0s autopkgtest [18:21:14]: starting date and time: 2025-12-04 18:21:14+0000 0s autopkgtest [18:21:14]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [18:21:14]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.qdf2qa9c/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade coot --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.9-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-13.secgroup --name adt-resolute-arm64-coot-20251204-182113-juju-7f2275-prod-proposed-migration-environment-2-673651bd-90c7-4da2-8cbe-de6274e05ec6 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 5s Creating nova instance adt-resolute-arm64-coot-20251204-182113-juju-7f2275-prod-proposed-migration-environment-2-673651bd-90c7-4da2-8cbe-de6274e05ec6 from image adt/ubuntu-resolute-arm64-server-20251204.img (UUID d10d485b-270b-4b77-bdc2-f40c1cd474cf)... 283s autopkgtest [18:25:57]: testbed dpkg architecture: arm64 284s autopkgtest [18:25:58]: testbed apt version: 3.1.12 286s autopkgtest [18:26:00]: @@@@@@@@@@@@@@@@@@@@ test bed setup 287s autopkgtest [18:26:01]: testbed release detected to be: None 288s autopkgtest [18:26:02]: updating testbed package index (apt update) 289s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 289s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 289s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 289s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 289s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [947 kB] 290s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.1 kB] 290s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [162 kB] 290s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [233 kB] 291s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [7012 B] 291s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [120 B] 291s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [759 kB] 291s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [20.6 kB] 291s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [8716 B] 291s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [644 B] 294s Fetched 2285 kB in 3s (852 kB/s) 295s Reading package lists... 299s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 299s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 300s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 300s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 301s Reading package lists... 301s Reading package lists... 301s Building dependency tree... 301s Reading state information... 302s Calculating upgrade... 302s The following packages will be upgraded: 302s libpython3-stdlib python3 python3-gdbm python3-minimal 302s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 302s Need to get 72.9 kB of archives. 302s After this operation, 2048 B of additional disk space will be used. 302s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.13.9-2 [28.1 kB] 302s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.13.9-2 [23.0 kB] 302s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.13.9-2 [10.8 kB] 302s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-gdbm arm64 3.13.9-2 [11.0 kB] 303s dpkg-preconfigure: unable to re-open stdin: No such file or directory 303s Fetched 72.9 kB in 1s (71.6 kB/s) 303s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 88300 files and directories currently installed.) 303s Preparing to unpack .../python3-minimal_3.13.9-2_arm64.deb ... 303s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 303s Setting up python3-minimal (3.13.9-2) ... 303s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 88300 files and directories currently installed.) 303s Preparing to unpack .../python3_3.13.9-2_arm64.deb ... 303s running python pre-rtupdate hooks for python3.13... 303s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 304s Preparing to unpack .../libpython3-stdlib_3.13.9-2_arm64.deb ... 304s Unpacking libpython3-stdlib:arm64 (3.13.9-2) over (3.13.7-1) ... 304s Preparing to unpack .../python3-gdbm_3.13.9-2_arm64.deb ... 304s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 304s Setting up python3-gdbm (3.13.9-2) ... 304s Setting up libpython3-stdlib:arm64 (3.13.9-2) ... 304s Setting up python3 (3.13.9-2) ... 304s running python rtupdate hooks for python3.13... 304s running python post-rtupdate hooks for python3.13... 304s Processing triggers for man-db (2.13.1-1) ... 305s autopkgtest [18:26:19]: upgrading testbed (apt dist-upgrade and autopurge) 305s Reading package lists... 305s Building dependency tree... 305s Reading state information... 305s Calculating upgrade... 306s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 306s Reading package lists... 306s Building dependency tree... 306s Reading state information... 306s Solving dependencies... 307s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 310s autopkgtest [18:26:24]: testbed running kernel: Linux 6.17.0-6-generic #6-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 7 14:22:06 UTC 2025 310s autopkgtest [18:26:24]: @@@@@@@@@@@@@@@@@@@@ apt-source coot 327s Get:1 http://ftpmaster.internal/ubuntu resolute/universe coot 1.1.18+dfsg-2build1 (dsc) [2996 B] 327s Get:2 http://ftpmaster.internal/ubuntu resolute/universe coot 1.1.18+dfsg-2build1 (tar) [97.7 MB] 327s Get:3 http://ftpmaster.internal/ubuntu resolute/universe coot 1.1.18+dfsg-2build1 (diff) [54.5 kB] 327s gpgv: Signature made Thu Nov 27 07:12:11 2025 UTC 327s gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9 327s gpgv: Can't check signature: No public key 327s dpkg-source: warning: cannot verify inline signature for ./coot_1.1.18+dfsg-2build1.dsc: no acceptable signature found 330s autopkgtest [18:26:44]: testing package coot version 1.1.18+dfsg-2build1 333s autopkgtest [18:26:47]: build not needed 397s autopkgtest [18:27:51]: test command1: preparing testbed 397s Reading package lists... 397s Building dependency tree... 397s Reading state information... 397s Solving dependencies... 398s The following NEW packages will be installed: 398s adwaita-icon-theme coot coot-data coot-doc dconf-gsettings-backend 398s dconf-service fontconfig fontconfig-config fonts-freefont-ttf 398s fonts-noto-core fonts-noto-mono gir1.2-freedesktop gir1.2-gdkpixbuf-2.0 398s gir1.2-graphene-1.0 gir1.2-gtk-4.0 gir1.2-harfbuzz-0.0 gir1.2-pango-1.0 398s gtk-update-icon-cache hicolor-icon-theme libamd-comgr3 libamdhip64-6 398s libasound2-data libasound2t64 libblas3 libboost-iostreams1.88.0 398s libboost-numpy1.88.0 libboost-python1.88.0 libboost-serialization1.88.0 398s libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libccp4-data 398s libccp4c0t64 libclipper2 libcoordgen3 libcootapi-dev libcootapi1.1 398s libcpdb-frontend2t64 libcpdb2t64 libdatrie1 libdconf1 libdeflate0 398s libegl-mesa0 libegl1 libepoxy0 libevent-pthreads-2.1-7t64 libfabric1 398s libfontconfig1 libgbm1 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common 398s libgfortran5 libgl1 libgl1-mesa-dri libgles2 libglvnd0 libglx-mesa0 libglx0 398s libgomp1 libgraphene-1.0-0 libgraphite2-3 libgsl28 libgslcblas0 398s libgstreamer-gl1.0-0 libgstreamer-plugins-base1.0-0 libgstreamer1.0-0 398s libgtk-4-1 libgtk-4-common libharfbuzz-gobject0 libharfbuzz-subset0 398s libharfbuzz0b libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 398s libibmad5 libibumad3 libinchi1.07 libjbig0 libjpeg-turbo8 libjpeg8 398s liblapack3 liblerc4 libllvm21 libmaeparser1 libmmdb2-0 libogg0 libopenmpi40 398s liborc-0.4-0t64 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 398s libpangoxft-1.0-0 libpciaccess0 libpixman-1-0 librdkit1t64 librdmacm1t64 398s librsvg2-2 libsharpyuv0 libssm2 libthai-data libthai0 libtiff6 libucx0 398s libvorbis0a libvorbisfile3 libvulkan1 libwayland-client0 libwayland-cursor0 398s libwayland-egl1 libwebp7 libx11-xcb1 libxcb-dri3-0 libxcb-glx0 398s libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 398s libxcb-xfixes0 libxcursor1 libxdamage1 libxfixes3 libxft2 libxi6 398s libxinerama1 libxnvctrl0 libxrandr2 libxrender1 libxshmfence1 libxxf86vm1 398s mesa-libgallium ocl-icd-libopencl1 python3-numpy python3-numpy-dev 398s python3-rdkit rdkit-data refmac-dictionary sfftw2 ttf-bitstream-vera 400s 0 upgraded, 140 newly installed, 0 to remove and 0 not upgraded. 400s Need to get 189 MB of archives. 400s After this operation, 920 MB of additional disk space will be used. 400s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 402s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7 [181 kB] 405s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-9ubuntu1 [450 kB] 405s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7 [2300 kB] 406s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 407s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libgdk-pixbuf2.0-common all 2.44.4+dfsg-1 [8584 B] 407s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu2 [165 kB] 407s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 407s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 407s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 407s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 407s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 407s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 407s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 407s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libgdk-pixbuf-2.0-0 arm64 2.44.4+dfsg-1 [149 kB] 407s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 gtk-update-icon-cache arm64 4.20.3+ds-2 [54.6 kB] 407s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 hicolor-icon-theme all 0.18-2 [13.3 kB] 407s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 adwaita-icon-theme all 49.0-1 [581 kB] 407s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-noto-mono all 20201225-2 [435 kB] 407s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-noto-core all 20201225-2 [13.3 MB] 409s Get:21 http://ftpmaster.internal/ubuntu resolute/universe arm64 ttf-bitstream-vera all 1.10-11 [242 kB] 409s Get:22 http://ftpmaster.internal/ubuntu resolute/universe arm64 coot-data all 1.1.18+dfsg-2build1 [14.5 MB] 412s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-freefont-ttf all 20211204+svn4273-4 [5649 kB] 413s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.15.0-2.3ubuntu1 [38.1 kB] 413s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.15.0-2.3ubuntu1 [144 kB] 413s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 413s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2build1 [18.1 kB] 413s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2build1 [6234 B] 413s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 413s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-1build1 [592 kB] 413s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo-gobject2 arm64 1.18.4-1build1 [128 kB] 413s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 gir1.2-freedesktop arm64 1.86.0-6 [65.9 kB] 414s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 gir1.2-gdkpixbuf-2.0 arm64 2.44.4+dfsg-1 [9302 B] 414s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphene-1.0-0 arm64 1.10.8-5 [48.0 kB] 414s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 gir1.2-graphene-1.0 arm64 1.10.8-5 [11.1 kB] 414s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 414s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.1.0-1 [523 kB] 414s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz-gobject0 arm64 12.1.0-1 [32.8 kB] 414s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 gir1.2-harfbuzz-0.0 arm64 12.1.0-1 [44.5 kB] 414s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig arm64 2.15.0-2.3ubuntu1 [191 kB] 414s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai-data all 0.1.29-2build2 [153 kB] 414s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libdatrie1 arm64 0.2.14-1 [19.6 kB] 414s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai0 arm64 0.1.29-2build2 [18.4 kB] 414s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 libpango-1.0-0 arm64 1.56.3-2 [237 kB] 414s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangoft2-1.0-0 arm64 1.56.3-2 [50.2 kB] 414s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangocairo-1.0-0 arm64 1.56.3-2 [27.7 kB] 414s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 414s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangoxft-1.0-0 arm64 1.56.3-2 [20.0 kB] 414s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 gir1.2-pango-1.0 arm64 1.56.3-2 [34.7 kB] 414s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo-script-interpreter2 arm64 1.18.4-1build1 [67.0 kB] 414s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 libcpdb2t64 arm64 2.0~b7-0ubuntu3 [31.1 kB] 414s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 libcpdb-frontend2t64 arm64 2.0~b7-0ubuntu3 [22.1 kB] 414s Get:53 http://ftpmaster.internal/ubuntu resolute/main arm64 libepoxy0 arm64 1.5.10-2 [236 kB] 414s Get:54 http://ftpmaster.internal/ubuntu resolute/main arm64 libglvnd0 arm64 1.7.0-1build2 [59.2 kB] 414s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 libx11-xcb1 arm64 2:1.8.12-1build1 [8216 B] 414s Get:56 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-dri3-0 arm64 1.17.0-2build1 [8120 B] 414s Get:57 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-present0 arm64 1.17.0-2build1 [6560 B] 414s Get:58 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-randr0 arm64 1.17.0-2build1 [20.2 kB] 414s Get:59 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-sync1 arm64 1.17.0-2build1 [10.4 kB] 414s Get:60 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-xfixes0 arm64 1.17.0-2build1 [11.4 kB] 414s Get:61 http://ftpmaster.internal/ubuntu resolute/main arm64 libxshmfence1 arm64 1.3.3-1 [5378 B] 414s Get:62 http://ftpmaster.internal/ubuntu resolute/main arm64 mesa-libgallium arm64 25.2.7-1ubuntu1 [12.1 MB] 415s Get:63 http://ftpmaster.internal/ubuntu resolute/main arm64 libgbm1 arm64 25.2.7-1ubuntu1 [34.5 kB] 415s Get:64 http://ftpmaster.internal/ubuntu resolute/main arm64 libwayland-client0 arm64 1.24.0-2 [27.6 kB] 415s Get:65 http://ftpmaster.internal/ubuntu resolute/main arm64 libegl-mesa0 arm64 25.2.7-1ubuntu1 [115 kB] 415s Get:66 http://ftpmaster.internal/ubuntu resolute/main arm64 libegl1 arm64 1.7.0-1build2 [31.9 kB] 415s Get:67 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-glx0 arm64 1.17.0-2build1 [27.8 kB] 415s Get:68 http://ftpmaster.internal/ubuntu resolute/main arm64 libxxf86vm1 arm64 1:1.1.4-2 [10.2 kB] 415s Get:69 http://ftpmaster.internal/ubuntu resolute/main arm64 libvulkan1 arm64 1.4.328.1-1 [169 kB] 415s Get:70 http://ftpmaster.internal/ubuntu resolute/main arm64 libgl1-mesa-dri arm64 25.2.7-1ubuntu1 [35.9 kB] 415s Get:71 http://ftpmaster.internal/ubuntu resolute/main arm64 libglx-mesa0 arm64 25.2.7-1ubuntu1 [110 kB] 415s Get:72 http://ftpmaster.internal/ubuntu resolute/main arm64 libglx0 arm64 1.7.0-1build2 [34.5 kB] 415s Get:73 http://ftpmaster.internal/ubuntu resolute/main arm64 libgl1 arm64 1.7.0-1build2 [104 kB] 415s Get:74 http://ftpmaster.internal/ubuntu resolute/main arm64 libgstreamer1.0-0 arm64 1.27.2-2 [1162 kB] 415s Get:75 http://ftpmaster.internal/ubuntu resolute/main arm64 liborc-0.4-0t64 arm64 1:0.4.41-1 [202 kB] 415s Get:76 http://ftpmaster.internal/ubuntu resolute/main arm64 libgstreamer-plugins-base1.0-0 arm64 1.27.2-3build1 [854 kB] 415s Get:77 http://ftpmaster.internal/ubuntu resolute/main arm64 libwayland-cursor0 arm64 1.24.0-2 [10.6 kB] 415s Get:78 http://ftpmaster.internal/ubuntu resolute/main arm64 libwayland-egl1 arm64 1.24.0-2 [6172 B] 415s Get:79 http://ftpmaster.internal/ubuntu resolute/main arm64 libgstreamer-gl1.0-0 arm64 1.27.2-3build1 [220 kB] 415s Get:80 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz-subset0 arm64 12.1.0-1 [503 kB] 415s Get:81 http://ftpmaster.internal/ubuntu resolute/main arm64 librsvg2-2 arm64 2.61.3+dfsg-2 [1752 kB] 415s Get:82 http://ftpmaster.internal/ubuntu resolute/main arm64 libxfixes3 arm64 1:6.0.0-2build1 [11.2 kB] 415s Get:83 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcursor1 arm64 1:1.2.3-1 [22.2 kB] 415s Get:84 http://ftpmaster.internal/ubuntu resolute/main arm64 libxdamage1 arm64 1:1.1.6-1build1 [6236 B] 415s Get:85 http://ftpmaster.internal/ubuntu resolute/main arm64 libxi6 arm64 2:1.8.2-1 [32.4 kB] 415s Get:86 http://ftpmaster.internal/ubuntu resolute/main arm64 libxinerama1 arm64 2:1.1.4-3build1 [6394 B] 415s Get:87 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrandr2 arm64 2:1.5.4-1 [19.6 kB] 415s Get:88 http://ftpmaster.internal/ubuntu resolute/main arm64 libgles2 arm64 1.7.0-1build2 [17.9 kB] 415s Get:89 http://ftpmaster.internal/ubuntu resolute/main arm64 libdconf1 arm64 0.49.0-2 [40.7 kB] 415s Get:90 http://ftpmaster.internal/ubuntu resolute/main arm64 dconf-service arm64 0.49.0-2 [27.2 kB] 415s Get:91 http://ftpmaster.internal/ubuntu resolute/main arm64 dconf-gsettings-backend arm64 0.49.0-2 [21.9 kB] 415s Get:92 http://ftpmaster.internal/ubuntu resolute/main arm64 libgtk-4-common all 4.20.3+ds-2 [1545 kB] 416s Get:93 http://ftpmaster.internal/ubuntu resolute/main arm64 libgtk-4-1 arm64 4.20.3+ds-2 [3304 kB] 416s Get:94 http://ftpmaster.internal/ubuntu resolute/main arm64 gir1.2-gtk-4.0 arm64 4.20.3+ds-2 [220 kB] 416s Get:95 http://ftpmaster.internal/ubuntu resolute/universe arm64 rdkit-data all 202503.6-3ubuntu2 [12.6 MB] 417s Get:96 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-python1.88.0 arm64 1.88.0-1.4ubuntu2 [350 kB] 417s Get:97 http://ftpmaster.internal/ubuntu resolute/universe arm64 libboost-numpy1.88.0 arm64 1.88.0-1.4ubuntu2 [247 kB] 417s Get:98 http://ftpmaster.internal/ubuntu resolute/universe arm64 libboost-serialization1.88.0 arm64 1.88.0-1.4ubuntu2 [343 kB] 417s Get:99 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcoordgen3 arm64 3.0.2-1 [207 kB] 417s Get:100 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-iostreams1.88.0 arm64 1.88.0-1.4ubuntu2 [261 kB] 417s Get:101 http://ftpmaster.internal/ubuntu resolute/universe arm64 libinchi1.07 arm64 1.07.3+dfsg-1 [573 kB] 417s Get:102 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmaeparser1 arm64 1.3.3-3 [86.2 kB] 418s Get:103 http://ftpmaster.internal/ubuntu resolute/universe arm64 librdkit1t64 arm64 202503.6-3ubuntu2 [5799 kB] 418s Get:104 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-rdkit arm64 202503.6-3ubuntu2 [4725 kB] 419s Get:105 http://ftpmaster.internal/ubuntu resolute/universe arm64 refmac-dictionary all 5.41-3 [16.7 MB] 421s Get:106 http://ftpmaster.internal/ubuntu resolute/main arm64 libasound2-data all 1.2.14-2ubuntu1 [21.3 kB] 421s Get:107 http://ftpmaster.internal/ubuntu resolute/main arm64 libasound2t64 arm64 1.2.14-2ubuntu1 [390 kB] 421s Get:108 http://ftpmaster.internal/ubuntu resolute/universe arm64 libccp4-data all 8.0.0-5 [65.2 kB] 421s Get:109 http://ftpmaster.internal/ubuntu resolute/universe arm64 libccp4c0t64 arm64 8.0.0-5 [99.8 kB] 421s Get:110 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmmdb2-0 arm64 2.0.22-1 [347 kB] 421s Get:111 http://ftpmaster.internal/ubuntu resolute/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10build1 [8272 B] 421s Get:112 http://ftpmaster.internal/ubuntu resolute/main arm64 librdmacm1t64 arm64 56.1-1ubuntu1 [71.4 kB] 421s Get:113 http://ftpmaster.internal/ubuntu resolute/universe arm64 libfabric1 arm64 2.1.0-1.1 [622 kB] 421s Get:114 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhwloc15 arm64 2.12.2-1 [169 kB] 421s Get:115 http://ftpmaster.internal/ubuntu resolute/main arm64 libllvm21 arm64 1:21.1.2-2ubuntu6 [29.4 MB] 423s Get:116 http://ftpmaster.internal/ubuntu resolute/universe arm64 libamd-comgr3 arm64 7.0.2+dfsg-2 [14.8 MB] 425s Get:117 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhsakmt1 arm64 6.4.3+dfsg-3 [67.5 kB] 425s Get:118 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhsa-runtime64-1 arm64 6.4.3+dfsg-3 [366 kB] 425s Get:119 http://ftpmaster.internal/ubuntu resolute/universe arm64 libamdhip64-6 arm64 6.4.3-4 [10.4 MB] 426s Get:120 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-9ubuntu1 [147 kB] 426s Get:121 http://ftpmaster.internal/ubuntu resolute/main arm64 libibumad3 arm64 56.1-1ubuntu1 [31.3 kB] 426s Get:122 http://ftpmaster.internal/ubuntu resolute/main arm64 libibmad5 arm64 56.1-1ubuntu1 [44.1 kB] 426s Get:123 http://ftpmaster.internal/ubuntu resolute/universe arm64 libucx0 arm64 1.19.0+ds-1build1 [1187 kB] 426s Get:124 http://ftpmaster.internal/ubuntu resolute/main arm64 libpciaccess0 arm64 0.18.1-1ubuntu2 [19.4 kB] 426s Get:125 http://ftpmaster.internal/ubuntu resolute/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu4 [12.4 kB] 426s Get:126 http://ftpmaster.internal/ubuntu resolute/main arm64 ocl-icd-libopencl1 arm64 2.3.4-1 [41.1 kB] 426s Get:127 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhwloc-plugins arm64 2.12.2-1 [16.6 kB] 426s Get:128 http://ftpmaster.internal/ubuntu resolute/universe arm64 libopenmpi40 arm64 5.0.8-8ubuntu1 [3274 kB] 426s Get:129 http://ftpmaster.internal/ubuntu resolute/universe arm64 sfftw2 arm64 2.1.5-7build1 [184 kB] 426s Get:130 http://ftpmaster.internal/ubuntu resolute/universe arm64 libclipper2 arm64 2.1.20201109-2build1 [1150 kB] 427s Get:131 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgslcblas0 arm64 2.8+dfsg-5.1ubuntu1 [96.3 kB] 427s Get:132 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgsl28 arm64 2.8+dfsg-5.1ubuntu1 [1029 kB] 427s Get:133 http://ftpmaster.internal/ubuntu resolute/universe arm64 libssm2 arm64 1.4.0-2build1 [83.8 kB] 427s Get:134 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcootapi1.1 arm64 1.1.18+dfsg-2build1 [3808 kB] 427s Get:135 http://ftpmaster.internal/ubuntu resolute/main arm64 libogg0 arm64 1.3.6-2 [23.0 kB] 427s Get:136 http://ftpmaster.internal/ubuntu resolute/main arm64 libvorbis0a arm64 1.3.7-3build1 [99.3 kB] 427s Get:137 http://ftpmaster.internal/ubuntu resolute/main arm64 libvorbisfile3 arm64 1.3.7-3build1 [18.0 kB] 427s Get:138 http://ftpmaster.internal/ubuntu resolute/universe arm64 coot arm64 1.1.18+dfsg-2build1 [8262 kB] 429s Get:139 http://ftpmaster.internal/ubuntu resolute/universe arm64 coot-doc all 1.1.18+dfsg-2build1 [2048 kB] 430s Get:140 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcootapi-dev arm64 1.1.18+dfsg-2build1 [24.0 kB] 430s Fetched 189 MB in 32s (5920 kB/s) 430s Selecting previously unselected package python3-numpy-dev:arm64. 430s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 88300 files and directories currently installed.) 430s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 430s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 430s Selecting previously unselected package libblas3:arm64. 430s Preparing to unpack .../001-libblas3_3.12.1-7_arm64.deb ... 430s Unpacking libblas3:arm64 (3.12.1-7) ... 431s Selecting previously unselected package libgfortran5:arm64. 431s Preparing to unpack .../002-libgfortran5_15.2.0-9ubuntu1_arm64.deb ... 431s Unpacking libgfortran5:arm64 (15.2.0-9ubuntu1) ... 431s Selecting previously unselected package liblapack3:arm64. 431s Preparing to unpack .../003-liblapack3_3.12.1-7_arm64.deb ... 431s Unpacking liblapack3:arm64 (3.12.1-7) ... 431s Selecting previously unselected package python3-numpy. 431s Preparing to unpack .../004-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 431s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 431s Selecting previously unselected package libgdk-pixbuf2.0-common. 431s Preparing to unpack .../005-libgdk-pixbuf2.0-common_2.44.4+dfsg-1_all.deb ... 431s Unpacking libgdk-pixbuf2.0-common (2.44.4+dfsg-1) ... 431s Selecting previously unselected package libjpeg-turbo8:arm64. 431s Preparing to unpack .../006-libjpeg-turbo8_2.1.5-4ubuntu2_arm64.deb ... 431s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 431s Selecting previously unselected package libjpeg8:arm64. 431s Preparing to unpack .../007-libjpeg8_8c-2ubuntu11_arm64.deb ... 431s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 431s Selecting previously unselected package libdeflate0:arm64. 431s Preparing to unpack .../008-libdeflate0_1.23-2_arm64.deb ... 431s Unpacking libdeflate0:arm64 (1.23-2) ... 431s Selecting previously unselected package libjbig0:arm64. 431s Preparing to unpack .../009-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 431s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 431s Selecting previously unselected package liblerc4:arm64. 431s Preparing to unpack .../010-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 431s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 431s Selecting previously unselected package libsharpyuv0:arm64. 431s Preparing to unpack .../011-libsharpyuv0_1.5.0-0.1_arm64.deb ... 431s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 431s Selecting previously unselected package libwebp7:arm64. 431s Preparing to unpack .../012-libwebp7_1.5.0-0.1_arm64.deb ... 431s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 431s Selecting previously unselected package libtiff6:arm64. 431s Preparing to unpack .../013-libtiff6_4.7.0-3ubuntu3_arm64.deb ... 431s Unpacking libtiff6:arm64 (4.7.0-3ubuntu3) ... 431s Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64. 431s Preparing to unpack .../014-libgdk-pixbuf-2.0-0_2.44.4+dfsg-1_arm64.deb ... 431s Unpacking libgdk-pixbuf-2.0-0:arm64 (2.44.4+dfsg-1) ... 431s Selecting previously unselected package gtk-update-icon-cache. 431s Preparing to unpack .../015-gtk-update-icon-cache_4.20.3+ds-2_arm64.deb ... 431s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 431s 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. 431s Unpacking gtk-update-icon-cache (4.20.3+ds-2) ... 431s Selecting previously unselected package hicolor-icon-theme. 431s Preparing to unpack .../016-hicolor-icon-theme_0.18-2_all.deb ... 431s Unpacking hicolor-icon-theme (0.18-2) ... 431s Selecting previously unselected package adwaita-icon-theme. 431s Preparing to unpack .../017-adwaita-icon-theme_49.0-1_all.deb ... 431s Unpacking adwaita-icon-theme (49.0-1) ... 432s Selecting previously unselected package fonts-noto-mono. 432s Preparing to unpack .../018-fonts-noto-mono_20201225-2_all.deb ... 432s Unpacking fonts-noto-mono (20201225-2) ... 432s Selecting previously unselected package fonts-noto-core. 432s Preparing to unpack .../019-fonts-noto-core_20201225-2_all.deb ... 432s Unpacking fonts-noto-core (20201225-2) ... 432s Selecting previously unselected package ttf-bitstream-vera. 432s Preparing to unpack .../020-ttf-bitstream-vera_1.10-11_all.deb ... 432s Unpacking ttf-bitstream-vera (1.10-11) ... 432s Selecting previously unselected package coot-data. 432s Preparing to unpack .../021-coot-data_1.1.18+dfsg-2build1_all.deb ... 432s Unpacking coot-data (1.1.18+dfsg-2build1) ... 432s Selecting previously unselected package fonts-freefont-ttf. 432s Preparing to unpack .../022-fonts-freefont-ttf_20211204+svn4273-4_all.deb ... 432s Unpacking fonts-freefont-ttf (20211204+svn4273-4) ... 433s Selecting previously unselected package fontconfig-config. 433s Preparing to unpack .../023-fontconfig-config_2.15.0-2.3ubuntu1_arm64.deb ... 433s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 433s Selecting previously unselected package libfontconfig1:arm64. 433s Preparing to unpack .../024-libfontconfig1_2.15.0-2.3ubuntu1_arm64.deb ... 433s Unpacking libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 433s Selecting previously unselected package libpixman-1-0:arm64. 433s Preparing to unpack .../025-libpixman-1-0_0.46.4-1_arm64.deb ... 433s Unpacking libpixman-1-0:arm64 (0.46.4-1) ... 433s Selecting previously unselected package libxcb-render0:arm64. 433s Preparing to unpack .../026-libxcb-render0_1.17.0-2build1_arm64.deb ... 433s Unpacking libxcb-render0:arm64 (1.17.0-2build1) ... 433s Selecting previously unselected package libxcb-shm0:arm64. 433s Preparing to unpack .../027-libxcb-shm0_1.17.0-2build1_arm64.deb ... 433s Unpacking libxcb-shm0:arm64 (1.17.0-2build1) ... 433s Selecting previously unselected package libxrender1:arm64. 433s Preparing to unpack .../028-libxrender1_1%3a0.9.12-1_arm64.deb ... 433s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 433s Selecting previously unselected package libcairo2:arm64. 433s Preparing to unpack .../029-libcairo2_1.18.4-1build1_arm64.deb ... 433s Unpacking libcairo2:arm64 (1.18.4-1build1) ... 433s Selecting previously unselected package libcairo-gobject2:arm64. 433s Preparing to unpack .../030-libcairo-gobject2_1.18.4-1build1_arm64.deb ... 433s Unpacking libcairo-gobject2:arm64 (1.18.4-1build1) ... 433s Selecting previously unselected package gir1.2-freedesktop:arm64. 433s Preparing to unpack .../031-gir1.2-freedesktop_1.86.0-6_arm64.deb ... 433s Unpacking gir1.2-freedesktop:arm64 (1.86.0-6) ... 433s Selecting previously unselected package gir1.2-gdkpixbuf-2.0:arm64. 433s Preparing to unpack .../032-gir1.2-gdkpixbuf-2.0_2.44.4+dfsg-1_arm64.deb ... 433s Unpacking gir1.2-gdkpixbuf-2.0:arm64 (2.44.4+dfsg-1) ... 433s Selecting previously unselected package libgraphene-1.0-0:arm64. 433s Preparing to unpack .../033-libgraphene-1.0-0_1.10.8-5_arm64.deb ... 433s Unpacking libgraphene-1.0-0:arm64 (1.10.8-5) ... 433s Selecting previously unselected package gir1.2-graphene-1.0:arm64. 433s Preparing to unpack .../034-gir1.2-graphene-1.0_1.10.8-5_arm64.deb ... 433s Unpacking gir1.2-graphene-1.0:arm64 (1.10.8-5) ... 433s Selecting previously unselected package libgraphite2-3:arm64. 433s Preparing to unpack .../035-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 433s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 433s Selecting previously unselected package libharfbuzz0b:arm64. 434s Preparing to unpack .../036-libharfbuzz0b_12.1.0-1_arm64.deb ... 434s Unpacking libharfbuzz0b:arm64 (12.1.0-1) ... 434s Selecting previously unselected package libharfbuzz-gobject0:arm64. 434s Preparing to unpack .../037-libharfbuzz-gobject0_12.1.0-1_arm64.deb ... 434s Unpacking libharfbuzz-gobject0:arm64 (12.1.0-1) ... 434s Selecting previously unselected package gir1.2-harfbuzz-0.0:arm64. 434s Preparing to unpack .../038-gir1.2-harfbuzz-0.0_12.1.0-1_arm64.deb ... 434s Unpacking gir1.2-harfbuzz-0.0:arm64 (12.1.0-1) ... 434s Selecting previously unselected package fontconfig. 434s Preparing to unpack .../039-fontconfig_2.15.0-2.3ubuntu1_arm64.deb ... 434s Unpacking fontconfig (2.15.0-2.3ubuntu1) ... 434s Selecting previously unselected package libthai-data. 434s Preparing to unpack .../040-libthai-data_0.1.29-2build2_all.deb ... 434s Unpacking libthai-data (0.1.29-2build2) ... 434s Selecting previously unselected package libdatrie1:arm64. 434s Preparing to unpack .../041-libdatrie1_0.2.14-1_arm64.deb ... 434s Unpacking libdatrie1:arm64 (0.2.14-1) ... 434s Selecting previously unselected package libthai0:arm64. 434s Preparing to unpack .../042-libthai0_0.1.29-2build2_arm64.deb ... 434s Unpacking libthai0:arm64 (0.1.29-2build2) ... 434s Selecting previously unselected package libpango-1.0-0:arm64. 434s Preparing to unpack .../043-libpango-1.0-0_1.56.3-2_arm64.deb ... 434s Unpacking libpango-1.0-0:arm64 (1.56.3-2) ... 434s Selecting previously unselected package libpangoft2-1.0-0:arm64. 434s Preparing to unpack .../044-libpangoft2-1.0-0_1.56.3-2_arm64.deb ... 434s Unpacking libpangoft2-1.0-0:arm64 (1.56.3-2) ... 434s Selecting previously unselected package libpangocairo-1.0-0:arm64. 434s Preparing to unpack .../045-libpangocairo-1.0-0_1.56.3-2_arm64.deb ... 434s Unpacking libpangocairo-1.0-0:arm64 (1.56.3-2) ... 434s Selecting previously unselected package libxft2:arm64. 434s Preparing to unpack .../046-libxft2_2.3.6-1build1_arm64.deb ... 434s Unpacking libxft2:arm64 (2.3.6-1build1) ... 434s Selecting previously unselected package libpangoxft-1.0-0:arm64. 434s Preparing to unpack .../047-libpangoxft-1.0-0_1.56.3-2_arm64.deb ... 434s Unpacking libpangoxft-1.0-0:arm64 (1.56.3-2) ... 434s Selecting previously unselected package gir1.2-pango-1.0:arm64. 434s Preparing to unpack .../048-gir1.2-pango-1.0_1.56.3-2_arm64.deb ... 434s Unpacking gir1.2-pango-1.0:arm64 (1.56.3-2) ... 434s Selecting previously unselected package libcairo-script-interpreter2:arm64. 434s Preparing to unpack .../049-libcairo-script-interpreter2_1.18.4-1build1_arm64.deb ... 434s Unpacking libcairo-script-interpreter2:arm64 (1.18.4-1build1) ... 434s Selecting previously unselected package libcpdb2t64:arm64. 434s Preparing to unpack .../050-libcpdb2t64_2.0~b7-0ubuntu3_arm64.deb ... 434s Unpacking libcpdb2t64:arm64 (2.0~b7-0ubuntu3) ... 434s Selecting previously unselected package libcpdb-frontend2t64:arm64. 434s Preparing to unpack .../051-libcpdb-frontend2t64_2.0~b7-0ubuntu3_arm64.deb ... 434s Unpacking libcpdb-frontend2t64:arm64 (2.0~b7-0ubuntu3) ... 434s Selecting previously unselected package libepoxy0:arm64. 434s Preparing to unpack .../052-libepoxy0_1.5.10-2_arm64.deb ... 434s Unpacking libepoxy0:arm64 (1.5.10-2) ... 434s Selecting previously unselected package libglvnd0:arm64. 434s Preparing to unpack .../053-libglvnd0_1.7.0-1build2_arm64.deb ... 434s Unpacking libglvnd0:arm64 (1.7.0-1build2) ... 434s Selecting previously unselected package libx11-xcb1:arm64. 434s Preparing to unpack .../054-libx11-xcb1_2%3a1.8.12-1build1_arm64.deb ... 434s Unpacking libx11-xcb1:arm64 (2:1.8.12-1build1) ... 434s Selecting previously unselected package libxcb-dri3-0:arm64. 434s Preparing to unpack .../055-libxcb-dri3-0_1.17.0-2build1_arm64.deb ... 434s Unpacking libxcb-dri3-0:arm64 (1.17.0-2build1) ... 434s Selecting previously unselected package libxcb-present0:arm64. 434s Preparing to unpack .../056-libxcb-present0_1.17.0-2build1_arm64.deb ... 434s Unpacking libxcb-present0:arm64 (1.17.0-2build1) ... 434s Selecting previously unselected package libxcb-randr0:arm64. 435s Preparing to unpack .../057-libxcb-randr0_1.17.0-2build1_arm64.deb ... 435s Unpacking libxcb-randr0:arm64 (1.17.0-2build1) ... 435s Selecting previously unselected package libxcb-sync1:arm64. 435s Preparing to unpack .../058-libxcb-sync1_1.17.0-2build1_arm64.deb ... 435s Unpacking libxcb-sync1:arm64 (1.17.0-2build1) ... 435s Selecting previously unselected package libxcb-xfixes0:arm64. 435s Preparing to unpack .../059-libxcb-xfixes0_1.17.0-2build1_arm64.deb ... 435s Unpacking libxcb-xfixes0:arm64 (1.17.0-2build1) ... 435s Selecting previously unselected package libxshmfence1:arm64. 435s Preparing to unpack .../060-libxshmfence1_1.3.3-1_arm64.deb ... 435s Unpacking libxshmfence1:arm64 (1.3.3-1) ... 435s Selecting previously unselected package mesa-libgallium:arm64. 435s Preparing to unpack .../061-mesa-libgallium_25.2.7-1ubuntu1_arm64.deb ... 435s Unpacking mesa-libgallium:arm64 (25.2.7-1ubuntu1) ... 435s Selecting previously unselected package libgbm1:arm64. 435s Preparing to unpack .../062-libgbm1_25.2.7-1ubuntu1_arm64.deb ... 435s Unpacking libgbm1:arm64 (25.2.7-1ubuntu1) ... 435s Selecting previously unselected package libwayland-client0:arm64. 435s Preparing to unpack .../063-libwayland-client0_1.24.0-2_arm64.deb ... 435s Unpacking libwayland-client0:arm64 (1.24.0-2) ... 435s Selecting previously unselected package libegl-mesa0:arm64. 435s Preparing to unpack .../064-libegl-mesa0_25.2.7-1ubuntu1_arm64.deb ... 435s Unpacking libegl-mesa0:arm64 (25.2.7-1ubuntu1) ... 435s Selecting previously unselected package libegl1:arm64. 435s Preparing to unpack .../065-libegl1_1.7.0-1build2_arm64.deb ... 435s Unpacking libegl1:arm64 (1.7.0-1build2) ... 435s Selecting previously unselected package libxcb-glx0:arm64. 435s Preparing to unpack .../066-libxcb-glx0_1.17.0-2build1_arm64.deb ... 435s Unpacking libxcb-glx0:arm64 (1.17.0-2build1) ... 435s Selecting previously unselected package libxxf86vm1:arm64. 435s Preparing to unpack .../067-libxxf86vm1_1%3a1.1.4-2_arm64.deb ... 435s Unpacking libxxf86vm1:arm64 (1:1.1.4-2) ... 435s Selecting previously unselected package libvulkan1:arm64. 435s Preparing to unpack .../068-libvulkan1_1.4.328.1-1_arm64.deb ... 435s Unpacking libvulkan1:arm64 (1.4.328.1-1) ... 435s Selecting previously unselected package libgl1-mesa-dri:arm64. 435s Preparing to unpack .../069-libgl1-mesa-dri_25.2.7-1ubuntu1_arm64.deb ... 435s Unpacking libgl1-mesa-dri:arm64 (25.2.7-1ubuntu1) ... 435s Selecting previously unselected package libglx-mesa0:arm64. 435s Preparing to unpack .../070-libglx-mesa0_25.2.7-1ubuntu1_arm64.deb ... 435s Unpacking libglx-mesa0:arm64 (25.2.7-1ubuntu1) ... 435s Selecting previously unselected package libglx0:arm64. 435s Preparing to unpack .../071-libglx0_1.7.0-1build2_arm64.deb ... 435s Unpacking libglx0:arm64 (1.7.0-1build2) ... 435s Selecting previously unselected package libgl1:arm64. 435s Preparing to unpack .../072-libgl1_1.7.0-1build2_arm64.deb ... 435s Unpacking libgl1:arm64 (1.7.0-1build2) ... 435s Selecting previously unselected package libgstreamer1.0-0:arm64. 435s Preparing to unpack .../073-libgstreamer1.0-0_1.27.2-2_arm64.deb ... 435s Unpacking libgstreamer1.0-0:arm64 (1.27.2-2) ... 436s Selecting previously unselected package liborc-0.4-0t64:arm64. 436s Preparing to unpack .../074-liborc-0.4-0t64_1%3a0.4.41-1_arm64.deb ... 436s Unpacking liborc-0.4-0t64:arm64 (1:0.4.41-1) ... 436s Selecting previously unselected package libgstreamer-plugins-base1.0-0:arm64. 436s Preparing to unpack .../075-libgstreamer-plugins-base1.0-0_1.27.2-3build1_arm64.deb ... 436s Unpacking libgstreamer-plugins-base1.0-0:arm64 (1.27.2-3build1) ... 436s Selecting previously unselected package libwayland-cursor0:arm64. 436s Preparing to unpack .../076-libwayland-cursor0_1.24.0-2_arm64.deb ... 436s Unpacking libwayland-cursor0:arm64 (1.24.0-2) ... 436s Selecting previously unselected package libwayland-egl1:arm64. 436s Preparing to unpack .../077-libwayland-egl1_1.24.0-2_arm64.deb ... 436s Unpacking libwayland-egl1:arm64 (1.24.0-2) ... 436s Selecting previously unselected package libgstreamer-gl1.0-0:arm64. 436s Preparing to unpack .../078-libgstreamer-gl1.0-0_1.27.2-3build1_arm64.deb ... 436s Unpacking libgstreamer-gl1.0-0:arm64 (1.27.2-3build1) ... 436s Selecting previously unselected package libharfbuzz-subset0:arm64. 436s Preparing to unpack .../079-libharfbuzz-subset0_12.1.0-1_arm64.deb ... 436s Unpacking libharfbuzz-subset0:arm64 (12.1.0-1) ... 436s Selecting previously unselected package librsvg2-2:arm64. 436s Preparing to unpack .../080-librsvg2-2_2.61.3+dfsg-2_arm64.deb ... 436s Unpacking librsvg2-2:arm64 (2.61.3+dfsg-2) ... 436s Selecting previously unselected package libxfixes3:arm64. 436s Preparing to unpack .../081-libxfixes3_1%3a6.0.0-2build1_arm64.deb ... 436s Unpacking libxfixes3:arm64 (1:6.0.0-2build1) ... 436s Selecting previously unselected package libxcursor1:arm64. 436s Preparing to unpack .../082-libxcursor1_1%3a1.2.3-1_arm64.deb ... 436s Unpacking libxcursor1:arm64 (1:1.2.3-1) ... 436s Selecting previously unselected package libxdamage1:arm64. 436s Preparing to unpack .../083-libxdamage1_1%3a1.1.6-1build1_arm64.deb ... 436s Unpacking libxdamage1:arm64 (1:1.1.6-1build1) ... 436s Selecting previously unselected package libxi6:arm64. 436s Preparing to unpack .../084-libxi6_2%3a1.8.2-1_arm64.deb ... 436s Unpacking libxi6:arm64 (2:1.8.2-1) ... 436s Selecting previously unselected package libxinerama1:arm64. 436s Preparing to unpack .../085-libxinerama1_2%3a1.1.4-3build1_arm64.deb ... 436s Unpacking libxinerama1:arm64 (2:1.1.4-3build1) ... 436s Selecting previously unselected package libxrandr2:arm64. 436s Preparing to unpack .../086-libxrandr2_2%3a1.5.4-1_arm64.deb ... 436s Unpacking libxrandr2:arm64 (2:1.5.4-1) ... 436s Selecting previously unselected package libgles2:arm64. 436s Preparing to unpack .../087-libgles2_1.7.0-1build2_arm64.deb ... 436s Unpacking libgles2:arm64 (1.7.0-1build2) ... 436s Selecting previously unselected package libdconf1:arm64. 436s Preparing to unpack .../088-libdconf1_0.49.0-2_arm64.deb ... 436s Unpacking libdconf1:arm64 (0.49.0-2) ... 436s Selecting previously unselected package dconf-service. 436s Preparing to unpack .../089-dconf-service_0.49.0-2_arm64.deb ... 436s Unpacking dconf-service (0.49.0-2) ... 436s Selecting previously unselected package dconf-gsettings-backend:arm64. 436s Preparing to unpack .../090-dconf-gsettings-backend_0.49.0-2_arm64.deb ... 436s Unpacking dconf-gsettings-backend:arm64 (0.49.0-2) ... 436s Selecting previously unselected package libgtk-4-common. 436s Preparing to unpack .../091-libgtk-4-common_4.20.3+ds-2_all.deb ... 436s Unpacking libgtk-4-common (4.20.3+ds-2) ... 436s Selecting previously unselected package libgtk-4-1:arm64. 437s Preparing to unpack .../092-libgtk-4-1_4.20.3+ds-2_arm64.deb ... 437s Unpacking libgtk-4-1:arm64 (4.20.3+ds-2) ... 437s Selecting previously unselected package gir1.2-gtk-4.0:arm64. 437s Preparing to unpack .../093-gir1.2-gtk-4.0_4.20.3+ds-2_arm64.deb ... 437s Unpacking gir1.2-gtk-4.0:arm64 (4.20.3+ds-2) ... 437s Selecting previously unselected package rdkit-data. 437s Preparing to unpack .../094-rdkit-data_202503.6-3ubuntu2_all.deb ... 437s Unpacking rdkit-data (202503.6-3ubuntu2) ... 437s Selecting previously unselected package libboost-python1.88.0. 437s Preparing to unpack .../095-libboost-python1.88.0_1.88.0-1.4ubuntu2_arm64.deb ... 437s Unpacking libboost-python1.88.0 (1.88.0-1.4ubuntu2) ... 437s Selecting previously unselected package libboost-numpy1.88.0. 437s Preparing to unpack .../096-libboost-numpy1.88.0_1.88.0-1.4ubuntu2_arm64.deb ... 437s Unpacking libboost-numpy1.88.0 (1.88.0-1.4ubuntu2) ... 437s Selecting previously unselected package libboost-serialization1.88.0:arm64. 437s Preparing to unpack .../097-libboost-serialization1.88.0_1.88.0-1.4ubuntu2_arm64.deb ... 437s Unpacking libboost-serialization1.88.0:arm64 (1.88.0-1.4ubuntu2) ... 437s Selecting previously unselected package libcoordgen3:arm64. 437s Preparing to unpack .../098-libcoordgen3_3.0.2-1_arm64.deb ... 437s Unpacking libcoordgen3:arm64 (3.0.2-1) ... 437s Selecting previously unselected package libboost-iostreams1.88.0:arm64. 437s Preparing to unpack .../099-libboost-iostreams1.88.0_1.88.0-1.4ubuntu2_arm64.deb ... 437s Unpacking libboost-iostreams1.88.0:arm64 (1.88.0-1.4ubuntu2) ... 437s Selecting previously unselected package libinchi1.07. 437s Preparing to unpack .../100-libinchi1.07_1.07.3+dfsg-1_arm64.deb ... 437s Unpacking libinchi1.07 (1.07.3+dfsg-1) ... 437s Selecting previously unselected package libmaeparser1:arm64. 437s Preparing to unpack .../101-libmaeparser1_1.3.3-3_arm64.deb ... 437s Unpacking libmaeparser1:arm64 (1.3.3-3) ... 437s Selecting previously unselected package librdkit1t64. 437s Preparing to unpack .../102-librdkit1t64_202503.6-3ubuntu2_arm64.deb ... 437s Unpacking librdkit1t64 (202503.6-3ubuntu2) ... 438s Selecting previously unselected package python3-rdkit. 438s Preparing to unpack .../103-python3-rdkit_202503.6-3ubuntu2_arm64.deb ... 438s Unpacking python3-rdkit (202503.6-3ubuntu2) ... 438s Selecting previously unselected package refmac-dictionary. 438s Preparing to unpack .../104-refmac-dictionary_5.41-3_all.deb ... 438s Unpacking refmac-dictionary (5.41-3) ... 439s Selecting previously unselected package libasound2-data. 439s Preparing to unpack .../105-libasound2-data_1.2.14-2ubuntu1_all.deb ... 439s Unpacking libasound2-data (1.2.14-2ubuntu1) ... 439s Selecting previously unselected package libasound2t64:arm64. 439s Preparing to unpack .../106-libasound2t64_1.2.14-2ubuntu1_arm64.deb ... 439s Unpacking libasound2t64:arm64 (1.2.14-2ubuntu1) ... 439s Selecting previously unselected package libccp4-data. 439s Preparing to unpack .../107-libccp4-data_8.0.0-5_all.deb ... 439s Unpacking libccp4-data (8.0.0-5) ... 439s Selecting previously unselected package libccp4c0t64:arm64. 439s Preparing to unpack .../108-libccp4c0t64_8.0.0-5_arm64.deb ... 439s Unpacking libccp4c0t64:arm64 (8.0.0-5) ... 440s Selecting previously unselected package libmmdb2-0:arm64. 440s Preparing to unpack .../109-libmmdb2-0_2.0.22-1_arm64.deb ... 440s Unpacking libmmdb2-0:arm64 (2.0.22-1) ... 440s Selecting previously unselected package libevent-pthreads-2.1-7t64:arm64. 440s Preparing to unpack .../110-libevent-pthreads-2.1-7t64_2.1.12-stable-10build1_arm64.deb ... 440s Unpacking libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10build1) ... 440s Selecting previously unselected package librdmacm1t64:arm64. 440s Preparing to unpack .../111-librdmacm1t64_56.1-1ubuntu1_arm64.deb ... 440s Unpacking librdmacm1t64:arm64 (56.1-1ubuntu1) ... 440s Selecting previously unselected package libfabric1:arm64. 440s Preparing to unpack .../112-libfabric1_2.1.0-1.1_arm64.deb ... 440s Unpacking libfabric1:arm64 (2.1.0-1.1) ... 440s Selecting previously unselected package libhwloc15:arm64. 440s Preparing to unpack .../113-libhwloc15_2.12.2-1_arm64.deb ... 440s Unpacking libhwloc15:arm64 (2.12.2-1) ... 440s Selecting previously unselected package libllvm21:arm64. 440s Preparing to unpack .../114-libllvm21_1%3a21.1.2-2ubuntu6_arm64.deb ... 440s Unpacking libllvm21:arm64 (1:21.1.2-2ubuntu6) ... 440s Selecting previously unselected package libamd-comgr3:arm64. 440s Preparing to unpack .../115-libamd-comgr3_7.0.2+dfsg-2_arm64.deb ... 440s Unpacking libamd-comgr3:arm64 (7.0.2+dfsg-2) ... 441s Selecting previously unselected package libhsakmt1:arm64. 441s Preparing to unpack .../116-libhsakmt1_6.4.3+dfsg-3_arm64.deb ... 441s Unpacking libhsakmt1:arm64 (6.4.3+dfsg-3) ... 441s Selecting previously unselected package libhsa-runtime64-1:arm64. 441s Preparing to unpack .../117-libhsa-runtime64-1_6.4.3+dfsg-3_arm64.deb ... 441s Unpacking libhsa-runtime64-1:arm64 (6.4.3+dfsg-3) ... 441s Selecting previously unselected package libamdhip64-6:arm64. 441s Preparing to unpack .../118-libamdhip64-6_6.4.3-4_arm64.deb ... 441s Unpacking libamdhip64-6:arm64 (6.4.3-4) ... 441s Selecting previously unselected package libgomp1:arm64. 441s Preparing to unpack .../119-libgomp1_15.2.0-9ubuntu1_arm64.deb ... 441s Unpacking libgomp1:arm64 (15.2.0-9ubuntu1) ... 441s Selecting previously unselected package libibumad3:arm64. 441s Preparing to unpack .../120-libibumad3_56.1-1ubuntu1_arm64.deb ... 441s Unpacking libibumad3:arm64 (56.1-1ubuntu1) ... 441s Selecting previously unselected package libibmad5:arm64. 441s Preparing to unpack .../121-libibmad5_56.1-1ubuntu1_arm64.deb ... 441s Unpacking libibmad5:arm64 (56.1-1ubuntu1) ... 441s Selecting previously unselected package libucx0:arm64. 441s Preparing to unpack .../122-libucx0_1.19.0+ds-1build1_arm64.deb ... 441s Unpacking libucx0:arm64 (1.19.0+ds-1build1) ... 441s Selecting previously unselected package libpciaccess0:arm64. 441s Preparing to unpack .../123-libpciaccess0_0.18.1-1ubuntu2_arm64.deb ... 441s Unpacking libpciaccess0:arm64 (0.18.1-1ubuntu2) ... 441s Selecting previously unselected package libxnvctrl0:arm64. 441s Preparing to unpack .../124-libxnvctrl0_510.47.03-0ubuntu4_arm64.deb ... 441s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 441s Selecting previously unselected package ocl-icd-libopencl1:arm64. 441s Preparing to unpack .../125-ocl-icd-libopencl1_2.3.4-1_arm64.deb ... 441s Unpacking ocl-icd-libopencl1:arm64 (2.3.4-1) ... 441s Selecting previously unselected package libhwloc-plugins:arm64. 442s Preparing to unpack .../126-libhwloc-plugins_2.12.2-1_arm64.deb ... 442s Unpacking libhwloc-plugins:arm64 (2.12.2-1) ... 442s Selecting previously unselected package libopenmpi40:arm64. 442s Preparing to unpack .../127-libopenmpi40_5.0.8-8ubuntu1_arm64.deb ... 442s Unpacking libopenmpi40:arm64 (5.0.8-8ubuntu1) ... 442s Selecting previously unselected package sfftw2. 442s Preparing to unpack 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(1.1.18+dfsg-2build1) ... 443s Selecting previously unselected package libcootapi-dev. 443s Preparing to unpack .../139-libcootapi-dev_1.1.18+dfsg-2build1_arm64.deb ... 443s Unpacking libcootapi-dev (1.1.18+dfsg-2build1) ... 443s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 443s Setting up libxcb-dri3-0:arm64 (1.17.0-2build1) ... 443s Setting up libpixman-1-0:arm64 (0.46.4-1) ... 443s Setting up coot-doc (1.1.18+dfsg-2build1) ... 443s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 443s Setting up libx11-xcb1:arm64 (2:1.8.12-1build1) ... 443s Setting up libpciaccess0:arm64 (0.18.1-1ubuntu2) ... 443s Setting up libboost-python1.88.0 (1.88.0-1.4ubuntu2) ... 443s Setting up ttf-bitstream-vera (1.10-11) ... 443s Setting up libxdamage1:arm64 (1:1.1.6-1build1) ... 443s Setting up libxcb-xfixes0:arm64 (1.17.0-2build1) ... 443s Setting up libogg0:arm64 (1.3.6-2) ... 443s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 443s Setting up fonts-noto-mono (20201225-2) ... 443s Setting up hicolor-icon-theme (0.18-2) ... 443s Setting up libxi6:arm64 (2:1.8.2-1) ... 443s Setting up libxrender1:arm64 (1:0.9.12-1) ... 443s Setting up libdatrie1:arm64 (0.2.14-1) ... 443s Setting up libgslcblas0:arm64 (2.8+dfsg-5.1ubuntu1) ... 443s Setting up libmmdb2-0:arm64 (2.0.22-1) ... 443s Setting up libxcb-render0:arm64 (1.17.0-2build1) ... 443s Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10build1) ... 443s Setting up libglvnd0:arm64 (1.7.0-1build2) ... 443s Setting up libxcb-glx0:arm64 (1.17.0-2build1) ... 443s Setting up libgdk-pixbuf2.0-common (2.44.4+dfsg-1) ... 443s Setting up libibumad3:arm64 (56.1-1ubuntu1) ... 443s Setting up libdeflate0:arm64 (1.23-2) ... 443s Setting up fonts-freefont-ttf (20211204+svn4273-4) ... 443s Setting up libcpdb2t64:arm64 (2.0~b7-0ubuntu3) ... 443s Setting up libxcb-shm0:arm64 (1.17.0-2build1) ... 443s Setting up libibmad5:arm64 (56.1-1ubuntu1) ... 443s Setting up libcpdb-frontend2t64:arm64 (2.0~b7-0ubuntu3) ... 443s Setting up libboost-iostreams1.88.0:arm64 (1.88.0-1.4ubuntu2) ... 443s Setting up libccp4-data (8.0.0-5) ... 443s Setting up libgomp1:arm64 (15.2.0-9ubuntu1) ... 443s Setting up rdkit-data (202503.6-3ubuntu2) ... 443s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 443s Setting up libboost-serialization1.88.0:arm64 (1.88.0-1.4ubuntu2) ... 443s Setting up libxxf86vm1:arm64 (1:1.1.4-2) ... 443s Setting up liborc-0.4-0t64:arm64 (1:0.4.41-1) ... 443s Setting up libmaeparser1:arm64 (1.3.3-3) ... 443s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 443s Setting up refmac-dictionary (5.41-3) ... 443s Setting up libxcb-present0:arm64 (1.17.0-2build1) ... 443s Setting up libdconf1:arm64 (0.49.0-2) ... 443s Setting up libasound2-data (1.2.14-2ubuntu1) ... 443s Setting up libblas3:arm64 (3.12.1-7) ... 443s 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 443s Setting up libgles2:arm64 (1.7.0-1build2) ... 443s Setting up libasound2t64:arm64 (1.2.14-2ubuntu1) ... 443s Setting up libepoxy0:arm64 (1.5.10-2) ... 443s Setting up libxfixes3:arm64 (1:6.0.0-2build1) ... 443s Setting up libxcb-sync1:arm64 (1.17.0-2build1) ... 443s Setting up libllvm21:arm64 (1:21.1.2-2ubuntu6) ... 443s Setting up libxinerama1:arm64 (2:1.1.4-3build1) ... 443s Setting up libhwloc15:arm64 (2.12.2-1) ... 443s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 443s Setting up libvorbis0a:arm64 (1.3.7-3build1) ... 443s Setting up libxrandr2:arm64 (2:1.5.4-1) ... 443s Setting up libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 443s Setting up libgfortran5:arm64 (15.2.0-9ubuntu1) ... 443s Setting up libvulkan1:arm64 (1.4.328.1-1) ... 443s Setting up libwebp7:arm64 (1.5.0-0.1) ... 443s Setting up ocl-icd-libopencl1:arm64 (2.3.4-1) ... 443s Setting up libboost-numpy1.88.0 (1.88.0-1.4ubuntu2) ... 443s Setting up libxshmfence1:arm64 (1.3.3-1) ... 443s Setting up libccp4c0t64:arm64 (8.0.0-5) ... 443s Setting up libxcb-randr0:arm64 (1.17.0-2build1) ... 443s Setting up libamd-comgr3:arm64 (7.0.2+dfsg-2) ... 443s Setting up librdmacm1t64:arm64 (56.1-1ubuntu1) ... 443s Setting up libharfbuzz0b:arm64 (12.1.0-1) ... 443s Setting up libthai-data (0.1.29-2build2) ... 443s Setting up libwayland-egl1:arm64 (1.24.0-2) ... 443s Setting up libcoordgen3:arm64 (3.0.2-1) ... 443s Setting up libgsl28:arm64 (2.8+dfsg-5.1ubuntu1) ... 443s Setting up libinchi1.07 (1.07.3+dfsg-1) ... 443s Setting up fonts-noto-core (20201225-2) ... 443s Setting up libhsakmt1:arm64 (6.4.3+dfsg-3) ... 443s Setting up libgstreamer1.0-0:arm64 (1.27.2-2) ... 443s Setcap worked! gst-ptp-helper is not suid! 443s Setting up libgraphene-1.0-0:arm64 (1.10.8-5) ... 443s Setting up libwayland-client0:arm64 (1.24.0-2) ... 443s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 443s Setting up gir1.2-graphene-1.0:arm64 (1.10.8-5) ... 443s Setting up libfabric1:arm64 (2.1.0-1.1) ... 443s Setting up mesa-libgallium:arm64 (25.2.7-1ubuntu1) ... 443s Setting up liblapack3:arm64 (3.12.1-7) ... 443s 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 443s Setting up libssm2:arm64 (1.4.0-2build1) ... 443s Setting up libgbm1:arm64 (25.2.7-1ubuntu1) ... 443s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 443s Setting up libxcursor1:arm64 (1:1.2.3-1) ... 443s Setting up libgl1-mesa-dri:arm64 (25.2.7-1ubuntu1) ... 443s Setting up libgstreamer-plugins-base1.0-0:arm64 (1.27.2-3build1) ... 443s Setting up dconf-service (0.49.0-2) ... 443s Setting up libharfbuzz-gobject0:arm64 (12.1.0-1) ... 443s Setting up libhwloc-plugins:arm64 (2.12.2-1) ... 443s Setting up libthai0:arm64 (0.1.29-2build2) ... 443s Setting up libvorbisfile3:arm64 (1.3.7-3build1) ... 443s Setting up libegl-mesa0:arm64 (25.2.7-1ubuntu1) ... 443s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 445s Setting up libtiff6:arm64 (4.7.0-3ubuntu3) ... 445s Setting up libwayland-cursor0:arm64 (1.24.0-2) ... 445s Setting up libhsa-runtime64-1:arm64 (6.4.3+dfsg-3) ... 445s Setting up libegl1:arm64 (1.7.0-1build2) ... 445s Setting up libharfbuzz-subset0:arm64 (12.1.0-1) ... 445s Setting up libgdk-pixbuf-2.0-0:arm64 (2.44.4+dfsg-1) ... 445s Setting up libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 445s Setting up coot-data (1.1.18+dfsg-2build1) ... 445s Setting up gtk-update-icon-cache (4.20.3+ds-2) ... 445s Setting up fontconfig (2.15.0-2.3ubuntu1) ... 447s Regenerating fonts cache... done. 447s Setting up libxft2:arm64 (2.3.6-1build1) ... 447s Setting up libglx-mesa0:arm64 (25.2.7-1ubuntu1) ... 447s Setting up libglx0:arm64 (1.7.0-1build2) ... 447s Setting up dconf-gsettings-backend:arm64 (0.49.0-2) ... 447s Setting up gir1.2-gdkpixbuf-2.0:arm64 (2.44.4+dfsg-1) ... 447s Setting up libpango-1.0-0:arm64 (1.56.3-2) ... 447s Setting up libcairo2:arm64 (1.18.4-1build1) ... 447s Setting up libgl1:arm64 (1.7.0-1build2) ... 447s Setting up adwaita-icon-theme (49.0-1) ... 447s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 447s Setting up libamdhip64-6:arm64 (6.4.3-4) ... 447s Setting up libcairo-gobject2:arm64 (1.18.4-1build1) ... 447s Setting up libgtk-4-common (4.20.3+ds-2) ... 447s Setting up libpangoft2-1.0-0:arm64 (1.56.3-2) ... 447s Setting up libpangocairo-1.0-0:arm64 (1.56.3-2) ... 447s Setting up libcairo-script-interpreter2:arm64 (1.18.4-1build1) ... 447s Setting up libucx0:arm64 (1.19.0+ds-1build1) ... 447s Setting up gir1.2-freedesktop:arm64 (1.86.0-6) ... 447s Setting up libpangoxft-1.0-0:arm64 (1.56.3-2) ... 447s Setting up librdkit1t64 (202503.6-3ubuntu2) ... 447s Setting up gir1.2-harfbuzz-0.0:arm64 (12.1.0-1) ... 447s Setting up librsvg2-2:arm64 (2.61.3+dfsg-2) ... 447s Setting up gir1.2-pango-1.0:arm64 (1.56.3-2) ... 447s Setting up libgstreamer-gl1.0-0:arm64 (1.27.2-3build1) ... 447s Setting up python3-rdkit (202503.6-3ubuntu2) ... 447s Setting up libopenmpi40:arm64 (5.0.8-8ubuntu1) ... 447s Setting up sfftw2 (2.1.5-7build1) ... 447s Setting up libclipper2:arm64 (2.1.20201109-2build1) ... 447s Setting up libcootapi1.1 (1.1.18+dfsg-2build1) ... 448s Setting up libcootapi-dev (1.1.18+dfsg-2build1) ... 448s Processing triggers for libc-bin (2.42-2ubuntu2) ... 448s Processing triggers for man-db (2.13.1-1) ... 449s Processing triggers for libglib2.0-0t64:arm64 (2.86.2-1) ... 449s Setting up libgtk-4-1:arm64 (4.20.3+ds-2) ... 449s Setting up gir1.2-gtk-4.0:arm64 (4.20.3+ds-2) ... 449s Setting up coot (1.1.18+dfsg-2build1) ... 449s Processing triggers for libc-bin (2.42-2ubuntu2) ... 451s autopkgtest [18:28:45]: test command1: coot --self-test 451s autopkgtest [18:28:45]: test command1: [----------------------- 451s INFO:: Running internal self tests 456s INFO:: Test Clipper core : OK 456s INFO:: Test Clipper contrib: OK 456s run_internal_tests() --------- we have 8 internal test functionns 456s Entering test: kevin's torsion test 456s PASS: kevin's torsion test 456s Entering test: test_alt_conf_rotamers 456s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 456s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 456s chis.size() 2 (should be 2) 456s DEBUG:: i_rot 0 chi: alt-conf: A chi-1: 65.911 456s DEBUG:: i_rot 1 chi: alt-conf: B chi-1: -144.68 456s For residue 80 chis size 1 456s residue 80 chis: -56.8781 -80.8484 456s PASS: test_alt_conf_rotamers 456s Entering test: test_fragmemt_atom_selection 456s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 456s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 456s ----------------- create_mmdbmanager_from_inverted_atom_selection() 456s n_initial: 1465 n_1: 1401 n_2: 64 456s PASS: test_fragmemt_atom_selection 456s Entering test: test_add_atom 456s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 456s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 456s PASS: test_add_atom 456s Entering test: test segid exchange 456s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 456s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 456s Test with a rogue segid 456s INFO:: No consistent segids for residue 1 456s PASS: test segid exchange 456s Entering test: test peak search non-close 456s mtz_file_name /usr/share/coot/data/rnasa-1.8-all_refmac1.mtz 456s INFO:: FFT Resolution: 0.444444 456s INFO:: Map Sampling Rate: 1.500000 456s INFO:: Grid: Nuvw = ( 132, 160, 80) 456s INFO:: Cell: Cell (64.897,78.323,38.792, 90, 90, 90) 456s INFO:: Spacegroup: P 21 21 21 456s There are 2260 peaks and 0 problem peaks 456s PASS: test peak search non-close 456s Entering test: test symop card 456s 1 0 0 456s 0 1 0 456s 0 0 1 456s translations: -1 0 0 456s PASS: test symop card 456s Entering test: SSM sequence alignment output 456s 456s -- 456s Moving: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNR--ESVLPTQSYGYYHEYTVITP--GARTRG 456s Target: ---SGTVCLSALPPEATDTLNLIASDGPFPYSQDG 456s 456s Moving: TRRI.ICGEATQEDY..YTGDHYATFSLIDQTC 456s 456s -- 456s Moving: D 456s Target: --SGTVCLSALPPEATDTLNLIASDGPFPYSQDG 456s 456s -- 456s Moving: DVSGTVCLSALPPEATDTLNIASDGPFPYSQDGVVFQNR--ESVLPQSYG 456s Target: --SGTVCLSALPPEATDTLNIASDGPFPYSQDXXxxxxxxxxxxxxxxxG 456s 456s -- 456s PASS: SSM sequence alignment output 457s autopkgtest [18:28:51]: test command1: -----------------------] 458s command1 PASS 458s autopkgtest [18:28:52]: test command1: - - - - - - - - - - results - - - - - - - - - - 458s autopkgtest [18:28:52]: test command2: preparing testbed 459s Reading package lists... 459s Building dependency tree... 459s Reading state information... 459s Solving dependencies... 459s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 461s autopkgtest [18:28:55]: test command2: pyrogen --help 461s autopkgtest [18:28:55]: test command2: [----------------------- 462s Usage: pyrogen [options] file-or-SMILES 462s if file-or-SMILES has extension ".smi" or ".smiles" then it is treated as a file 462s 462s Options: 462s -h, --help show this help message and exit 462s -c FILE, --mmcif=FILE 462s Make restraints from input mmcif FILE 462s -m FILE, --mol=FILE Make restraints from input sdf/mol FILE 462s -r COMP_ID, --residue-type=COMP_ID 462s Create restraints for this type. Default is LIG 462s -4, --quartet-planes Use 4-atom plane restraints, 462s forces --quartet-hydrogens 462s -H, --quartet-hydrogens 462s Use 4-atom hydrogen plane restraints 462s -b, --no-shift-hydrogen-atoms 462s Stop addition or deletion of Hydrogen atoms for 462s formally-charged atoms 462s -n, --no-mogul Don't run CSD Mogul to update bond and angle 462s restraints 462s -N COMPOUND_NAME, --name=COMPOUND_NAME 462s Compound name 462s -S, --smiles Write the SMILES for the input molecule 462s -t, --tautomers Show SMILES for tautomers, don't generate restraints 462s -T MOGUL_DIR, --tmp-directory=MOGUL_DIR 462s Directory into which the tmp files (e.g. for mogul) 462s are written 462s -d OUTPUT_DIR, --directory=OUTPUT_DIR 462s Directory into which the output files (e.g. mmCIF and 462s PDB) are written 462s -o OUTPUT_POSTFIX, --output-postfix=OUTPUT_POSTFIX 462s string to add to output file names, default is 462s "pyrogen" 462s -p, --picture Additionally output a chemical diagram PNG 462s -P, --preserve-input-coordinates 462s Preserve the inputput coordinates (if possible) 462s -v, --version Print version information 462s -a, --no-match-vs-reference-dictionaries 462s Don't match atom names vs. dictionary molecules 462s (default False) 462s -R DICT_FILES_FOR_NAMES_MATCH, --reference-dictionary-files=DICT_FILES_FOR_NAMES_MATCH 462s Try to match the atom names of the output molecule to 462s this dictionary in these files (comma-separated list) 462s -C COMP_ID_LIST_FOR_NAMES_MATCH, --reference-dictionary-comp-ids=COMP_ID_LIST_FOR_NAMES_MATCH 462s Try to match the atom names of the output molecule to 462s these comp-ids (comma-separated list) 462s -w, --wwPDB Fetch the wwPDB ligand definition and use that 462s -f FETCH (Just) fetch from the PDBe the CCD entry for the given 462s compound-id 462s -q, --quiet print less messages 462s autopkgtest [18:28:56]: test command2: -----------------------] 463s autopkgtest [18:28:57]: test command2: - - - - - - - - - - results - - - - - - - - - - 463s command2 PASS 463s autopkgtest [18:28:57]: @@@@@@@@@@@@@@@@@@@@ summary 463s command1 PASS 463s command2 PASS