0s autopkgtest [15:27:23]: starting date and time: 2025-10-18 15:27:23+0000 0s autopkgtest [15:27:23]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [15:27:23]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5z4fdv83/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/3.13.7-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-8.secgroup --name adt-resolute-arm64-coot-20251018-152723-juju-7f2275-prod-proposed-migration-environment-15-dae285d8-8137-42a1-b4d7-b0028a22b763 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-coot-20251018-152723-juju-7f2275-prod-proposed-migration-environment-15-dae285d8-8137-42a1-b4d7-b0028a22b763 from image adt/ubuntu-resolute-arm64-server-20251018.img (UUID f7a49384-4e4d-4350-9a26-1f59236f89dd)... 58s autopkgtest [15:28:21]: testbed dpkg architecture: arm64 58s autopkgtest [15:28:21]: testbed apt version: 3.1.6ubuntu2 58s autopkgtest [15:28:21]: @@@@@@@@@@@@@@@@@@@@ test bed setup 59s autopkgtest [15:28:22]: testbed release detected to be: None 59s autopkgtest [15:28:22]: updating testbed package index (apt update) 60s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 60s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 60s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 60s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 60s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [345 kB] 60s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.4 kB] 60s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 60s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [28.4 kB] 60s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [81.1 kB] 60s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [43.8 kB] 60s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [223 kB] 60s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [5672 B] 60s Fetched 831 kB in 1s (938 kB/s) 61s Reading package lists... 62s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 62s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 62s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 62s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 63s Reading package lists... 63s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s Calculating upgrade... 64s The following packages will be upgraded: 64s apt flash-kernel gir1.2-girepository-2.0 libapt-pkg7.0 libgirepository-1.0-1 64s libpython3-stdlib lto-disabled-list python3 python3-minimal 64s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 64s Need to get 2671 kB of archives. 64s After this operation, 66.6 kB of additional disk space will be used. 64s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.13.7-2 [27.8 kB] 64s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.13.7-2 [23.9 kB] 64s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.13.7-2 [10.6 kB] 64s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libapt-pkg7.0 arm64 3.1.8ubuntu1 [1055 kB] 65s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 apt arm64 3.1.8ubuntu1 [1373 kB] 65s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libgirepository-1.0-1 arm64 1.86.0-6 [84.5 kB] 65s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 gir1.2-girepository-2.0 arm64 1.86.0-6 [25.3 kB] 65s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 flash-kernel arm64 3.109ubuntu7 [58.8 kB] 65s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 lto-disabled-list all 71 [12.5 kB] 65s dpkg-preconfigure: unable to re-open stdin: No such file or directory 65s Fetched 2671 kB in 1s (2507 kB/s) 66s (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 ... 83359 files and directories currently installed.) 66s Preparing to unpack .../python3-minimal_3.13.7-2_arm64.deb ... 66s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 66s Setting up python3-minimal (3.13.7-2) ... 66s (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 ... 83359 files and directories currently installed.) 66s Preparing to unpack .../0-python3_3.13.7-2_arm64.deb ... 66s running python pre-rtupdate hooks for python3.13... 66s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 66s Preparing to unpack .../1-libpython3-stdlib_3.13.7-2_arm64.deb ... 66s Unpacking libpython3-stdlib:arm64 (3.13.7-2) over (3.13.7-1) ... 66s Preparing to unpack .../2-libapt-pkg7.0_3.1.8ubuntu1_arm64.deb ... 66s Unpacking libapt-pkg7.0:arm64 (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 66s Preparing to unpack .../3-apt_3.1.8ubuntu1_arm64.deb ... 66s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 67s Preparing to unpack .../4-libgirepository-1.0-1_1.86.0-6_arm64.deb ... 67s Unpacking libgirepository-1.0-1:arm64 (1.86.0-6) over (1.84.0-1) ... 67s Preparing to unpack .../5-gir1.2-girepository-2.0_1.86.0-6_arm64.deb ... 67s Unpacking gir1.2-girepository-2.0:arm64 (1.86.0-6) over (1.84.0-1) ... 67s Preparing to unpack .../6-flash-kernel_3.109ubuntu7_arm64.deb ... 67s Unpacking flash-kernel (3.109ubuntu7) over (3.109ubuntu6) ... 67s Preparing to unpack .../7-lto-disabled-list_71_all.deb ... 67s Unpacking lto-disabled-list (71) over (69) ... 67s Setting up lto-disabled-list (71) ... 67s Setting up libgirepository-1.0-1:arm64 (1.86.0-6) ... 67s Setting up libapt-pkg7.0:arm64 (3.1.8ubuntu1) ... 67s Setting up libpython3-stdlib:arm64 (3.13.7-2) ... 67s Setting up apt (3.1.8ubuntu1) ... 68s Setting up python3 (3.13.7-2) ... 68s running python rtupdate hooks for python3.13... 68s running python post-rtupdate hooks for python3.13... 68s Setting up gir1.2-girepository-2.0:arm64 (1.86.0-6) ... 68s Setting up flash-kernel (3.109ubuntu7) ... 69s flash-kernel: deferring update (trigger activated) 69s Processing triggers for libc-bin (2.42-0ubuntu3) ... 69s Processing triggers for man-db (2.13.1-1) ... 71s Processing triggers for initramfs-tools (0.150ubuntu3) ... 71s update-initramfs: Generating /boot/initrd.img-6.17.0-5-generic 88s System running in EFI mode, skipping. 88s Processing triggers for flash-kernel (3.109ubuntu7) ... 88s System running in EFI mode, skipping. 89s autopkgtest [15:28:52]: upgrading testbed (apt dist-upgrade and autopurge) 90s Reading package lists... 90s Building dependency tree... 90s Reading state information... 90s Calculating upgrade... 91s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 91s Reading package lists... 91s Building dependency tree... 91s Reading state information... 91s Solving dependencies... 91s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s autopkgtest [15:28:55]: rebooting testbed after setup commands that affected boot 119s autopkgtest [15:29:22]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 122s autopkgtest [15:29:25]: @@@@@@@@@@@@@@@@@@@@ apt-source coot 130s Get:1 http://ftpmaster.internal/ubuntu resolute/universe coot 1.1.15+dfsg-1build1 (dsc) [2996 B] 130s Get:2 http://ftpmaster.internal/ubuntu resolute/universe coot 1.1.15+dfsg-1build1 (tar) [89.2 MB] 130s Get:3 http://ftpmaster.internal/ubuntu resolute/universe coot 1.1.15+dfsg-1build1 (diff) [53.7 kB] 130s gpgv: Signature made Fri Aug 8 03:34:32 2025 UTC 130s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 130s gpgv: Can't check signature: No public key 130s dpkg-source: warning: cannot verify inline signature for ./coot_1.1.15+dfsg-1build1.dsc: no acceptable signature found 133s autopkgtest [15:29:36]: testing package coot version 1.1.15+dfsg-1build1 134s autopkgtest [15:29:37]: build not needed 145s autopkgtest [15:29:48]: test command1: preparing testbed 145s Reading package lists... 145s Building dependency tree... 145s Reading state information... 146s Solving dependencies... 146s The following NEW packages will be installed: 146s adwaita-icon-theme coot coot-data coot-doc dconf-gsettings-backend 146s dconf-service fontconfig fontconfig-config fonts-freefont-ttf 146s fonts-noto-core fonts-noto-mono gir1.2-freedesktop gir1.2-gdkpixbuf-2.0 146s gir1.2-graphene-1.0 gir1.2-gtk-4.0 gir1.2-harfbuzz-0.0 gir1.2-pango-1.0 146s gtk-update-icon-cache hicolor-icon-theme libamd-comgr2 libamdhip64-5 146s libasound2-data libasound2t64 libblas3 libboost-iostreams1.83.0 146s libboost-iostreams1.88.0 libboost-numpy1.83.0 libboost-python1.83.0 146s libboost-python1.88.0 libboost-serialization1.83.0 146s libboost-serialization1.88.0 libcairo-gobject2 libcairo-script-interpreter2 146s libcairo2 libccp4-data libccp4c0t64 libclipper2 libcoordgen3 libcootapi-dev 146s libcootapi1.1 libcpdb-frontend2t64 libcpdb2t64 libdatrie1 libdconf1 146s libdeflate0 libdrm-amdgpu1 libegl-mesa0 libegl1 libepoxy0 146s libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libfontconfig1 146s libgbm1 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgl1 146s libgl1-mesa-dri libgles2 libglvnd0 libglx-mesa0 libglx0 libgomp1 146s libgraphene-1.0-0 libgraphite2-3 libgsl28 libgslcblas0 libgstreamer-gl1.0-0 146s libgstreamer-plugins-base1.0-0 libgstreamer1.0-0 libgtk-4-1 libgtk-4-common 146s libgudev-1.0-0 libharfbuzz-gobject0 libharfbuzz-subset0 libharfbuzz0b 146s libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 146s libibumad3 libinchi1.07 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 146s libllvm17t64 libmaeparser1 libmmdb2-0 libogg0 libopenmpi40 liborc-0.4-0t64 146s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpangoxft-1.0-0 146s libpciaccess0 libpixman-1-0 librdkit1t64 librdmacm1t64 librsvg2-2 146s libsharpyuv0 libssm2 libthai-data libthai0 libtiff6 libucx0 libvorbis0a 146s libvorbisfile3 libvulkan1 libwayland-client0 libwayland-cursor0 146s libwayland-egl1 libwebp7 libx11-xcb1 libxcb-dri3-0 libxcb-glx0 146s libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 146s libxcb-xfixes0 libxcursor1 libxdamage1 libxfixes3 libxft2 libxi6 146s libxinerama1 libxnvctrl0 libxrandr2 libxrender1 libxshmfence1 libxxf86vm1 146s mesa-libgallium ocl-icd-libopencl1 python3-numpy python3-numpy-dev 146s python3-rdkit rdkit-data refmac-dictionary sfftw2 ttf-bitstream-vera 146s 0 upgraded, 146 newly installed, 0 to remove and 0 not upgraded. 146s Need to get 181 MB of archives. 146s After this operation, 895 MB of additional disk space will be used. 146s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 146s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-6build1 [186 kB] 147s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-5ubuntu1 [450 kB] 147s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-6build1 [2340 kB] 147s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 147s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-5 [8326 B] 147s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu2 [165 kB] 147s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 147s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 147s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 147s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 147s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 147s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 147s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 147s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-5 [156 kB] 147s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 gtk-update-icon-cache arm64 4.20.1+ds-2 [54.4 kB] 147s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 hicolor-icon-theme all 0.18-2 [13.3 kB] 147s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 adwaita-icon-theme all 49.0-1 [581 kB] 147s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-noto-mono all 20201225-2 [435 kB] 147s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-noto-core all 20201225-2 [13.3 MB] 148s Get:21 http://ftpmaster.internal/ubuntu resolute/universe arm64 ttf-bitstream-vera all 1.10-8.2 [244 kB] 148s Get:22 http://ftpmaster.internal/ubuntu resolute/universe arm64 coot-data all 1.1.15+dfsg-1build1 [11.9 MB] 148s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-freefont-ttf all 20211204+svn4273-2 [5641 kB] 148s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.15.0-2.3ubuntu1 [38.1 kB] 148s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.15.0-2.3ubuntu1 [144 kB] 148s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 148s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2build1 [18.1 kB] 148s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2build1 [6234 B] 148s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 148s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-1build1 [592 kB] 148s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo-gobject2 arm64 1.18.4-1build1 [128 kB] 148s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 gir1.2-freedesktop arm64 1.86.0-6 [65.9 kB] 148s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 gir1.2-gdkpixbuf-2.0 arm64 2.42.12+dfsg-5 [9282 B] 148s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphene-1.0-0 arm64 1.10.8-5 [48.0 kB] 148s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 gir1.2-graphene-1.0 arm64 1.10.8-5 [11.1 kB] 148s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 148s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 148s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz-gobject0 arm64 10.2.0-1 [34.2 kB] 148s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 gir1.2-harfbuzz-0.0 arm64 10.2.0-1 [45.0 kB] 148s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig arm64 2.15.0-2.3ubuntu1 [191 kB] 148s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 148s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libdatrie1 arm64 0.2.13-4 [19.1 kB] 148s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 148s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 libpango-1.0-0 arm64 1.56.3-1build1 [247 kB] 148s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangoft2-1.0-0 arm64 1.56.3-1build1 [53.5 kB] 148s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangocairo-1.0-0 arm64 1.56.3-1build1 [29.6 kB] 148s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 148s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangoxft-1.0-0 arm64 1.56.3-1build1 [21.3 kB] 148s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 gir1.2-pango-1.0 arm64 1.56.3-1build1 [34.6 kB] 149s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo-script-interpreter2 arm64 1.18.4-1build1 [67.0 kB] 149s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 libcpdb2t64 arm64 2.0~b7-0ubuntu3 [31.1 kB] 149s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 libcpdb-frontend2t64 arm64 2.0~b7-0ubuntu3 [22.1 kB] 149s Get:53 http://ftpmaster.internal/ubuntu resolute/main arm64 libepoxy0 arm64 1.5.10-2 [236 kB] 149s Get:54 http://ftpmaster.internal/ubuntu resolute/main arm64 libglvnd0 arm64 1.7.0-1build2 [59.2 kB] 149s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 libdrm-amdgpu1 arm64 2.4.125-1 [21.6 kB] 149s Get:56 http://ftpmaster.internal/ubuntu resolute/main arm64 libx11-xcb1 arm64 2:1.8.12-1build1 [8216 B] 149s Get:57 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-dri3-0 arm64 1.17.0-2build1 [8120 B] 149s Get:58 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-present0 arm64 1.17.0-2build1 [6560 B] 149s Get:59 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-randr0 arm64 1.17.0-2build1 [20.2 kB] 149s Get:60 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-sync1 arm64 1.17.0-2build1 [10.4 kB] 149s Get:61 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-xfixes0 arm64 1.17.0-2build1 [11.4 kB] 149s Get:62 http://ftpmaster.internal/ubuntu resolute/main arm64 libxshmfence1 arm64 1.3.3-1 [5378 B] 149s Get:63 http://ftpmaster.internal/ubuntu resolute/main arm64 mesa-libgallium arm64 25.2.3-1ubuntu1 [12.1 MB] 149s Get:64 http://ftpmaster.internal/ubuntu resolute/main arm64 libgbm1 arm64 25.2.3-1ubuntu1 [34.4 kB] 149s Get:65 http://ftpmaster.internal/ubuntu resolute/main arm64 libwayland-client0 arm64 1.24.0-1build1 [28.9 kB] 149s Get:66 http://ftpmaster.internal/ubuntu resolute/main arm64 libegl-mesa0 arm64 25.2.3-1ubuntu1 [115 kB] 149s Get:67 http://ftpmaster.internal/ubuntu resolute/main arm64 libegl1 arm64 1.7.0-1build2 [31.9 kB] 149s Get:68 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-glx0 arm64 1.17.0-2build1 [27.8 kB] 149s Get:69 http://ftpmaster.internal/ubuntu resolute/main arm64 libxxf86vm1 arm64 1:1.1.4-1build4 [9130 B] 149s Get:70 http://ftpmaster.internal/ubuntu resolute/main arm64 libvulkan1 arm64 1.4.321.0-1 [169 kB] 149s Get:71 http://ftpmaster.internal/ubuntu resolute/main arm64 libgl1-mesa-dri arm64 25.2.3-1ubuntu1 [34.9 kB] 149s Get:72 http://ftpmaster.internal/ubuntu resolute/main arm64 libglx-mesa0 arm64 25.2.3-1ubuntu1 [110 kB] 149s Get:73 http://ftpmaster.internal/ubuntu resolute/main arm64 libglx0 arm64 1.7.0-1build2 [34.5 kB] 149s Get:74 http://ftpmaster.internal/ubuntu resolute/main arm64 libgl1 arm64 1.7.0-1build2 [104 kB] 149s Get:75 http://ftpmaster.internal/ubuntu resolute/main arm64 libgstreamer1.0-0 arm64 1.26.6-1 [1160 kB] 149s Get:76 http://ftpmaster.internal/ubuntu resolute/main arm64 liborc-0.4-0t64 arm64 1:0.4.41-1 [202 kB] 149s Get:77 http://ftpmaster.internal/ubuntu resolute/main arm64 libgstreamer-plugins-base1.0-0 arm64 1.26.6-1 [850 kB] 149s Get:78 http://ftpmaster.internal/ubuntu resolute/main arm64 libgudev-1.0-0 arm64 1:238-7 [16.5 kB] 149s Get:79 http://ftpmaster.internal/ubuntu resolute/main arm64 libwayland-cursor0 arm64 1.24.0-1build1 [11.1 kB] 149s Get:80 http://ftpmaster.internal/ubuntu resolute/main arm64 libwayland-egl1 arm64 1.24.0-1build1 [6500 B] 149s Get:81 http://ftpmaster.internal/ubuntu resolute/main arm64 libgstreamer-gl1.0-0 arm64 1.26.6-1 [220 kB] 149s Get:82 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz-subset0 arm64 10.2.0-1 [502 kB] 149s Get:83 http://ftpmaster.internal/ubuntu resolute/main arm64 librsvg2-2 arm64 2.60.0+dfsg-1build1 [1720 kB] 149s Get:84 http://ftpmaster.internal/ubuntu resolute/main arm64 libxfixes3 arm64 1:6.0.0-2build1 [11.2 kB] 149s Get:85 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcursor1 arm64 1:1.2.3-1 [22.2 kB] 149s Get:86 http://ftpmaster.internal/ubuntu resolute/main arm64 libxdamage1 arm64 1:1.1.6-1build1 [6236 B] 149s Get:87 http://ftpmaster.internal/ubuntu resolute/main arm64 libxi6 arm64 2:1.8.2-1 [32.4 kB] 149s Get:88 http://ftpmaster.internal/ubuntu resolute/main arm64 libxinerama1 arm64 2:1.1.4-3build1 [6394 B] 149s Get:89 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrandr2 arm64 2:1.5.4-1 [19.6 kB] 149s Get:90 http://ftpmaster.internal/ubuntu resolute/main arm64 libgles2 arm64 1.7.0-1build2 [17.9 kB] 149s Get:91 http://ftpmaster.internal/ubuntu resolute/main arm64 libdconf1 arm64 0.40.0-5willsync1 [42.3 kB] 149s Get:92 http://ftpmaster.internal/ubuntu resolute/main arm64 dconf-service arm64 0.40.0-5willsync1 [28.8 kB] 149s Get:93 http://ftpmaster.internal/ubuntu resolute/main arm64 dconf-gsettings-backend arm64 0.40.0-5willsync1 [23.8 kB] 149s Get:94 http://ftpmaster.internal/ubuntu resolute/main arm64 libgtk-4-common all 4.20.1+ds-2 [1528 kB] 149s Get:95 http://ftpmaster.internal/ubuntu resolute/main arm64 libgtk-4-1 arm64 4.20.1+ds-2 [3298 kB] 149s Get:96 http://ftpmaster.internal/ubuntu resolute/main arm64 gir1.2-gtk-4.0 arm64 4.20.1+ds-2 [220 kB] 149s Get:97 http://ftpmaster.internal/ubuntu resolute/universe arm64 rdkit-data all 202503.1-4 [12.6 MB] 150s Get:98 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-python1.83.0 arm64 1.83.0-5ubuntu1 [313 kB] 150s Get:99 http://ftpmaster.internal/ubuntu resolute/universe arm64 libboost-numpy1.83.0 arm64 1.83.0-5ubuntu1 [244 kB] 150s Get:100 http://ftpmaster.internal/ubuntu resolute/universe arm64 libboost-serialization1.83.0 arm64 1.83.0-5ubuntu1 [350 kB] 150s Get:101 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcoordgen3 arm64 3.0.2-1 [207 kB] 150s Get:102 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-5ubuntu1 [262 kB] 150s Get:103 http://ftpmaster.internal/ubuntu resolute/universe arm64 libinchi1.07 arm64 1.07.3+dfsg-1 [573 kB] 150s Get:104 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-iostreams1.88.0 arm64 1.88.0-1.4ubuntu1 [263 kB] 150s Get:105 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmaeparser1 arm64 1.3.1-1build3 [86.4 kB] 150s Get:106 http://ftpmaster.internal/ubuntu resolute/universe arm64 librdkit1t64 arm64 202503.1-4 [5454 kB] 151s Get:107 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-rdkit arm64 202503.1-4 [4683 kB] 151s Get:108 http://ftpmaster.internal/ubuntu resolute/universe arm64 refmac-dictionary all 5.41-3 [16.7 MB] 152s Get:109 http://ftpmaster.internal/ubuntu resolute/main arm64 libasound2-data all 1.2.14-1ubuntu1 [21.2 kB] 152s Get:110 http://ftpmaster.internal/ubuntu resolute/main arm64 libasound2t64 arm64 1.2.14-1ubuntu1 [394 kB] 152s Get:111 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-python1.88.0 arm64 1.88.0-1.4ubuntu1 [317 kB] 152s Get:112 http://ftpmaster.internal/ubuntu resolute/universe arm64 libboost-serialization1.88.0 arm64 1.88.0-1.4ubuntu1 [353 kB] 152s Get:113 http://ftpmaster.internal/ubuntu resolute/universe arm64 libccp4-data all 8.0.0-5 [65.2 kB] 152s Get:114 http://ftpmaster.internal/ubuntu resolute/universe arm64 libccp4c0t64 arm64 8.0.0-5 [99.8 kB] 152s Get:115 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmmdb2-0 arm64 2.0.22-1 [347 kB] 152s Get:116 http://ftpmaster.internal/ubuntu resolute/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-10build1 [97.5 kB] 152s Get:117 http://ftpmaster.internal/ubuntu resolute/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10build1 [8272 B] 152s Get:118 http://ftpmaster.internal/ubuntu resolute/main arm64 librdmacm1t64 arm64 56.1-1ubuntu1 [71.4 kB] 152s Get:119 http://ftpmaster.internal/ubuntu resolute/universe arm64 libfabric1 arm64 2.1.0-1.1 [622 kB] 152s Get:120 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhwloc15 arm64 2.12.2-1 [169 kB] 152s Get:121 http://ftpmaster.internal/ubuntu resolute/universe arm64 libllvm17t64 arm64 1:17.0.6-22build1 [24.8 MB] 152s Get:122 http://ftpmaster.internal/ubuntu resolute/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3build3 [14.0 MB] 153s Get:123 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhsakmt1 arm64 6.2.4+ds-1 [64.7 kB] 153s Get:124 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhsa-runtime64-1 arm64 6.1.2-3 [305 kB] 153s Get:125 http://ftpmaster.internal/ubuntu resolute/universe arm64 libamdhip64-5 arm64 5.7.1-6 [9707 kB] 153s Get:126 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-5ubuntu1 [148 kB] 153s Get:127 http://ftpmaster.internal/ubuntu resolute/main arm64 libibumad3 arm64 56.1-1ubuntu1 [31.3 kB] 153s Get:128 http://ftpmaster.internal/ubuntu resolute/main arm64 libibmad5 arm64 56.1-1ubuntu1 [44.1 kB] 153s Get:129 http://ftpmaster.internal/ubuntu resolute/universe arm64 libucx0 arm64 1.19.0+ds-1 [1242 kB] 153s Get:130 http://ftpmaster.internal/ubuntu resolute/main arm64 libpciaccess0 arm64 0.18.1-1ubuntu2 [19.4 kB] 153s Get:131 http://ftpmaster.internal/ubuntu resolute/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu4 [12.4 kB] 153s Get:132 http://ftpmaster.internal/ubuntu resolute/main arm64 ocl-icd-libopencl1 arm64 2.3.3-1 [42.2 kB] 153s Get:133 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhwloc-plugins arm64 2.12.2-1 [16.6 kB] 153s Get:134 http://ftpmaster.internal/ubuntu resolute/universe arm64 libopenmpi40 arm64 5.0.8-8ubuntu1 [3274 kB] 153s Get:135 http://ftpmaster.internal/ubuntu resolute/universe arm64 sfftw2 arm64 2.1.5-7build1 [184 kB] 153s Get:136 http://ftpmaster.internal/ubuntu resolute/universe arm64 libclipper2 arm64 2.1.20201109-2build1 [1150 kB] 153s Get:137 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgslcblas0 arm64 2.8+dfsg-5.1ubuntu1 [96.3 kB] 153s Get:138 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgsl28 arm64 2.8+dfsg-5.1ubuntu1 [1029 kB] 153s Get:139 http://ftpmaster.internal/ubuntu resolute/universe arm64 libssm2 arm64 1.4.0-2build1 [83.8 kB] 153s Get:140 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcootapi1.1 arm64 1.1.15+dfsg-1build1 [3583 kB] 153s Get:141 http://ftpmaster.internal/ubuntu resolute/main arm64 libogg0 arm64 1.3.5-3build1 [22.6 kB] 153s Get:142 http://ftpmaster.internal/ubuntu resolute/main arm64 libvorbis0a arm64 1.3.7-3build1 [99.3 kB] 153s Get:143 http://ftpmaster.internal/ubuntu resolute/main arm64 libvorbisfile3 arm64 1.3.7-3build1 [18.0 kB] 153s Get:144 http://ftpmaster.internal/ubuntu resolute/universe arm64 coot arm64 1.1.15+dfsg-1build1 [8112 kB] 153s Get:145 http://ftpmaster.internal/ubuntu resolute/universe arm64 coot-doc all 1.1.15+dfsg-1build1 [2048 kB] 153s Get:146 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcootapi-dev arm64 1.1.15+dfsg-1build1 [25.5 kB] 154s Fetched 181 MB in 7s (24.6 MB/s) 154s Selecting previously unselected package python3-numpy-dev:arm64. 154s (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 ... 83359 files and directories currently installed.) 154s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 154s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 154s Selecting previously unselected package libblas3:arm64. 154s Preparing to unpack .../001-libblas3_3.12.1-6build1_arm64.deb ... 154s Unpacking libblas3:arm64 (3.12.1-6build1) ... 154s Selecting previously unselected package libgfortran5:arm64. 154s Preparing to unpack .../002-libgfortran5_15.2.0-5ubuntu1_arm64.deb ... 154s Unpacking libgfortran5:arm64 (15.2.0-5ubuntu1) ... 154s Selecting previously unselected package liblapack3:arm64. 154s Preparing to unpack .../003-liblapack3_3.12.1-6build1_arm64.deb ... 154s Unpacking liblapack3:arm64 (3.12.1-6build1) ... 154s Selecting previously unselected package python3-numpy. 154s Preparing to unpack .../004-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 154s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 154s Selecting previously unselected package libgdk-pixbuf2.0-common. 154s Preparing to unpack .../005-libgdk-pixbuf2.0-common_2.42.12+dfsg-5_all.deb ... 154s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-5) ... 154s Selecting previously unselected package libjpeg-turbo8:arm64. 154s Preparing to unpack .../006-libjpeg-turbo8_2.1.5-4ubuntu2_arm64.deb ... 154s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 154s Selecting previously unselected package libjpeg8:arm64. 154s Preparing to unpack .../007-libjpeg8_8c-2ubuntu11_arm64.deb ... 154s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 154s Selecting previously unselected package libdeflate0:arm64. 154s Preparing to unpack .../008-libdeflate0_1.23-2_arm64.deb ... 154s Unpacking libdeflate0:arm64 (1.23-2) ... 154s Selecting previously unselected package libjbig0:arm64. 154s Preparing to unpack .../009-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 154s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 154s Selecting previously unselected package liblerc4:arm64. 155s Preparing to unpack .../010-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 155s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 155s Selecting previously unselected package libsharpyuv0:arm64. 155s Preparing to unpack .../011-libsharpyuv0_1.5.0-0.1_arm64.deb ... 155s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 155s Selecting previously unselected package libwebp7:arm64. 155s Preparing to unpack .../012-libwebp7_1.5.0-0.1_arm64.deb ... 155s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 155s Selecting previously unselected package libtiff6:arm64. 155s Preparing to unpack .../013-libtiff6_4.7.0-3ubuntu3_arm64.deb ... 155s Unpacking libtiff6:arm64 (4.7.0-3ubuntu3) ... 155s Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64. 155s Preparing to unpack .../014-libgdk-pixbuf-2.0-0_2.42.12+dfsg-5_arm64.deb ... 155s Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-5) ... 155s Selecting previously unselected package gtk-update-icon-cache. 155s Preparing to unpack .../015-gtk-update-icon-cache_4.20.1+ds-2_arm64.deb ... 155s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 155s 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. 155s Unpacking gtk-update-icon-cache (4.20.1+ds-2) ... 155s Selecting previously unselected package hicolor-icon-theme. 155s Preparing to unpack .../016-hicolor-icon-theme_0.18-2_all.deb ... 155s Unpacking hicolor-icon-theme (0.18-2) ... 155s Selecting previously unselected package adwaita-icon-theme. 155s Preparing to unpack .../017-adwaita-icon-theme_49.0-1_all.deb ... 155s Unpacking adwaita-icon-theme (49.0-1) ... 155s Selecting previously unselected package fonts-noto-mono. 155s Preparing to unpack .../018-fonts-noto-mono_20201225-2_all.deb ... 155s Unpacking fonts-noto-mono (20201225-2) ... 155s Selecting previously unselected package fonts-noto-core. 155s Preparing to unpack .../019-fonts-noto-core_20201225-2_all.deb ... 155s Unpacking fonts-noto-core (20201225-2) ... 155s Selecting previously unselected package ttf-bitstream-vera. 155s Preparing to unpack .../020-ttf-bitstream-vera_1.10-8.2_all.deb ... 155s Unpacking ttf-bitstream-vera (1.10-8.2) ... 155s Selecting previously unselected package coot-data. 155s Preparing to unpack .../021-coot-data_1.1.15+dfsg-1build1_all.deb ... 155s Unpacking coot-data (1.1.15+dfsg-1build1) ... 156s Selecting previously unselected package fonts-freefont-ttf. 156s Preparing to unpack .../022-fonts-freefont-ttf_20211204+svn4273-2_all.deb ... 156s Unpacking fonts-freefont-ttf (20211204+svn4273-2) ... 156s Selecting previously unselected package fontconfig-config. 156s Preparing to unpack .../023-fontconfig-config_2.15.0-2.3ubuntu1_arm64.deb ... 156s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 156s Selecting previously unselected package libfontconfig1:arm64. 156s Preparing to unpack .../024-libfontconfig1_2.15.0-2.3ubuntu1_arm64.deb ... 156s Unpacking libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 156s Selecting previously unselected package libpixman-1-0:arm64. 156s Preparing to unpack .../025-libpixman-1-0_0.44.0-3_arm64.deb ... 156s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 156s Selecting previously unselected package libxcb-render0:arm64. 156s Preparing to unpack .../026-libxcb-render0_1.17.0-2build1_arm64.deb ... 156s Unpacking libxcb-render0:arm64 (1.17.0-2build1) ... 156s Selecting previously unselected package libxcb-shm0:arm64. 156s Preparing to unpack .../027-libxcb-shm0_1.17.0-2build1_arm64.deb ... 156s Unpacking libxcb-shm0:arm64 (1.17.0-2build1) ... 156s Selecting previously unselected package libxrender1:arm64. 156s Preparing to unpack .../028-libxrender1_1%3a0.9.12-1_arm64.deb ... 156s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 156s Selecting previously unselected package libcairo2:arm64. 156s Preparing to unpack .../029-libcairo2_1.18.4-1build1_arm64.deb ... 156s Unpacking libcairo2:arm64 (1.18.4-1build1) ... 156s Selecting previously unselected package libcairo-gobject2:arm64. 156s Preparing to unpack .../030-libcairo-gobject2_1.18.4-1build1_arm64.deb ... 156s Unpacking libcairo-gobject2:arm64 (1.18.4-1build1) ... 156s Selecting previously unselected package gir1.2-freedesktop:arm64. 156s Preparing to unpack .../031-gir1.2-freedesktop_1.86.0-6_arm64.deb ... 156s Unpacking gir1.2-freedesktop:arm64 (1.86.0-6) ... 156s Selecting previously unselected package gir1.2-gdkpixbuf-2.0:arm64. 156s Preparing to unpack .../032-gir1.2-gdkpixbuf-2.0_2.42.12+dfsg-5_arm64.deb ... 156s Unpacking gir1.2-gdkpixbuf-2.0:arm64 (2.42.12+dfsg-5) ... 156s Selecting previously unselected package libgraphene-1.0-0:arm64. 156s Preparing to unpack .../033-libgraphene-1.0-0_1.10.8-5_arm64.deb ... 156s Unpacking libgraphene-1.0-0:arm64 (1.10.8-5) ... 156s Selecting previously unselected package gir1.2-graphene-1.0:arm64. 156s Preparing to unpack .../034-gir1.2-graphene-1.0_1.10.8-5_arm64.deb ... 156s Unpacking gir1.2-graphene-1.0:arm64 (1.10.8-5) ... 156s Selecting previously unselected package libgraphite2-3:arm64. 156s Preparing to unpack .../035-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 156s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 156s Selecting previously unselected package libharfbuzz0b:arm64. 156s Preparing to unpack .../036-libharfbuzz0b_10.2.0-1_arm64.deb ... 156s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 156s Selecting previously unselected package libharfbuzz-gobject0:arm64. 156s Preparing to unpack .../037-libharfbuzz-gobject0_10.2.0-1_arm64.deb ... 156s Unpacking libharfbuzz-gobject0:arm64 (10.2.0-1) ... 156s Selecting previously unselected package gir1.2-harfbuzz-0.0:arm64. 156s Preparing to unpack .../038-gir1.2-harfbuzz-0.0_10.2.0-1_arm64.deb ... 156s Unpacking gir1.2-harfbuzz-0.0:arm64 (10.2.0-1) ... 156s Selecting previously unselected package fontconfig. 156s Preparing to unpack .../039-fontconfig_2.15.0-2.3ubuntu1_arm64.deb ... 156s Unpacking fontconfig (2.15.0-2.3ubuntu1) ... 156s Selecting previously unselected package libthai-data. 156s Preparing to unpack .../040-libthai-data_0.1.29-2build1_all.deb ... 156s Unpacking libthai-data (0.1.29-2build1) ... 156s Selecting previously unselected package libdatrie1:arm64. 156s Preparing to unpack .../041-libdatrie1_0.2.13-4_arm64.deb ... 156s Unpacking libdatrie1:arm64 (0.2.13-4) ... 157s Selecting previously unselected package libthai0:arm64. 157s Preparing to unpack .../042-libthai0_0.1.29-2build1_arm64.deb ... 157s Unpacking libthai0:arm64 (0.1.29-2build1) ... 157s Selecting previously unselected package libpango-1.0-0:arm64. 157s Preparing to unpack .../043-libpango-1.0-0_1.56.3-1build1_arm64.deb ... 157s Unpacking libpango-1.0-0:arm64 (1.56.3-1build1) ... 157s Selecting previously unselected package libpangoft2-1.0-0:arm64. 157s Preparing to unpack .../044-libpangoft2-1.0-0_1.56.3-1build1_arm64.deb ... 157s Unpacking libpangoft2-1.0-0:arm64 (1.56.3-1build1) ... 157s Selecting previously unselected package libpangocairo-1.0-0:arm64. 157s Preparing to unpack .../045-libpangocairo-1.0-0_1.56.3-1build1_arm64.deb ... 157s Unpacking libpangocairo-1.0-0:arm64 (1.56.3-1build1) ... 157s Selecting previously unselected package libxft2:arm64. 157s Preparing to unpack .../046-libxft2_2.3.6-1build1_arm64.deb ... 157s Unpacking libxft2:arm64 (2.3.6-1build1) ... 157s Selecting previously unselected package libpangoxft-1.0-0:arm64. 157s Preparing to unpack .../047-libpangoxft-1.0-0_1.56.3-1build1_arm64.deb ... 157s Unpacking libpangoxft-1.0-0:arm64 (1.56.3-1build1) ... 157s Selecting previously unselected package gir1.2-pango-1.0:arm64. 157s Preparing to unpack .../048-gir1.2-pango-1.0_1.56.3-1build1_arm64.deb ... 157s Unpacking gir1.2-pango-1.0:arm64 (1.56.3-1build1) ... 157s Selecting previously unselected package libcairo-script-interpreter2:arm64. 157s Preparing to unpack .../049-libcairo-script-interpreter2_1.18.4-1build1_arm64.deb ... 157s Unpacking libcairo-script-interpreter2:arm64 (1.18.4-1build1) ... 157s Selecting previously unselected package libcpdb2t64:arm64. 157s Preparing to unpack .../050-libcpdb2t64_2.0~b7-0ubuntu3_arm64.deb ... 157s Unpacking libcpdb2t64:arm64 (2.0~b7-0ubuntu3) ... 157s Selecting previously unselected package libcpdb-frontend2t64:arm64. 157s Preparing to unpack .../051-libcpdb-frontend2t64_2.0~b7-0ubuntu3_arm64.deb ... 157s Unpacking libcpdb-frontend2t64:arm64 (2.0~b7-0ubuntu3) ... 157s Selecting previously unselected package libepoxy0:arm64. 157s Preparing to unpack .../052-libepoxy0_1.5.10-2_arm64.deb ... 157s Unpacking libepoxy0:arm64 (1.5.10-2) ... 157s Selecting previously unselected package libglvnd0:arm64. 157s Preparing to unpack .../053-libglvnd0_1.7.0-1build2_arm64.deb ... 157s Unpacking libglvnd0:arm64 (1.7.0-1build2) ... 157s Selecting previously unselected package libdrm-amdgpu1:arm64. 157s Preparing to unpack .../054-libdrm-amdgpu1_2.4.125-1_arm64.deb ... 157s Unpacking libdrm-amdgpu1:arm64 (2.4.125-1) ... 157s Selecting previously unselected package libx11-xcb1:arm64. 157s Preparing to unpack .../055-libx11-xcb1_2%3a1.8.12-1build1_arm64.deb ... 157s Unpacking libx11-xcb1:arm64 (2:1.8.12-1build1) ... 157s Selecting previously unselected package libxcb-dri3-0:arm64. 157s Preparing to unpack .../056-libxcb-dri3-0_1.17.0-2build1_arm64.deb ... 157s Unpacking libxcb-dri3-0:arm64 (1.17.0-2build1) ... 157s Selecting previously unselected package libxcb-present0:arm64. 157s Preparing to unpack .../057-libxcb-present0_1.17.0-2build1_arm64.deb ... 157s Unpacking libxcb-present0:arm64 (1.17.0-2build1) ... 157s Selecting previously unselected package libxcb-randr0:arm64. 157s Preparing to unpack .../058-libxcb-randr0_1.17.0-2build1_arm64.deb ... 157s Unpacking libxcb-randr0:arm64 (1.17.0-2build1) ... 157s Selecting previously unselected package libxcb-sync1:arm64. 157s Preparing to unpack .../059-libxcb-sync1_1.17.0-2build1_arm64.deb ... 157s Unpacking libxcb-sync1:arm64 (1.17.0-2build1) ... 157s Selecting previously unselected package libxcb-xfixes0:arm64. 157s Preparing to unpack .../060-libxcb-xfixes0_1.17.0-2build1_arm64.deb ... 157s Unpacking libxcb-xfixes0:arm64 (1.17.0-2build1) ... 157s Selecting previously unselected package libxshmfence1:arm64. 157s Preparing to unpack .../061-libxshmfence1_1.3.3-1_arm64.deb ... 157s Unpacking libxshmfence1:arm64 (1.3.3-1) ... 157s Selecting previously unselected package mesa-libgallium:arm64. 157s Preparing to unpack .../062-mesa-libgallium_25.2.3-1ubuntu1_arm64.deb ... 157s Unpacking mesa-libgallium:arm64 (25.2.3-1ubuntu1) ... 157s Selecting previously unselected package libgbm1:arm64. 157s Preparing to unpack .../063-libgbm1_25.2.3-1ubuntu1_arm64.deb ... 157s Unpacking libgbm1:arm64 (25.2.3-1ubuntu1) ... 157s Selecting previously unselected package libwayland-client0:arm64. 157s Preparing to unpack .../064-libwayland-client0_1.24.0-1build1_arm64.deb ... 157s Unpacking libwayland-client0:arm64 (1.24.0-1build1) ... 157s Selecting previously unselected package libegl-mesa0:arm64. 158s Preparing to unpack .../065-libegl-mesa0_25.2.3-1ubuntu1_arm64.deb ... 158s Unpacking libegl-mesa0:arm64 (25.2.3-1ubuntu1) ... 158s Selecting previously unselected package libegl1:arm64. 158s Preparing to unpack .../066-libegl1_1.7.0-1build2_arm64.deb ... 158s Unpacking libegl1:arm64 (1.7.0-1build2) ... 158s Selecting previously unselected package libxcb-glx0:arm64. 158s Preparing to unpack .../067-libxcb-glx0_1.17.0-2build1_arm64.deb ... 158s Unpacking libxcb-glx0:arm64 (1.17.0-2build1) ... 158s Selecting previously unselected package libxxf86vm1:arm64. 158s Preparing to unpack .../068-libxxf86vm1_1%3a1.1.4-1build4_arm64.deb ... 158s Unpacking libxxf86vm1:arm64 (1:1.1.4-1build4) ... 158s Selecting previously unselected package libvulkan1:arm64. 158s Preparing to unpack .../069-libvulkan1_1.4.321.0-1_arm64.deb ... 158s Unpacking libvulkan1:arm64 (1.4.321.0-1) ... 158s Selecting previously unselected package libgl1-mesa-dri:arm64. 158s Preparing to unpack .../070-libgl1-mesa-dri_25.2.3-1ubuntu1_arm64.deb ... 158s Unpacking libgl1-mesa-dri:arm64 (25.2.3-1ubuntu1) ... 158s Selecting previously unselected package libglx-mesa0:arm64. 158s Preparing to unpack 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libharfbuzz-subset0:arm64. 158s Preparing to unpack .../081-libharfbuzz-subset0_10.2.0-1_arm64.deb ... 158s Unpacking libharfbuzz-subset0:arm64 (10.2.0-1) ... 158s Selecting previously unselected package librsvg2-2:arm64. 158s Preparing to unpack .../082-librsvg2-2_2.60.0+dfsg-1build1_arm64.deb ... 158s Unpacking librsvg2-2:arm64 (2.60.0+dfsg-1build1) ... 158s Selecting previously unselected package libxfixes3:arm64. 158s Preparing to unpack .../083-libxfixes3_1%3a6.0.0-2build1_arm64.deb ... 158s Unpacking libxfixes3:arm64 (1:6.0.0-2build1) ... 158s Selecting previously unselected package libxcursor1:arm64. 158s Preparing to unpack .../084-libxcursor1_1%3a1.2.3-1_arm64.deb ... 158s Unpacking libxcursor1:arm64 (1:1.2.3-1) ... 158s Selecting previously unselected package libxdamage1:arm64. 158s Preparing to unpack .../085-libxdamage1_1%3a1.1.6-1build1_arm64.deb ... 158s Unpacking libxdamage1:arm64 (1:1.1.6-1build1) ... 158s Selecting previously unselected package libxi6:arm64. 158s Preparing to unpack .../086-libxi6_2%3a1.8.2-1_arm64.deb ... 158s Unpacking libxi6:arm64 (2:1.8.2-1) ... 158s Selecting previously unselected package libxinerama1:arm64. 158s Preparing to unpack .../087-libxinerama1_2%3a1.1.4-3build1_arm64.deb ... 158s Unpacking libxinerama1:arm64 (2:1.1.4-3build1) ... 158s Selecting previously unselected package libxrandr2:arm64. 158s Preparing to unpack .../088-libxrandr2_2%3a1.5.4-1_arm64.deb ... 158s Unpacking libxrandr2:arm64 (2:1.5.4-1) ... 158s Selecting previously unselected package libgles2:arm64. 158s Preparing to unpack .../089-libgles2_1.7.0-1build2_arm64.deb ... 158s Unpacking libgles2:arm64 (1.7.0-1build2) ... 158s Selecting previously unselected package libdconf1:arm64. 158s Preparing to unpack .../090-libdconf1_0.40.0-5willsync1_arm64.deb ... 158s Unpacking libdconf1:arm64 (0.40.0-5willsync1) ... 158s Selecting previously unselected package dconf-service. 158s Preparing to unpack .../091-dconf-service_0.40.0-5willsync1_arm64.deb ... 158s Unpacking dconf-service (0.40.0-5willsync1) ... 159s Selecting previously unselected package dconf-gsettings-backend:arm64. 159s Preparing to unpack .../092-dconf-gsettings-backend_0.40.0-5willsync1_arm64.deb ... 159s Unpacking dconf-gsettings-backend:arm64 (0.40.0-5willsync1) ... 159s Selecting previously unselected package libgtk-4-common. 159s Preparing to unpack .../093-libgtk-4-common_4.20.1+ds-2_all.deb ... 159s Unpacking libgtk-4-common (4.20.1+ds-2) ... 159s Selecting previously unselected package libgtk-4-1:arm64. 159s Preparing to unpack .../094-libgtk-4-1_4.20.1+ds-2_arm64.deb ... 159s Unpacking libgtk-4-1:arm64 (4.20.1+ds-2) ... 159s Selecting previously unselected package gir1.2-gtk-4.0:arm64. 159s Preparing to unpack .../095-gir1.2-gtk-4.0_4.20.1+ds-2_arm64.deb ... 159s Unpacking gir1.2-gtk-4.0:arm64 (4.20.1+ds-2) ... 159s Selecting previously unselected package rdkit-data. 159s Preparing to unpack .../096-rdkit-data_202503.1-4_all.deb ... 159s Unpacking rdkit-data (202503.1-4) ... 159s Selecting previously unselected package libboost-python1.83.0. 159s Preparing to unpack .../097-libboost-python1.83.0_1.83.0-5ubuntu1_arm64.deb ... 159s Unpacking libboost-python1.83.0 (1.83.0-5ubuntu1) ... 159s Selecting previously unselected package libboost-numpy1.83.0. 159s Preparing to unpack .../098-libboost-numpy1.83.0_1.83.0-5ubuntu1_arm64.deb ... 159s Unpacking libboost-numpy1.83.0 (1.83.0-5ubuntu1) ... 159s Selecting previously unselected package libboost-serialization1.83.0:arm64. 159s Preparing to unpack .../099-libboost-serialization1.83.0_1.83.0-5ubuntu1_arm64.deb ... 159s Unpacking libboost-serialization1.83.0:arm64 (1.83.0-5ubuntu1) ... 159s Selecting previously unselected package libcoordgen3:arm64. 159s Preparing to unpack .../100-libcoordgen3_3.0.2-1_arm64.deb ... 159s Unpacking libcoordgen3:arm64 (3.0.2-1) ... 159s Selecting previously unselected package libboost-iostreams1.83.0:arm64. 159s Preparing to unpack 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unpack .../106-python3-rdkit_202503.1-4_arm64.deb ... 159s Unpacking python3-rdkit (202503.1-4) ... 160s Selecting previously unselected package refmac-dictionary. 160s Preparing to unpack .../107-refmac-dictionary_5.41-3_all.deb ... 160s Unpacking refmac-dictionary (5.41-3) ... 161s Selecting previously unselected package libasound2-data. 161s Preparing to unpack .../108-libasound2-data_1.2.14-1ubuntu1_all.deb ... 161s Unpacking libasound2-data (1.2.14-1ubuntu1) ... 161s Selecting previously unselected package libasound2t64:arm64. 161s Preparing to unpack .../109-libasound2t64_1.2.14-1ubuntu1_arm64.deb ... 161s Unpacking libasound2t64:arm64 (1.2.14-1ubuntu1) ... 161s Selecting previously unselected package libboost-python1.88.0. 161s Preparing to unpack .../110-libboost-python1.88.0_1.88.0-1.4ubuntu1_arm64.deb ... 161s Unpacking libboost-python1.88.0 (1.88.0-1.4ubuntu1) ... 161s Selecting previously unselected package libboost-serialization1.88.0:arm64. 161s Preparing to unpack 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Preparing to unpack .../116-libevent-pthreads-2.1-7t64_2.1.12-stable-10build1_arm64.deb ... 161s Unpacking libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10build1) ... 161s Selecting previously unselected package librdmacm1t64:arm64. 161s Preparing to unpack .../117-librdmacm1t64_56.1-1ubuntu1_arm64.deb ... 161s Unpacking librdmacm1t64:arm64 (56.1-1ubuntu1) ... 161s Selecting previously unselected package libfabric1:arm64. 162s Preparing to unpack .../118-libfabric1_2.1.0-1.1_arm64.deb ... 162s Unpacking libfabric1:arm64 (2.1.0-1.1) ... 162s Selecting previously unselected package libhwloc15:arm64. 162s Preparing to unpack .../119-libhwloc15_2.12.2-1_arm64.deb ... 162s Unpacking libhwloc15:arm64 (2.12.2-1) ... 162s Selecting previously unselected package libllvm17t64:arm64. 162s Preparing to unpack .../120-libllvm17t64_1%3a17.0.6-22build1_arm64.deb ... 162s Unpacking libllvm17t64:arm64 (1:17.0.6-22build1) ... 162s Selecting previously unselected package libamd-comgr2:arm64. 162s Preparing to unpack .../121-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build3_arm64.deb ... 162s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build3) ... 163s Selecting previously unselected package libhsakmt1:arm64. 163s Preparing to unpack .../122-libhsakmt1_6.2.4+ds-1_arm64.deb ... 163s Unpacking libhsakmt1:arm64 (6.2.4+ds-1) ... 163s Selecting previously unselected package libhsa-runtime64-1:arm64. 163s Preparing to unpack .../123-libhsa-runtime64-1_6.1.2-3_arm64.deb ... 163s Unpacking libhsa-runtime64-1:arm64 (6.1.2-3) ... 163s Selecting previously unselected package libamdhip64-5:arm64. 163s Preparing to unpack .../124-libamdhip64-5_5.7.1-6_arm64.deb ... 163s Unpacking libamdhip64-5:arm64 (5.7.1-6) ... 163s Selecting previously unselected package libgomp1:arm64. 163s Preparing to unpack .../125-libgomp1_15.2.0-5ubuntu1_arm64.deb ... 163s Unpacking libgomp1:arm64 (15.2.0-5ubuntu1) ... 163s Selecting previously unselected package libibumad3:arm64. 163s Preparing to unpack .../126-libibumad3_56.1-1ubuntu1_arm64.deb ... 163s Unpacking libibumad3:arm64 (56.1-1ubuntu1) ... 163s Selecting previously unselected package libibmad5:arm64. 163s Preparing to unpack .../127-libibmad5_56.1-1ubuntu1_arm64.deb ... 163s Unpacking libibmad5:arm64 (56.1-1ubuntu1) ... 163s Selecting previously unselected package libucx0:arm64. 163s Preparing to unpack .../128-libucx0_1.19.0+ds-1_arm64.deb ... 163s Unpacking libucx0:arm64 (1.19.0+ds-1) ... 163s Selecting previously unselected package libpciaccess0:arm64. 163s Preparing to unpack .../129-libpciaccess0_0.18.1-1ubuntu2_arm64.deb ... 163s Unpacking libpciaccess0:arm64 (0.18.1-1ubuntu2) ... 163s Selecting previously unselected package libxnvctrl0:arm64. 163s Preparing to unpack .../130-libxnvctrl0_510.47.03-0ubuntu4_arm64.deb ... 163s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 163s Selecting previously unselected package ocl-icd-libopencl1:arm64. 163s Preparing to unpack .../131-ocl-icd-libopencl1_2.3.3-1_arm64.deb ... 163s Unpacking ocl-icd-libopencl1:arm64 (2.3.3-1) ... 163s Selecting previously unselected package libhwloc-plugins:arm64. 163s Preparing to unpack .../132-libhwloc-plugins_2.12.2-1_arm64.deb ... 163s Unpacking libhwloc-plugins:arm64 (2.12.2-1) ... 163s Selecting previously unselected package libopenmpi40:arm64. 163s Preparing to unpack .../133-libopenmpi40_5.0.8-8ubuntu1_arm64.deb ... 163s Unpacking libopenmpi40:arm64 (5.0.8-8ubuntu1) ... 163s Selecting previously unselected package sfftw2. 163s Preparing to unpack .../134-sfftw2_2.1.5-7build1_arm64.deb ... 163s Unpacking sfftw2 (2.1.5-7build1) ... 163s Selecting previously unselected package libclipper2:arm64. 163s Preparing to unpack .../135-libclipper2_2.1.20201109-2build1_arm64.deb ... 163s Unpacking libclipper2:arm64 (2.1.20201109-2build1) ... 163s Selecting previously unselected package libgslcblas0:arm64. 163s Preparing to unpack .../136-libgslcblas0_2.8+dfsg-5.1ubuntu1_arm64.deb ... 163s Unpacking libgslcblas0:arm64 (2.8+dfsg-5.1ubuntu1) ... 163s Selecting previously unselected package libgsl28:arm64. 163s Preparing to unpack .../137-libgsl28_2.8+dfsg-5.1ubuntu1_arm64.deb ... 163s Unpacking libgsl28:arm64 (2.8+dfsg-5.1ubuntu1) ... 163s Selecting previously unselected package libssm2:arm64. 163s Preparing to unpack .../138-libssm2_1.4.0-2build1_arm64.deb ... 163s Unpacking libssm2:arm64 (1.4.0-2build1) ... 163s Selecting previously unselected package libcootapi1.1. 163s Preparing to unpack .../139-libcootapi1.1_1.1.15+dfsg-1build1_arm64.deb ... 163s Unpacking libcootapi1.1 (1.1.15+dfsg-1build1) ... 164s Selecting previously unselected package libogg0:arm64. 164s Preparing to unpack .../140-libogg0_1.3.5-3build1_arm64.deb ... 164s Unpacking libogg0:arm64 (1.3.5-3build1) ... 164s Selecting previously unselected package libvorbis0a:arm64. 164s Preparing to unpack .../141-libvorbis0a_1.3.7-3build1_arm64.deb ... 164s Unpacking libvorbis0a:arm64 (1.3.7-3build1) ... 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... 168s Setting up libucx0:arm64 (1.19.0+ds-1) ... 168s Setting up libopenmpi40:arm64 (5.0.8-8ubuntu1) ... 168s Setting up sfftw2 (2.1.5-7build1) ... 168s Setting up libclipper2:arm64 (2.1.20201109-2build1) ... 169s Setting up libcootapi1.1 (1.1.15+dfsg-1build1) ... 169s Setting up libcootapi-dev (1.1.15+dfsg-1build1) ... 169s Processing triggers for libc-bin (2.42-0ubuntu3) ... 169s Processing triggers for man-db (2.13.1-1) ... 170s Processing triggers for libglib2.0-0t64:arm64 (2.86.0-2) ... 170s Setting up libgtk-4-1:arm64 (4.20.1+ds-2) ... 170s Setting up gir1.2-gtk-4.0:arm64 (4.20.1+ds-2) ... 170s Setting up coot (1.1.15+dfsg-1build1) ... 171s Processing triggers for libc-bin (2.42-0ubuntu3) ... 172s autopkgtest [15:30:15]: test command1: coot --self-test 172s autopkgtest [15:30:15]: test command1: [----------------------- 173s INFO:: Running internal self tests 177s INFO:: Test Clipper core : OK 177s INFO:: Test Clipper contrib: OK 177s run_internal_tests() --------- we have 8 internal test functionns 177s Entering test: kevin's torsion test 177s PASS: kevin's torsion test 177s Entering test: test_alt_conf_rotamers 177s DEBUG:: get_atom_selection() with file "/usr/share/coot/data/tutorial-modern.pdb" use_gemmi: 0 177s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 177s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 177s chis.size() 2 (should be 2) 177s DEBUG:: i_rot 0 chi: alt-conf: A chi-1: 65.911 177s DEBUG:: i_rot 1 chi: alt-conf: B chi-1: -144.68 177s For residue 80 chis size 1 177s residue 80 chis: -56.8781 -80.8484 177s PASS: test_alt_conf_rotamers 177s Entering test: test_fragmemt_atom_selection 177s DEBUG:: get_atom_selection() with file "/usr/share/coot/data/tutorial-modern.pdb" use_gemmi: 0 177s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 177s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 177s ----------------- create_mmdbmanager_from_inverted_atom_selection() 177s n_initial: 1465 n_1: 1401 n_2: 64 177s PASS: test_fragmemt_atom_selection 177s Entering test: test_add_atom 177s DEBUG:: get_atom_selection() with file "/usr/share/coot/data/tutorial-modern.pdb" use_gemmi: 0 177s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 177s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 177s PASS: test_add_atom 177s Entering test: test segid exchange 177s DEBUG:: get_atom_selection() with file "/usr/share/coot/data/tutorial-modern.pdb" use_gemmi: 0 177s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 177s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 177s Test with a rogue segid 177s INFO:: No consistent segids for residue 1 177s PASS: test segid exchange 177s Entering test: test peak search non-close 177s mtz_file_name /usr/share/coot/data/rnasa-1.8-all_refmac1.mtz 178s FFT Reso...0.444444 178s Sampling rate...1.5 178s Grid...Nuvw = ( 132, 160, 80) 178s Cell... Cell (64.897,78.323,38.792, 90, 90, 90) 178s Spacegroup...P 21 21 21 178s There are 2260 peaks and 0 problem peaks 178s PASS: test peak search non-close 178s Entering test: test symop card 178s 1 0 0 178s 0 1 0 178s 0 0 1 178s translations: -1 0 0 178s PASS: test symop card 178s Entering test: SSM sequence alignment output 178s 178s -- 178s Moving: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNR--ESVLPTQSYGYYHEYTVITP--GARTRG 178s Target: ---SGTVCLSALPPEATDTLNLIASDGPFPYSQDG 178s 178s Moving: TRRI.ICGEATQEDY..YTGDHYATFSLIDQTC 178s 178s -- 178s Moving: D 178s Target: --SGTVCLSALPPEATDTLNLIASDGPFPYSQDG 178s 178s -- 178s Moving: DVSGTVCLSALPPEATDTLNIASDGPFPYSQDGVVFQNR--ESVLPQSYG 178s Target: --SGTVCLSALPPEATDTLNIASDGPFPYSQDXXxxxxxxxxxxxxxxxG 178s 178s -- 178s PASS: SSM sequence alignment output 178s autopkgtest [15:30:21]: test command1: -----------------------] 178s autopkgtest [15:30:21]: test command1: - - - - - - - - - - results - - - - - - - - - - 178s command1 PASS 179s autopkgtest [15:30:22]: test command2: preparing testbed 179s Reading package lists... 179s Building dependency tree... 179s Reading state information... 179s Solving dependencies... 180s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 181s autopkgtest [15:30:24]: test command2: pyrogen --help 181s autopkgtest [15:30:24]: test command2: [----------------------- 182s Usage: pyrogen [options] file-or-SMILES 182s if file-or-SMILES has extension ".smi" or ".smiles" then it is treated as a file 182s 182s Options: 182s -h, --help show this help message and exit 182s -c FILE, --mmcif=FILE 182s Make restraints from input mmcif FILE 182s -m FILE, --mol=FILE Make restraints from input sdf/mol FILE 182s -r COMP_ID, --residue-type=COMP_ID 182s Create restraints for this type. Default is LIG 182s -4, --quartet-planes Use 4-atom plane restraints, 182s forces --quartet-hydrogens 182s -H, --quartet-hydrogens 182s Use 4-atom hydrogen plane restraints 182s -b, --no-shift-hydrogen-atoms 182s Stop addition or deletion of Hydrogen atoms for 182s formally-charged atoms 182s -n, --no-mogul Don't run CSD Mogul to update bond and angle 182s restraints 182s -N COMPOUND_NAME, --name=COMPOUND_NAME 182s Compound name 182s -S, --smiles Write the SMILES for the input molecule 182s -t, --tautomers Show SMILES for tautomers, don't generate restraints 182s -T MOGUL_DIR, --tmp-directory=MOGUL_DIR 182s Directory into which the tmp files (e.g. for mogul) 182s are written 182s -d OUTPUT_DIR, --directory=OUTPUT_DIR 182s Directory into which the output files (e.g. mmCIF and 182s PDB) are written 182s -o OUTPUT_POSTFIX, --output-postfix=OUTPUT_POSTFIX 182s string to add to output file names, default is 182s "pyrogen" 182s -p, --picture Additionally output a chemical diagram PNG 182s -P, --preserve-input-coordinates 182s Preserve the inputput coordinates (if possible) 182s -v, --version Print version information 182s -a, --no-match-vs-reference-dictionaries 182s Don't match atom names vs. dictionary molecules 182s (default False) 182s -R DICT_FILES_FOR_NAMES_MATCH, --reference-dictionary-files=DICT_FILES_FOR_NAMES_MATCH 182s Try to match the atom names of the output molecule to 182s this dictionary in these files (comma-separated list) 182s -C COMP_ID_LIST_FOR_NAMES_MATCH, --reference-dictionary-comp-ids=COMP_ID_LIST_FOR_NAMES_MATCH 182s Try to match the atom names of the output molecule to 182s these comp-ids (comma-separated list) 182s -w, --wwPDB Fetch the wwPDB ligand definition and use that 182s -f FETCH (Just) fetch from the PDBe the CCD entry for the given 182s compound-id 182s -q, --quiet print less messages 182s autopkgtest [15:30:25]: test command2: -----------------------] 183s command2 PASS 183s autopkgtest [15:30:26]: test command2: - - - - - - - - - - results - - - - - - - - - - 183s autopkgtest [15:30:26]: @@@@@@@@@@@@@@@@@@@@ summary 183s command1 PASS 183s command2 PASS