecting previously unselected package libboost-numpy1.83.0.
177s Preparing to unpack .../074-libboost-numpy1.83.0_1.83.0-3.2ubuntu2_ppc64el.deb ...
177s Unpacking libboost-numpy1.83.0 (1.83.0-3.2ubuntu2) ...
177s Selecting previously unselected package libboost-serialization1.83.0:ppc64el.
177s Preparing to unpack .../075-libboost-serialization1.83.0_1.83.0-3.2ubuntu2_ppc64el.deb ...
177s Unpacking libboost-serialization1.83.0:ppc64el (1.83.0-3.2ubuntu2) ...
177s Selecting previously unselected package libcoordgen3:ppc64el.
177s Preparing to unpack .../076-libcoordgen3_3.0.2-1_ppc64el.deb ...
177s Unpacking libcoordgen3:ppc64el (3.0.2-1) ...
177s Selecting previously unselected package libboost-iostreams1.83.0:ppc64el.
177s Preparing to unpack .../077-libboost-iostreams1.83.0_1.83.0-3.2ubuntu2_ppc64el.deb ...
177s Unpacking libboost-iostreams1.83.0:ppc64el (1.83.0-3.2ubuntu2) ...
177s Selecting previously unselected package libinchi1.07.
177s Preparing to unpack .../078-libinchi1.07_1.07.1+dfsg-5_ppc64el.deb ...
177s Unpacking libinchi1.07 (1.07.1+dfsg-5) ...
177s Selecting previously unselected package libmaeparser1:ppc64el.
177s Preparing to unpack .../079-libmaeparser1_1.3.1-1build1_ppc64el.deb ...
177s Unpacking libmaeparser1:ppc64el (1.3.1-1build1) ...
177s Selecting previously unselected package librdkit1t64.
177s Preparing to unpack .../080-librdkit1t64_202409.2-2_ppc64el.deb ...
177s Unpacking librdkit1t64 (202409.2-2) ...
177s Selecting previously unselected package python3-rdkit.
177s Preparing to unpack .../081-python3-rdkit_202409.2-2_ppc64el.deb ...
177s Unpacking python3-rdkit (202409.2-2) ...
178s Selecting previously unselected package refmac-dictionary.
178s Preparing to unpack .../082-refmac-dictionary_5.41-3_all.deb ...
178s Unpacking refmac-dictionary (5.41-3) ...
180s Selecting previously unselected package libasound2-data.
180s Preparing to unpack .../083-libasound2-data_1.2.12-1_all.deb ...
180s Unpacking libasound2-data (1.2.12-1) ...
181s Selecting previously unselected package libasound2t64:ppc64el.
181s Preparing to unpack .../084-libasound2t64_1.2.12-1_ppc64el.deb ...
181s Unpacking libasound2t64:ppc64el (1.2.12-1) ...
181s Selecting previously unselected package libccp4-data.
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181s Unpacking libccp4-data (8.0.0-4) ...
181s Selecting previously unselected package libccp4c0t64:ppc64el.
181s Preparing to unpack .../086-libccp4c0t64_8.0.0-4_ppc64el.deb ...
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181s Selecting previously unselected package libmmdb2-0:ppc64el.
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181s Unpacking libmmdb2-0:ppc64el (2.0.22-1) ...
181s Selecting previously unselected package libevent-pthreads-2.1-7t64:ppc64el.
181s Preparing to unpack .../088-libevent-pthreads-2.1-7t64_2.1.12-stable-10_ppc64el.deb ...
181s Unpacking libevent-pthreads-2.1-7t64:ppc64el (2.1.12-stable-10) ...
181s Selecting previously unselected package librdmacm1t64:ppc64el.
181s Preparing to unpack .../089-librdmacm1t64_52.0-2ubuntu1_ppc64el.deb ...
181s Unpacking librdmacm1t64:ppc64el (52.0-2ubuntu1) ...
181s Selecting previously unselected package libfabric1:ppc64el.
181s Preparing to unpack .../090-libfabric1_1.17.0-3ubuntu1_ppc64el.deb ...
181s Unpacking libfabric1:ppc64el (1.17.0-3ubuntu1) ...
181s Selecting previously unselected package libhwloc15:ppc64el.
181s Preparing to unpack .../091-libhwloc15_2.11.2-1_ppc64el.deb ...
181s Unpacking libhwloc15:ppc64el (2.11.2-1) ...
181s Selecting previously unselected package libmunge2:ppc64el.
181s Preparing to unpack .../092-libmunge2_0.5.15-4build1_ppc64el.deb ...
181s Unpacking libmunge2:ppc64el (0.5.15-4build1) ...
181s Selecting previously unselected package libpciaccess0:ppc64el.
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181s Unpacking libpciaccess0:ppc64el (0.17-3build1) ...
181s Selecting previously unselected package libxnvctrl0:ppc64el.
181s Preparing to unpack .../094-libxnvctrl0_510.47.03-0ubuntu4_ppc64el.deb ...
181s Unpacking libxnvctrl0:ppc64el (510.47.03-0ubuntu4) ...
181s Selecting previously unselected package ocl-icd-libopencl1:ppc64el.
181s Preparing to unpack .../095-ocl-icd-libopencl1_2.3.2-1build1_ppc64el.deb ...
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181s Selecting previously unselected package libhwloc-plugins:ppc64el.
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181s Unpacking libhwloc-plugins:ppc64el (2.11.2-1) ...
181s Selecting previously unselected package libpmix2t64:ppc64el.
181s Preparing to unpack .../097-libpmix2t64_5.0.4-1_ppc64el.deb ...
181s Unpacking libpmix2t64:ppc64el (5.0.4-1) ...
181s Selecting previously unselected package libllvm17t64:ppc64el.
181s Preparing to unpack .../098-libllvm17t64_1%3a17.0.6-18_ppc64el.deb ...
181s Unpacking libllvm17t64:ppc64el (1:17.0.6-18) ...
182s Selecting previously unselected package libamd-comgr2:ppc64el.
182s Preparing to unpack .../099-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_ppc64el.deb ...
182s Unpacking libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3build2) ...
183s Selecting previously unselected package libhsakmt1:ppc64el.
183s Preparing to unpack .../100-libhsakmt1_5.7.0-1build1_ppc64el.deb ...
183s Unpacking libhsakmt1:ppc64el (5.7.0-1build1) ...
183s Selecting previously unselected package libhsa-runtime64-1.
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183s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ...
183s Selecting previously unselected package libamdhip64-5.
183s Preparing to unpack .../102-libamdhip64-5_5.7.1-5_ppc64el.deb ...
183s Unpacking libamdhip64-5 (5.7.1-5) ...
183s Selecting previously unselected package libgomp1:ppc64el.
183s Preparing to unpack .../103-libgomp1_14.2.0-9ubuntu1_ppc64el.deb ...
183s Unpacking libgomp1:ppc64el (14.2.0-9ubuntu1) ...
183s Selecting previously unselected package libibumad3:ppc64el.
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183s Unpacking libibumad3:ppc64el (52.0-2ubuntu1) ...
183s Selecting previously unselected package libibmad5:ppc64el.
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183s Unpacking libibmad5:ppc64el (52.0-2ubuntu1) ...
183s Selecting previously unselected package libucx0:ppc64el.
183s Preparing to unpack .../106-libucx0_1.17.0+ds-3build1_ppc64el.deb ...
183s Unpacking libucx0:ppc64el (1.17.0+ds-3build1) ...
183s Selecting previously unselected package libopenmpi3t64:ppc64el.
183s Preparing to unpack .../107-libopenmpi3t64_4.1.6-13.3ubuntu2_ppc64el.deb ...
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183s Selecting previously unselected package libclipper2:ppc64el.
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183s Unpacking libclipper2:ppc64el (2.1.20201109-2build1) ...
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183s Unpacking libgsl28:ppc64el (2.8+dfsg-5) ...
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183s Unpacking libssm2:ppc64el (1.4.0-2build1) ...
183s Selecting previously unselected package libcootapi1.1.
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183s Unpacking libcootapi1.1 (1.1.09+dfsg-2build1) ...
184s Selecting previously unselected package libogg0:ppc64el.
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184s Unpacking libogg0:ppc64el (1.3.5-3build1) ...
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184s Unpacking libvorbis0a:ppc64el (1.3.7-2) ...
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184s Unpacking libvorbisfile3:ppc64el (1.3.7-2) ...
184s Selecting previously unselected package coot.
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184s Unpacking coot (1.1.09+dfsg-2build1) ...
184s Selecting previously unselected package coot-doc.
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184s Unpacking libcootapi-dev (1.1.09+dfsg-2build1) ...
184s Setting up libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ...
184s Setting up libboost-python1.83.0 (1.83.0-3.2ubuntu2) ...
184s Setting up libpixman-1-0:ppc64el (0.44.0-3) ...
184s Setting up coot-doc (1.1.09+dfsg-2build1) ...
184s Setting up libsharpyuv0:ppc64el (1.4.0-0.1) ...
184s Setting up libpciaccess0:ppc64el (0.17-3build1) ...
184s Setting up ttf-bitstream-vera (1.10-8.2) ...
184s Setting up libxdamage1:ppc64el (1:1.1.6-1build1) ...
184s Setting up libogg0:ppc64el (1.3.5-3build1) ...
184s Setting up liblerc4:ppc64el (4.0.0+ds-5ubuntu1) ...
184s Setting up fonts-noto-mono (20201225-2) ...
184s Setting up hicolor-icon-theme (0.18-1) ...
184s Setting up libxi6:ppc64el (2:1.8.2-1) ...
184s Setting up libxrender1:ppc64el (1:0.9.10-1.1build1) ...
184s Setting up libdatrie1:ppc64el (0.2.13-3build1) ...
184s Setting up libgslcblas0:ppc64el (2.8+dfsg-5) ...
184s Setting up libmmdb2-0:ppc64el (2.0.22-1) ...
184s Setting up libxcb-render0:ppc64el (1.17.0-2) ...
184s Setting up libevent-pthreads-2.1-7t64:ppc64el (2.1.12-stable-10) ...
184s Setting up libglvnd0:ppc64el (1.7.0-1build1) ...
184s Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ...
184s Setting up libibumad3:ppc64el (52.0-2ubuntu1) ...
184s Setting up libdeflate0:ppc64el (1.22-1) ...
184s Setting up fonts-freefont-ttf (20211204+svn4273-2) ...
184s Setting up libcpdb2t64:ppc64el (2.0~b5-1.2build1) ...
184s Setting up libxcb-shm0:ppc64el (1.17.0-2) ...
184s Setting up libibmad5:ppc64el (52.0-2ubuntu1) ...
184s Setting up libcpdb-frontend2t64:ppc64el (2.0~b5-1.2build1) ...
184s Setting up libccp4-data (8.0.0-4) ...
184s Setting up libgomp1:ppc64el (14.2.0-9ubuntu1) ...
184s Setting up rdkit-data (202409.2-2) ...
184s Setting up libjbig0:ppc64el (2.1-6.1ubuntu2) ...
184s Setting up libxnvctrl0:ppc64el (510.47.03-0ubuntu4) ...
184s Setting up refmac-dictionary (5.41-3) ...
184s Setting up libdconf1:ppc64el (0.40.0-4build2) ...
184s Setting up libasound2-data (1.2.12-1) ...
184s Setting up libboost-serialization1.83.0:ppc64el (1.83.0-3.2ubuntu2) ...
184s Setting up libboost-numpy1.83.0 (1.83.0-3.2ubuntu2) ...
184s Setting up libblas3:ppc64el (3.12.0-4) ...
184s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode
184s Setting up libgles2:ppc64el (1.7.0-1build1) ...
184s Setting up libasound2t64:ppc64el (1.2.12-1) ...
184s Setting up libmunge2:ppc64el (0.5.15-4build1) ...
184s Setting up libllvm17t64:ppc64el (1:17.0.6-18) ...
184s Setting up libepoxy0:ppc64el (1.5.10-2) ...
184s Setting up libxfixes3:ppc64el (1:6.0.0-2build1) ...
184s Setting up libboost-iostreams1.83.0:ppc64el (1.83.0-3.2ubuntu2) ...
184s Setting up libxinerama1:ppc64el (2:1.1.4-3build1) ...
184s Setting up libhwloc15:ppc64el (2.11.2-1) ...
184s Setting up libvorbis0a:ppc64el (1.3.7-2) ...
184s Setting up libxrandr2:ppc64el (2:1.5.4-1) ...
184s Setting up libjpeg-turbo8:ppc64el (2.1.5-3ubuntu2) ...
184s Setting up libgfortran5:ppc64el (14.2.0-9ubuntu1) ...
184s Setting up libvulkan1:ppc64el (1.3.296.0-1) ...
184s Setting up libwebp7:ppc64el (1.4.0-0.1) ...
184s Setting up ocl-icd-libopencl1:ppc64el (2.3.2-1build1) ...
184s Setting up libccp4c0t64:ppc64el (8.0.0-4) ...
184s Setting up librdmacm1t64:ppc64el (52.0-2ubuntu1) ...
184s Setting up libharfbuzz0b:ppc64el (10.0.1-1) ...
184s Setting up libthai-data (0.1.29-2build1) ...
184s Setting up libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3build2) ...
184s Setting up libwayland-egl1:ppc64el (1.23.0-1) ...
184s Setting up libcoordgen3:ppc64el (3.0.2-1) ...
184s Setting up libgsl28:ppc64el (2.8+dfsg-5) ...
184s Setting up libinchi1.07 (1.07.1+dfsg-5) ...
184s Setting up fonts-noto-core (20201225-2) ...
184s Setting up libhsakmt1:ppc64el (5.7.0-1build1) ...
184s Setting up libgraphene-1.0-0:ppc64el (1.10.8-4) ...
184s Setting up libwayland-client0:ppc64el (1.23.0-1) ...
184s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ...
184s Setting up gir1.2-graphene-1.0:ppc64el (1.10.8-4) ...
184s Setting up libfabric1:ppc64el (1.17.0-3ubuntu1) ...
184s Setting up liblapack3:ppc64el (3.12.0-4) ...
184s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode
184s Setting up libssm2:ppc64el (1.4.0-2build1) ...
184s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
184s Setting up libxcursor1:ppc64el (1:1.2.2-1) ...
184s Setting up dconf-service (0.40.0-4build2) ...
184s Setting up libharfbuzz-gobject0:ppc64el (10.0.1-1) ...
184s Setting up libhwloc-plugins:ppc64el (2.11.2-1) ...
184s Setting up libmaeparser1:ppc64el (1.3.1-1build1) ...
184s Setting up libthai0:ppc64el (0.1.29-2build1) ...
184s Setting up libvorbisfile3:ppc64el (1.3.7-2) ...
184s Setting up libpmix2t64:ppc64el (5.0.4-1) ...
184s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ...
187s Setting up libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ...
187s Setting up libhsa-runtime64-1 (5.7.1-2build1) ...
187s Setting up libharfbuzz-subset0:ppc64el (10.0.1-1) ...
187s Setting up libgdk-pixbuf-2.0-0:ppc64el (2.42.12+dfsg-1) ...
187s Setting up coot-data (1.1.09+dfsg-2build1) ...
187s Setting up gtk-update-icon-cache (4.16.5+ds-2) ...
187s Setting up dconf-gsettings-backend:ppc64el (0.40.0-4build2) ...
187s Setting up gir1.2-gdkpixbuf-2.0:ppc64el (2.42.12+dfsg-1) ...
187s Setting up libamdhip64-5 (5.7.1-5) ...
187s Setting up libgtk-4-common (4.16.5+ds-2) ...
187s Setting up libucx0:ppc64el (1.17.0+ds-3build1) ...
187s Setting up libopenmpi3t64:ppc64el (4.1.6-13.3ubuntu2) ...
187s Setting up sfftw2 (2.1.5-7) ...
187s Setting up libclipper2:ppc64el (2.1.20201109-2build1) ...
187s Setting up libcootapi1.1 (1.1.09+dfsg-2build1) ...
187s Setting up libcootapi-dev (1.1.09+dfsg-2build1) ...
187s Setting up adwaita-icon-theme (47.0-2) ...
187s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
187s Setting up humanity-icon-theme (0.6.16) ...
188s Setting up ubuntu-mono (24.04-0ubuntu1) ...
188s Processing triggers for man-db (2.13.0-1) ...
191s Processing triggers for libglib2.0-0t64:ppc64el (2.82.2-3) ...
191s Processing triggers for sgml-base (1.31) ...
191s Setting up libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ...
191s Setting up fontconfig (2.15.0-1.1ubuntu2) ...
193s Regenerating fonts cache... done.
193s Setting up libxft2:ppc64el (2.3.6-1build1) ...
193s Processing triggers for libc-bin (2.40-1ubuntu3) ...
193s Setting up libpango-1.0-0:ppc64el (1.54.0+ds-3) ...
193s Setting up libcairo2:ppc64el (1.18.2-2) ...
193s Setting up libcairo-gobject2:ppc64el (1.18.2-2) ...
193s Setting up libpangoft2-1.0-0:ppc64el (1.54.0+ds-3) ...
193s Setting up libpangocairo-1.0-0:ppc64el (1.54.0+ds-3) ...
193s Setting up libcairo-script-interpreter2:ppc64el (1.18.2-2) ...
193s Setting up gir1.2-freedesktop:ppc64el (1.82.0-2) ...
193s Setting up libpangoxft-1.0-0:ppc64el (1.54.0+ds-3) ...
193s Setting up librdkit1t64 (202409.2-2) ...
193s Setting up gir1.2-harfbuzz-0.0:ppc64el (10.0.1-1) ...
193s Setting up gir1.2-pango-1.0:ppc64el (1.54.0+ds-3) ...
193s Setting up python3-rdkit (202409.2-2) ...
194s Setting up libgtk-4-1:ppc64el (4.16.5+ds-2) ...
194s Setting up gir1.2-gtk-4.0:ppc64el (4.16.5+ds-2) ...
194s Setting up coot (1.1.09+dfsg-2build1) ...
195s /usr/lib/python3/dist-packages/coot/tautomer.py:289: SyntaxWarning: invalid escape sequence '\C'
195s   ('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'}),
195s Processing triggers for libc-bin (2.40-1ubuntu3) ...
197s autopkgtest [09:57:21]: test command1: coot --self-test
197s autopkgtest [09:57:21]: test command1: [-----------------------
197s INFO:: Running internal self tests
205s  INFO:: Test Clipper core   : OK
205s  INFO:: Test Clipper contrib: OK
205s run_internal_tests() --------- we have 8 internal test functionns 
205s Entering test: kevin's torsion test
205s PASS: kevin's torsion test
205s Entering test: test_alt_conf_rotamers
205s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb
205s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read.
205s chis.size() 2 (should be 2)
205s DEBUG:: i_rot 0 chi: alt-conf: A chi-1: 65.911
205s DEBUG:: i_rot 1 chi: alt-conf: B chi-1: -144.68
205s For residue 80 chis size 1
205s   residue 80 chis: -56.8781 -80.8484
205s PASS: test_alt_conf_rotamers
205s Entering test: test_fragmemt_atom_selection
205s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb
205s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read.
205s ----------------- create_mmdbmanager_from_inverted_atom_selection() 
205s    n_initial: 1465   n_1: 1401   n_2: 64
205s PASS: test_fragmemt_atom_selection
205s Entering test: test_add_atom
205s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb
205s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read.
205s PASS: test_add_atom
205s Entering test: test segid exchange
205s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb
205s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read.
205s    Test with a rogue segid 
205s    INFO:: No consistent segids for residue 1
205s PASS: test segid exchange
205s Entering test: test peak search non-close
205s mtz_file_name /usr/share/coot/data/rnasa-1.8-all_refmac1.mtz
205s FFT Reso...0.444444
205s Sampling rate...1.5
205s Grid...Nuvw = ( 132, 160,  80)
205s Cell... Cell (64.897,78.323,38.792,    90,    90,    90)
205s Spacegroup...P 21 21 21
205s    There are 2260 peaks and 0 problem peaks
205s PASS: test peak search non-close
205s Entering test: test symop card
205s 1 0 0
205s 0 1 0
205s 0 0 1
205s translations: -1 0 0
205s PASS: test symop card
205s Entering test: SSM sequence alignment output
205s 
205s --
205s  Moving: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNR--ESVLPTQSYGYYHEYTVITP--GARTRG
205s  Target: ---SGTVCLSALPPEATDTLNLIASDGPFPYSQDG
205s 
205s  Moving: TRRI.ICGEATQEDY..YTGDHYATFSLIDQTC
205s 
205s --
205s  Moving: D
205s  Target: --SGTVCLSALPPEATDTLNLIASDGPFPYSQDG
205s 
205s --
205s  Moving: DVSGTVCLSALPPEATDTLNIASDGPFPYSQDGVVFQNR--ESVLPQSYG
205s  Target: --SGTVCLSALPPEATDTLNIASDGPFPYSQDXXxxxxxxxxxxxxxxxG
205s 
205s --
205s PASS: SSM sequence alignment output
205s autopkgtest [09:57:29]: test command1: -----------------------]
206s command1             PASS
206s autopkgtest [09:57:30]: test command1:  - - - - - - - - - - results - - - - - - - - - -
206s autopkgtest [09:57:30]: test command2: preparing testbed
207s Reading package lists...
207s Building dependency tree...
207s Reading state information...
207s Starting pkgProblemResolver with broken count: 0
207s Starting 2 pkgProblemResolver with broken count: 0
207s Done
208s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
209s autopkgtest [09:57:33]: test command2: pyrogen --help
209s autopkgtest [09:57:33]: test command2: [-----------------------
210s Traceback (most recent call last):
210s   File "<frozen runpy>", line 198, in _run_module_as_main
210s   File "<frozen runpy>", line 88, in _run_code
210s   File "/usr/lib/python3/dist-packages/coot/pyrogen.py", line 38, in <module>
210s     import pyrogen_swig as pysw # relies on above rdkit.Chem import AllChem (but ideally should not)
210s     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
210s   File "/usr/lib/python3/dist-packages/coot/pyrogen_swig.py", line 12, in <module>
210s     import _pyrogen_swig
210s ImportError: /usr/lib/powerpc64le-linux-gnu/coot/libcoot-lidia-core.so.0: undefined symbol: _ZN5RDKit9ConformerC1ERKS0_
210s autopkgtest [09:57:34]: test command2: -----------------------]
211s autopkgtest [09:57:35]: test command2:  - - - - - - - - - - results - - - - - - - - - -
211s command2             FAIL non-zero exit status 1
211s autopkgtest [09:57:35]: test command2:  - - - - - - - - - - stderr - - - - - - - - - -
211s Traceback (most recent call last):
211s   File "<frozen runpy>", line 198, in _run_module_as_main
211s   File "<frozen runpy>", line 88, in _run_code
211s   File "/usr/lib/python3/dist-packages/coot/pyrogen.py", line 38, in <module>
211s     import pyrogen_swig as pysw # relies on above rdkit.Chem import AllChem (but ideally should not)
211s     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
211s   File "/usr/lib/python3/dist-packages/coot/pyrogen_swig.py", line 12, in <module>
211s     import _pyrogen_swig
211s ImportError: /usr/lib/powerpc64le-linux-gnu/coot/libcoot-lidia-core.so.0: undefined symbol: _ZN5RDKit9ConformerC1ERKS0_
211s autopkgtest [09:57:35]: @@@@@@@@@@@@@@@@@@@@ summary
211s command1             PASS
211s command2             FAIL non-zero exit status 1
222s nova [W] Using flock in prodstack6-ppc64el
222s Creating nova instance adt-plucky-ppc64el-coot-20241203-093440-juju-7f2275-prod-proposed-migration-environment-15-e4d34576-cccb-4dde-a445-8f370574704d from image adt/ubuntu-plucky-ppc64el-server-20241203.img (UUID 71a10fe7-f168-4d19-8647-b89d09dd4cc0)...