0s autopkgtest [07:29:57]: starting date and time: 2025-12-04 07:29:57+0000 0s autopkgtest [07:29:57]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [07:29:57]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.dxr9386v/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade openstructure --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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-2.secgroup --name adt-resolute-amd64-openstructure-20251204-072956-juju-7f2275-prod-proposed-migration-environment-2-5b393080-1225-4b81-8a6a-ccca5d4fecf7 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 5s Creating nova instance adt-resolute-amd64-openstructure-20251204-072956-juju-7f2275-prod-proposed-migration-environment-2-5b393080-1225-4b81-8a6a-ccca5d4fecf7 from image adt/ubuntu-resolute-amd64-server-20251204.img (UUID da78d93c-25db-4f64-b2b3-5da4bc39127b)... 80s autopkgtest [07:31:17]: testbed dpkg architecture: amd64 80s autopkgtest [07:31:17]: testbed apt version: 3.1.12 80s autopkgtest [07:31:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup 80s autopkgtest [07:31:17]: testbed release detected to be: None 82s autopkgtest [07:31:19]: updating testbed package index (apt update) 90s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 90s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 90s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 90s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 90s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [152 kB] 90s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [928 kB] 91s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.1 kB] 91s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [162 kB] 91s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [218 kB] 91s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6652 B] 91s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B] 91s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [752 kB] 91s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [344 kB] 91s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [24.1 kB] 91s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [9636 B] 91s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4040 B] 91s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [748 B] 92s Fetched 2749 kB in 6s (430 kB/s) 93s Reading package lists... 94s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 94s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 95s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 95s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 96s Reading package lists... 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 97s Calculating upgrade... 97s The following packages will be upgraded: 97s libpython3-stdlib python3 python3-gdbm python3-minimal 98s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 98s Need to get 72.9 kB of archives. 98s After this operation, 2048 B of additional disk space will be used. 98s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.9-2 [28.1 kB] 98s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.9-2 [23.0 kB] 98s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.9-2 [10.8 kB] 98s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.13.9-2 [11.0 kB] 99s dpkg-preconfigure: unable to re-open stdin: No such file or directory 99s Fetched 72.9 kB in 2s (46.2 kB/s) 99s (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 ... 83537 files and directories currently installed.) 99s Preparing to unpack .../python3-minimal_3.13.9-2_amd64.deb ... 99s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 99s Setting up python3-minimal (3.13.9-2) ... 99s (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 ... 83537 files and directories currently installed.) 99s Preparing to unpack .../python3_3.13.9-2_amd64.deb ... 99s running python pre-rtupdate hooks for python3.13... 99s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 99s Preparing to unpack .../libpython3-stdlib_3.13.9-2_amd64.deb ... 99s Unpacking libpython3-stdlib:amd64 (3.13.9-2) over (3.13.7-1) ... 99s Preparing to unpack .../python3-gdbm_3.13.9-2_amd64.deb ... 100s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 100s Setting up python3-gdbm (3.13.9-2) ... 100s Setting up libpython3-stdlib:amd64 (3.13.9-2) ... 100s Setting up python3 (3.13.9-2) ... 100s running python rtupdate hooks for python3.13... 100s running python post-rtupdate hooks for python3.13... 100s Processing triggers for man-db (2.13.1-1) ... 101s autopkgtest [07:31:38]: upgrading testbed (apt dist-upgrade and autopurge) 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 102s Calculating upgrade... 102s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 104s Solving dependencies... 104s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s autopkgtest [07:31:49]: testbed running kernel: Linux 6.17.0-6-generic #6-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 7 13:34:17 UTC 2025 113s autopkgtest [07:31:50]: @@@@@@@@@@@@@@@@@@@@ apt-source openstructure 171s Get:1 http://ftpmaster.internal/ubuntu resolute/universe openstructure 2.9.3-2build1 (dsc) [4845 B] 171s Get:2 http://ftpmaster.internal/ubuntu resolute/universe openstructure 2.9.3-2build1 (tar) [27.0 MB] 171s Get:3 http://ftpmaster.internal/ubuntu resolute/universe openstructure 2.9.3-2build1 (diff) [92.3 MB] 171s gpgv: Signature made Thu May 8 22:34:39 2025 UTC 171s gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D 171s gpgv: Can't check signature: No public key 171s dpkg-source: warning: cannot verify inline signature for ./openstructure_2.9.3-2build1.dsc: no acceptable signature found 175s autopkgtest [07:32:52]: testing package openstructure version 2.9.3-2build1 208s autopkgtest [07:33:25]: build not needed 227s autopkgtest [07:33:44]: test python: preparing testbed 228s Reading package lists... 228s Building dependency tree... 228s Reading state information... 228s Solving dependencies... 229s The following NEW packages will be installed: 229s clustalw dssp fontconfig fontconfig-config fonts-dejavu-core 229s fonts-dejavu-mono fonts-lyx libavahi-client3 libavahi-common-data 229s libavahi-common3 libblas3 libboost-filesystem1.83.0 libboost-iostreams1.83.0 229s libboost-program-options1.83.0 libboost-python1.83.0 libboost-thread1.83.0 229s libcifpp-data libcifpp9 libcups2t64 libdeflate0 libdouble-conversion3 229s libdrm-intel1 libegl-mesa0 libegl1 libfftw3-single3 libfontconfig1 libgbm1 229s libgfortran5 libgl1 libgl1-mesa-dri libglu1-mesa libglvnd0 libglx-mesa0 229s libglx0 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libimagequant0 229s libinput-bin libinput10 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 229s liblcms2-2 liblerc4 libmbedcrypto16 libmbedtls21 libmbedx509-7 libmd4c0 229s libmtdev1t64 libncbi-vdb3 libopengl0 libopenjp2-7 libopenmm8.1 229s libost-base-dev libost-base2.9 libost-bindings-dev libost-bindings2.9 229s libost-conop-dev libost-conop2.9 libost-db-dev libost-db2.9 libost-geom-dev 229s libost-geom2.9 libost-gfx-dev libost-gfx2.9 libost-gui-dev libost-gui2.9 229s libost-img-alg-dev libost-img-alg2.9 libost-img-dev libost-img2.9 229s libost-info-dev libost-info2.9 libost-io-dev libost-io2.9 libost-mol-alg-dev 229s libost-mol-alg2.9 libost-mol-dev libost-mol-mm-dev libost-mol-mm2.9 229s libost-mol2.9 libost-seq-alg-dev libost-seq-alg2.9 libost-seq-dev 229s libost-seq2.9 libparasail8 libpciaccess0 libpcre2-16-0 libqhull-r8.0 229s libqt5core5t64 libqt5dbus5t64 libqt5designer5 libqt5gui5t64 libqt5help5 229s libqt5network5t64 libqt5printsupport5t64 libqt5sql5t64 libqt5test5t64 229s libqt5widgets5t64 libqt5xml5t64 libraqm0 libsharpyuv0 libsm6 libtcl8.6 229s libtiff6 libtk8.6 libvulkan1 libwacom-common libwacom9 libwayland-client0 229s libwebp7 libwebpdemux2 libwebpmux3 libx11-xcb1 libxcb-dri3-0 libxcb-glx0 229s libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present0 libxcb-randr0 229s libxcb-render-util0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 229s libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 229s libxft2 libxkbcommon-x11-0 libxrender1 libxshmfence1 libxslt1.1 libxss1 229s libxxf86vm1 libzopfli1 mesa-libgallium ncbi-blast+ ncbi-data ncbi-vdb-data 229s openstructure python-matplotlib-data python3-brotli python3-contourpy 229s python3-cycler python3-fonttools python3-fs python3-kiwisolver python3-lxml 229s python3-lz4 python3-matplotlib python3-mpmath python3-munkres python3-numpy 229s python3-numpy-dev python3-ost python3-pil python3-pil.imagetk 229s python3-platformdirs python3-pyqt5 python3-pyqt5.sip python3-sympy 229s python3-tk python3-ufolib2 python3-unicodedata2 python3-zopfli python3.13-tk 229s python3.14-tk unicode-data voronota x11-common 229s 0 upgraded, 177 newly installed, 0 to remove and 0 not upgraded. 229s Need to get 218 MB of archives. 229s After this operation, 632 MB of additional disk space will be used. 229s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 230s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7 [259 kB] 230s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-9ubuntu1 [939 kB] 231s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7 [2739 kB] 232s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 233s Get:6 http://ftpmaster.internal/ubuntu resolute/universe amd64 clustalw amd64 2.1+lgpl-7build1 [254 kB] 233s Get:7 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcifpp-data all 9.0.5-2 [483 kB] 234s Get:8 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcifpp9 amd64 9.0.5-2 [1089 kB] 234s Get:9 http://ftpmaster.internal/ubuntu resolute/universe amd64 dssp amd64 4.5.7-1 [645 kB] 234s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 234s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 235s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB] 235s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB] 235s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.15.0-2.3ubuntu1 [180 kB] 235s Get:15 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-lyx all 2.4.4-2 [171 kB] 235s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libavahi-common-data amd64 0.8-16ubuntu3 [31.1 kB] 235s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libavahi-common3 amd64 0.8-16ubuntu3 [25.3 kB] 235s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libavahi-client3 amd64 0.8-16ubuntu3 [28.8 kB] 235s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-5ubuntu2 [289 kB] 235s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-5ubuntu2 [261 kB] 235s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost-program-options1.83.0 amd64 1.83.0-5ubuntu2 [324 kB] 235s Get:22 http://ftpmaster.internal/ubuntu resolute/universe amd64 libboost-python1.83.0 amd64 1.83.0-5ubuntu2 [357 kB] 235s Get:23 http://ftpmaster.internal/ubuntu resolute/universe amd64 libboost-thread1.83.0 amd64 1.83.0-5ubuntu2 [278 kB] 235s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libcups2t64 amd64 2.4.12-0ubuntu3 [272 kB] 235s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 235s Get:26 http://ftpmaster.internal/ubuntu resolute/universe amd64 libdouble-conversion3 amd64 3.3.1-2 [41.4 kB] 235s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libpciaccess0 amd64 0.18.1-1ubuntu2 [19.0 kB] 235s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-intel1 amd64 2.4.127-1ubuntu1 [69.2 kB] 235s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libx11-xcb1 amd64 2:1.8.12-1build1 [8044 B] 235s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-dri3-0 amd64 1.17.0-2build1 [8036 B] 235s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-present0 amd64 1.17.0-2build1 [6446 B] 235s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-randr0 amd64 1.17.0-2build1 [19.7 kB] 235s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-sync1 amd64 1.17.0-2build1 [10.1 kB] 235s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-xfixes0 amd64 1.17.0-2build1 [11.1 kB] 235s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libxshmfence1 amd64 1.3.3-1 [5262 B] 235s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 mesa-libgallium amd64 25.2.7-1ubuntu1 [11.1 MB] 238s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libgbm1 amd64 25.2.7-1ubuntu1 [34.0 kB] 238s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libwayland-client0 amd64 1.24.0-2 [28.5 kB] 238s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B] 238s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libegl-mesa0 amd64 25.2.7-1ubuntu1 [117 kB] 238s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-9ubuntu1 [151 kB] 238s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libfftw3-single3 amd64 3.3.10-2fakesync1build2 [894 kB] 238s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libvulkan1 amd64 1.4.328.1-1 [156 kB] 239s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libgl1-mesa-dri amd64 25.2.7-1ubuntu1 [36.9 kB] 239s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-glx0 amd64 1.17.0-2build1 [27.6 kB] 239s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libxxf86vm1 amd64 1:1.1.4-2 [10.6 kB] 239s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libglx-mesa0 amd64 25.2.7-1ubuntu1 [110 kB] 239s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 239s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.1.0-1 [535 kB] 239s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 239s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 239s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 239s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libwacom-common all 2.16.1-1 [113 kB] 239s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libwacom9 amd64 2.16.1-1 [28.3 kB] 239s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libinput-bin amd64 1.30.0-1 [24.6 kB] 239s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libmtdev1t64 amd64 1.1.7-1 [16.3 kB] 239s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libinput10 amd64 1.30.0-1 [160 kB] 239s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 239s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 239s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.17-1 [170 kB] 239s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 239s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmbedcrypto16 amd64 3.6.2-3ubuntu1 [276 kB] 239s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmbedx509-7 amd64 3.6.2-3ubuntu1 [37.1 kB] 239s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmbedtls21 amd64 3.6.2-3ubuntu1 [126 kB] 239s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmd4c0 amd64 0.5.2-2 [50.1 kB] 239s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [81.3 kB] 239s Get:67 http://ftpmaster.internal/ubuntu resolute/universe amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1376 kB] 239s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 libopenmm8.1 amd64 8.1.2+dfsg-12 [1045 kB] 240s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-base2.9 amd64 2.9.3-2build1 [25.4 kB] 240s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-base-dev amd64 2.9.3-2build1 [17.9 kB] 240s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-geom2.9 amd64 2.9.3-2build1 [57.7 kB] 240s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-mol2.9 amd64 2.9.3-2build1 [328 kB] 240s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-16-0 amd64 10.46-1 [243 kB] 240s Get:74 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqt5core5t64 amd64 5.15.17+dfsg-1ubuntu1 [2036 kB] 240s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqt5xml5t64 amd64 5.15.17+dfsg-1ubuntu1 [123 kB] 240s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-info2.9 amd64 2.9.3-2build1 [146 kB] 240s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-seq2.9 amd64 2.9.3-2build1 [63.9 kB] 240s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-bindings2.9 amd64 2.9.3-2build1 [199 kB] 240s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-bindings-dev amd64 2.9.3-2build1 [5218 B] 240s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-conop2.9 amd64 2.9.3-2build1 [176 kB] 240s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-conop-dev amd64 2.9.3-2build1 [12.2 kB] 240s Get:82 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-db2.9 amd64 2.9.3-2build1 [34.5 kB] 240s Get:83 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-db-dev amd64 2.9.3-2build1 [7608 B] 240s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-geom-dev amd64 2.9.3-2build1 [19.2 kB] 240s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 libglvnd0 amd64 1.7.0-1build2 [65.1 kB] 241s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 libopengl0 amd64 1.7.0-1build2 [32.6 kB] 241s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 libglu1-mesa amd64 9.0.2-1.1build1 [152 kB] 241s Get:88 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-img2.9 amd64 2.9.3-2build1 [135 kB] 241s Get:89 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-img-alg2.9 amd64 2.9.3-2build1 [146 kB] 241s Get:90 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-gfx2.9 amd64 2.9.3-2build1 [404 kB] 241s Get:91 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-gfx-dev amd64 2.9.3-2build1 [56.4 kB] 241s Get:92 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-mol-alg2.9 amd64 2.9.3-2build1 [324 kB] 241s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 241s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 241s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 241s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 241s Get:97 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-io2.9 amd64 2.9.3-2build1 [756 kB] 241s Get:98 http://ftpmaster.internal/ubuntu resolute/universe amd64 libparasail8 amd64 2.6.2+dfsg-2ubuntu2 [1977 kB] 242s Get:99 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-seq-alg2.9 amd64 2.9.3-2build1 [273 kB] 242s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 libegl1 amd64 1.7.0-1build2 [31.2 kB] 242s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 libglx0 amd64 1.7.0-1build2 [40.3 kB] 242s Get:102 http://ftpmaster.internal/ubuntu resolute/main amd64 libgl1 amd64 1.7.0-1build2 [101 kB] 242s Get:103 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqt5dbus5t64 amd64 5.15.17+dfsg-1ubuntu1 [221 kB] 243s Get:104 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqt5network5t64 amd64 5.15.17+dfsg-1ubuntu1 [723 kB] 243s Get:105 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1 [16.4 kB] 243s Get:106 http://ftpmaster.internal/ubuntu resolute/universe amd64 libxcb-icccm4 amd64 0.4.2-1 [11.1 kB] 243s Get:107 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-util1 amd64 0.4.1-1 [11.2 kB] 243s Get:108 http://ftpmaster.internal/ubuntu resolute/universe amd64 libxcb-image0 amd64 0.4.0-2build1 [10.8 kB] 243s Get:109 http://ftpmaster.internal/ubuntu resolute/universe amd64 libxcb-keysyms1 amd64 0.4.1-1 [8738 B] 243s Get:110 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB] 243s Get:111 http://ftpmaster.internal/ubuntu resolute/universe amd64 libxcb-render-util0 amd64 0.3.10-1 [10.8 kB] 243s Get:112 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shape0 amd64 1.17.0-2build1 [6544 B] 243s Get:113 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-xinerama0 amd64 1.17.0-2build1 [5752 B] 243s Get:114 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-xinput0 amd64 1.17.0-2build1 [36.7 kB] 243s Get:115 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-xkb1 amd64 1.17.0-2build1 [35.3 kB] 243s Get:116 http://ftpmaster.internal/ubuntu resolute/main amd64 libxkbcommon-x11-0 amd64 1.12.3-1 [15.0 kB] 243s Get:117 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 243s Get:118 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqt5gui5t64 amd64 5.15.17+dfsg-1ubuntu1 [3790 kB] 244s Get:119 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqt5widgets5t64 amd64 5.15.17+dfsg-1ubuntu1 [2559 kB] 245s Get:120 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-gui2.9 amd64 2.9.3-2build1 [454 kB] 245s Get:121 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-gui-dev amd64 2.9.3-2build1 [43.9 kB] 245s Get:122 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-img-alg-dev amd64 2.9.3-2build1 [19.7 kB] 245s Get:123 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-img-dev amd64 2.9.3-2build1 [33.9 kB] 245s Get:124 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-info-dev amd64 2.9.3-2build1 [10.5 kB] 245s Get:125 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-io-dev amd64 2.9.3-2build1 [43.2 kB] 245s Get:126 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-mol-alg-dev amd64 2.9.3-2build1 [21.6 kB] 245s Get:127 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-mol-dev amd64 2.9.3-2build1 [48.7 kB] 245s Get:128 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-mol-mm2.9 amd64 2.9.3-2build1 [254 kB] 245s Get:129 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-mol-mm-dev amd64 2.9.3-2build1 [18.6 kB] 245s Get:130 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-seq-alg-dev amd64 2.9.3-2build1 [182 kB] 245s Get:131 http://ftpmaster.internal/ubuntu resolute/universe amd64 libost-seq-dev amd64 2.9.3-2build1 [14.8 kB] 245s Get:132 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqhull-r8.0 amd64 2020.2-7 [197 kB] 245s Get:133 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqt5designer5 amd64 5.15.17-4 [2836 kB] 246s Get:134 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqt5sql5t64 amd64 5.15.17+dfsg-1ubuntu1 [121 kB] 246s Get:135 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqt5help5 amd64 5.15.17-4 [163 kB] 246s Get:136 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqt5printsupport5t64 amd64 5.15.17+dfsg-1ubuntu1 [207 kB] 246s Get:137 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqt5test5t64 amd64 5.15.17+dfsg-1ubuntu1 [148 kB] 246s Get:138 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1 [15.4 kB] 246s Get:139 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1036 kB] 246s Get:140 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 246s Get:141 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 246s Get:142 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 246s Get:143 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 246s Get:144 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 246s Get:145 http://ftpmaster.internal/ubuntu resolute/main amd64 libxslt1.1 amd64 1.1.43-0.3 [172 kB] 246s Get:146 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzopfli1 amd64 1.0.3-3 [141 kB] 246s Get:147 http://ftpmaster.internal/ubuntu resolute/universe amd64 ncbi-data all 6.1.20170106+dfsg2-6 [3969 kB] 247s Get:148 http://ftpmaster.internal/ubuntu resolute/universe amd64 ncbi-blast+ amd64 2.16.0+ds-7 [16.0 MB] 247s Get:149 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 248s Get:150 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [188 kB] 248s Get:151 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 12.0.0-1ubuntu1 [494 kB] 248s Get:152 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-tk amd64 3.13.9-1 [108 kB] 248s Get:153 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-tk amd64 3.14.0-4 [108 kB] 248s Get:154 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-tk amd64 3.13.9-2 [11.1 kB] 248s Get:155 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pil.imagetk amd64 12.0.0-1ubuntu1 [9700 B] 248s Get:156 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-contourpy amd64 1.3.3-1 [255 kB] 248s Get:157 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cycler all 0.12.1-2 [9850 B] 248s Get:158 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-brotli amd64 1.1.0-2build6 [340 kB] 248s Get:159 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-platformdirs all 4.4.0-1 [16.9 kB] 248s Get:160 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fs all 2.4.16-9ubuntu1 [91.5 kB] 248s Get:161 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-lxml amd64 6.0.2-1 [2333 kB] 248s Get:162 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-lz4 amd64 4.4.4+dfsg-3 [27.5 kB] 248s Get:163 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-munkres all 1.1.4-3 [9236 B] 248s Get:164 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mpmath all 1.3.0-2 [423 kB] 248s Get:165 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sympy all 1.14.0-2 [4306 kB] 248s Get:166 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 248s Get:167 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-unicodedata2 amd64 16.0.0+ds-1build1 [400 kB] 248s Get:168 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-zopfli amd64 0.4.0-1 [11.1 kB] 248s Get:169 http://ftpmaster.internal/ubuntu resolute/universe amd64 unicode-data all 16.0.0-1 [9513 kB] 248s Get:170 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fonttools amd64 4.57.0-3 [1705 kB] 248s Get:171 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-kiwisolver amd64 1.4.10~rc0-1 [65.5 kB] 248s Get:172 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-matplotlib amd64 3.10.7+dfsg1-1 [17.2 MB] 249s Get:173 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pyqt5.sip amd64 12.17.1-1 [81.1 kB] 249s Get:174 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pyqt5 amd64 5.15.11+dfsg-3 [2737 kB] 249s Get:175 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ost amd64 2.9.3-2build1 [3666 kB] 249s Get:176 http://ftpmaster.internal/ubuntu resolute/universe amd64 openstructure amd64 2.9.3-2build1 [92.4 MB] 253s Get:177 http://ftpmaster.internal/ubuntu resolute/universe amd64 voronota amd64 1.29.4415+ds-1 [2607 kB] 254s Preconfiguring packages ... 254s Fetched 218 MB in 24s (9002 kB/s) 254s Selecting previously unselected package python3-numpy-dev:amd64. 254s (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 ... 83537 files and directories currently installed.) 254s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 254s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 254s Selecting previously unselected package libblas3:amd64. 254s Preparing to unpack .../001-libblas3_3.12.1-7_amd64.deb ... 254s Unpacking libblas3:amd64 (3.12.1-7) ... 254s Selecting previously unselected package libgfortran5:amd64. 254s Preparing to unpack .../002-libgfortran5_15.2.0-9ubuntu1_amd64.deb ... 254s Unpacking libgfortran5:amd64 (15.2.0-9ubuntu1) ... 254s Selecting previously unselected package liblapack3:amd64. 254s Preparing to unpack .../003-liblapack3_3.12.1-7_amd64.deb ... 254s Unpacking liblapack3:amd64 (3.12.1-7) ... 254s Selecting previously unselected package python3-numpy. 254s Preparing to unpack .../004-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 254s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 254s Selecting previously unselected package clustalw. 254s Preparing to unpack .../005-clustalw_2.1+lgpl-7build1_amd64.deb ... 254s Unpacking clustalw (2.1+lgpl-7build1) ... 254s Selecting previously unselected package libcifpp-data. 254s Preparing to unpack .../006-libcifpp-data_9.0.5-2_all.deb ... 254s Unpacking libcifpp-data (9.0.5-2) ... 254s Selecting previously unselected package libcifpp9:amd64. 254s Preparing to unpack .../007-libcifpp9_9.0.5-2_amd64.deb ... 254s Unpacking libcifpp9:amd64 (9.0.5-2) ... 255s Selecting previously unselected package dssp. 255s Preparing to unpack .../008-dssp_4.5.7-1_amd64.deb ... 255s Unpacking dssp (4.5.7-1) ... 255s Selecting previously unselected package fonts-dejavu-mono. 255s Preparing to unpack .../009-fonts-dejavu-mono_2.37-8_all.deb ... 255s Unpacking fonts-dejavu-mono (2.37-8) ... 255s Selecting previously unselected package fonts-dejavu-core. 255s Preparing to unpack .../010-fonts-dejavu-core_2.37-8_all.deb ... 255s Unpacking fonts-dejavu-core (2.37-8) ... 255s Selecting previously unselected package fontconfig-config. 255s Preparing to unpack .../011-fontconfig-config_2.15.0-2.3ubuntu1_amd64.deb ... 255s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 255s Selecting previously unselected package libfontconfig1:amd64. 255s Preparing to unpack .../012-libfontconfig1_2.15.0-2.3ubuntu1_amd64.deb ... 255s Unpacking libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 255s Selecting previously unselected package fontconfig. 255s Preparing to unpack .../013-fontconfig_2.15.0-2.3ubuntu1_amd64.deb ... 255s Unpacking fontconfig (2.15.0-2.3ubuntu1) ... 255s Selecting previously unselected package fonts-lyx. 255s Preparing to unpack .../014-fonts-lyx_2.4.4-2_all.deb ... 255s Unpacking fonts-lyx (2.4.4-2) ... 255s Selecting previously unselected package libavahi-common-data:amd64. 255s Preparing to unpack .../015-libavahi-common-data_0.8-16ubuntu3_amd64.deb ... 255s Unpacking libavahi-common-data:amd64 (0.8-16ubuntu3) ... 255s Selecting previously unselected package libavahi-common3:amd64. 255s Preparing to unpack .../016-libavahi-common3_0.8-16ubuntu3_amd64.deb ... 255s Unpacking libavahi-common3:amd64 (0.8-16ubuntu3) ... 255s Selecting previously unselected package libavahi-client3:amd64. 255s Preparing to unpack .../017-libavahi-client3_0.8-16ubuntu3_amd64.deb ... 255s Unpacking libavahi-client3:amd64 (0.8-16ubuntu3) ... 255s Selecting previously unselected package libboost-filesystem1.83.0:amd64. 255s Preparing to unpack .../018-libboost-filesystem1.83.0_1.83.0-5ubuntu2_amd64.deb ... 255s Unpacking libboost-filesystem1.83.0:amd64 (1.83.0-5ubuntu2) ... 255s Selecting previously unselected package libboost-iostreams1.83.0:amd64. 255s Preparing to unpack .../019-libboost-iostreams1.83.0_1.83.0-5ubuntu2_amd64.deb ... 255s Unpacking libboost-iostreams1.83.0:amd64 (1.83.0-5ubuntu2) ... 255s Selecting previously unselected package libboost-program-options1.83.0:amd64. 255s Preparing to unpack .../020-libboost-program-options1.83.0_1.83.0-5ubuntu2_amd64.deb ... 255s Unpacking libboost-program-options1.83.0:amd64 (1.83.0-5ubuntu2) ... 255s Selecting previously unselected package libboost-python1.83.0. 255s Preparing to unpack .../021-libboost-python1.83.0_1.83.0-5ubuntu2_amd64.deb ... 255s Unpacking libboost-python1.83.0 (1.83.0-5ubuntu2) ... 255s Selecting previously unselected package libboost-thread1.83.0:amd64. 255s Preparing to unpack .../022-libboost-thread1.83.0_1.83.0-5ubuntu2_amd64.deb ... 255s Unpacking libboost-thread1.83.0:amd64 (1.83.0-5ubuntu2) ... 255s Selecting previously unselected package libcups2t64:amd64. 255s Preparing to unpack .../023-libcups2t64_2.4.12-0ubuntu3_amd64.deb ... 255s Unpacking libcups2t64:amd64 (2.4.12-0ubuntu3) ... 255s Selecting previously unselected package libdeflate0:amd64. 255s Preparing to unpack .../024-libdeflate0_1.23-2_amd64.deb ... 255s Unpacking libdeflate0:amd64 (1.23-2) ... 255s Selecting previously unselected package libdouble-conversion3:amd64. 255s Preparing to unpack .../025-libdouble-conversion3_3.3.1-2_amd64.deb ... 255s Unpacking libdouble-conversion3:amd64 (3.3.1-2) ... 255s Selecting previously unselected package libpciaccess0:amd64. 255s Preparing to unpack .../026-libpciaccess0_0.18.1-1ubuntu2_amd64.deb ... 255s Unpacking libpciaccess0:amd64 (0.18.1-1ubuntu2) ... 255s Selecting previously unselected package libdrm-intel1:amd64. 255s Preparing to unpack .../027-libdrm-intel1_2.4.127-1ubuntu1_amd64.deb ... 255s Unpacking libdrm-intel1:amd64 (2.4.127-1ubuntu1) ... 256s Selecting previously unselected package libx11-xcb1:amd64. 256s Preparing to unpack .../028-libx11-xcb1_2%3a1.8.12-1build1_amd64.deb ... 256s Unpacking libx11-xcb1:amd64 (2:1.8.12-1build1) ... 256s Selecting previously unselected package libxcb-dri3-0:amd64. 256s Preparing to unpack .../029-libxcb-dri3-0_1.17.0-2build1_amd64.deb ... 256s Unpacking libxcb-dri3-0:amd64 (1.17.0-2build1) ... 256s Selecting previously unselected package libxcb-present0:amd64. 256s Preparing to unpack .../030-libxcb-present0_1.17.0-2build1_amd64.deb ... 256s Unpacking libxcb-present0:amd64 (1.17.0-2build1) ... 256s Selecting previously unselected package libxcb-randr0:amd64. 256s Preparing to unpack .../031-libxcb-randr0_1.17.0-2build1_amd64.deb ... 256s Unpacking libxcb-randr0:amd64 (1.17.0-2build1) ... 256s Selecting previously unselected package libxcb-sync1:amd64. 256s Preparing to unpack .../032-libxcb-sync1_1.17.0-2build1_amd64.deb ... 256s Unpacking libxcb-sync1:amd64 (1.17.0-2build1) ... 256s Selecting previously unselected package libxcb-xfixes0:amd64. 256s Preparing to unpack .../033-libxcb-xfixes0_1.17.0-2build1_amd64.deb ... 256s Unpacking libxcb-xfixes0:amd64 (1.17.0-2build1) ... 256s Selecting previously unselected package libxshmfence1:amd64. 256s Preparing to unpack .../034-libxshmfence1_1.3.3-1_amd64.deb ... 256s Unpacking libxshmfence1:amd64 (1.3.3-1) ... 256s Selecting previously unselected package mesa-libgallium:amd64. 256s Preparing to unpack .../035-mesa-libgallium_25.2.7-1ubuntu1_amd64.deb ... 256s Unpacking mesa-libgallium:amd64 (25.2.7-1ubuntu1) ... 256s Selecting previously unselected package libgbm1:amd64. 256s Preparing to unpack .../036-libgbm1_25.2.7-1ubuntu1_amd64.deb ... 256s Unpacking libgbm1:amd64 (25.2.7-1ubuntu1) ... 256s Selecting previously unselected package libwayland-client0:amd64. 256s Preparing to unpack .../037-libwayland-client0_1.24.0-2_amd64.deb ... 256s Unpacking libwayland-client0:amd64 (1.24.0-2) ... 256s Selecting previously unselected package libxcb-shm0:amd64. 256s Preparing to unpack .../038-libxcb-shm0_1.17.0-2build1_amd64.deb ... 256s Unpacking libxcb-shm0:amd64 (1.17.0-2build1) ... 256s Selecting previously unselected package libegl-mesa0:amd64. 256s Preparing to unpack .../039-libegl-mesa0_25.2.7-1ubuntu1_amd64.deb ... 256s Unpacking libegl-mesa0:amd64 (25.2.7-1ubuntu1) ... 256s Selecting previously unselected package libgomp1:amd64. 256s Preparing to unpack .../040-libgomp1_15.2.0-9ubuntu1_amd64.deb ... 256s Unpacking libgomp1:amd64 (15.2.0-9ubuntu1) ... 256s Selecting previously unselected package libfftw3-single3:amd64. 256s Preparing to unpack .../041-libfftw3-single3_3.3.10-2fakesync1build2_amd64.deb ... 256s Unpacking libfftw3-single3:amd64 (3.3.10-2fakesync1build2) ... 256s Selecting previously unselected package libvulkan1:amd64. 256s Preparing to unpack .../042-libvulkan1_1.4.328.1-1_amd64.deb ... 256s Unpacking 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unpack .../069-libost-base-dev_2.9.3-2build1_amd64.deb ... 257s Unpacking libost-base-dev (2.9.3-2build1) ... 257s Selecting previously unselected package libost-geom2.9:amd64. 257s Preparing to unpack .../070-libost-geom2.9_2.9.3-2build1_amd64.deb ... 257s Unpacking libost-geom2.9:amd64 (2.9.3-2build1) ... 257s Selecting previously unselected package libost-mol2.9. 257s Preparing to unpack .../071-libost-mol2.9_2.9.3-2build1_amd64.deb ... 257s Unpacking libost-mol2.9 (2.9.3-2build1) ... 257s Selecting previously unselected package libpcre2-16-0:amd64. 257s Preparing to unpack .../072-libpcre2-16-0_10.46-1_amd64.deb ... 257s Unpacking libpcre2-16-0:amd64 (10.46-1) ... 257s Selecting previously unselected package libqt5core5t64:amd64. 257s Preparing to unpack .../073-libqt5core5t64_5.15.17+dfsg-1ubuntu1_amd64.deb ... 257s Unpacking libqt5core5t64:amd64 (5.15.17+dfsg-1ubuntu1) ... 257s Selecting previously unselected package libqt5xml5t64:amd64. 257s Preparing to unpack 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libglvnd0:amd64 (1.7.0-1build2) ... 258s Selecting previously unselected package libopengl0:amd64. 258s Preparing to unpack .../085-libopengl0_1.7.0-1build2_amd64.deb ... 258s Unpacking libopengl0:amd64 (1.7.0-1build2) ... 258s Selecting previously unselected package libglu1-mesa:amd64. 258s Preparing to unpack .../086-libglu1-mesa_9.0.2-1.1build1_amd64.deb ... 258s Unpacking libglu1-mesa:amd64 (9.0.2-1.1build1) ... 258s Selecting previously unselected package libost-img2.9. 258s Preparing to unpack .../087-libost-img2.9_2.9.3-2build1_amd64.deb ... 258s Unpacking libost-img2.9 (2.9.3-2build1) ... 258s Selecting previously unselected package libost-img-alg2.9. 258s Preparing to unpack .../088-libost-img-alg2.9_2.9.3-2build1_amd64.deb ... 258s Unpacking libost-img-alg2.9 (2.9.3-2build1) ... 258s Selecting previously unselected package libost-gfx2.9. 258s Preparing to unpack .../089-libost-gfx2.9_2.9.3-2build1_amd64.deb ... 258s Unpacking libost-gfx2.9 (2.9.3-2build1) ... 258s Selecting previously unselected package libost-gfx-dev. 258s Preparing to unpack .../090-libost-gfx-dev_2.9.3-2build1_amd64.deb ... 258s Unpacking libost-gfx-dev (2.9.3-2build1) ... 258s Selecting previously unselected package libost-mol-alg2.9. 258s Preparing to unpack .../091-libost-mol-alg2.9_2.9.3-2build1_amd64.deb ... 258s Unpacking libost-mol-alg2.9 (2.9.3-2build1) ... 258s Selecting previously unselected package libjbig0:amd64. 258s Preparing to unpack .../092-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 258s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 258s Selecting previously unselected package libsharpyuv0:amd64. 258s Preparing to unpack .../093-libsharpyuv0_1.5.0-0.1_amd64.deb ... 258s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 258s Selecting previously unselected package libwebp7:amd64. 258s Preparing to unpack .../094-libwebp7_1.5.0-0.1_amd64.deb ... 258s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 258s Selecting previously unselected package libtiff6:amd64. 258s Preparing to unpack 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unselected package libxcb-shape0:amd64. 258s Preparing to unpack .../111-libxcb-shape0_1.17.0-2build1_amd64.deb ... 258s Unpacking libxcb-shape0:amd64 (1.17.0-2build1) ... 258s Selecting previously unselected package libxcb-xinerama0:amd64. 258s Preparing to unpack .../112-libxcb-xinerama0_1.17.0-2build1_amd64.deb ... 258s Unpacking libxcb-xinerama0:amd64 (1.17.0-2build1) ... 258s Selecting previously unselected package libxcb-xinput0:amd64. 258s Preparing to unpack .../113-libxcb-xinput0_1.17.0-2build1_amd64.deb ... 258s Unpacking libxcb-xinput0:amd64 (1.17.0-2build1) ... 258s Selecting previously unselected package libxcb-xkb1:amd64. 259s Preparing to unpack .../114-libxcb-xkb1_1.17.0-2build1_amd64.deb ... 259s Unpacking libxcb-xkb1:amd64 (1.17.0-2build1) ... 259s Selecting previously unselected package libxkbcommon-x11-0:amd64. 259s Preparing to unpack .../115-libxkbcommon-x11-0_1.12.3-1_amd64.deb ... 259s Unpacking libxkbcommon-x11-0:amd64 (1.12.3-1) ... 259s Selecting previously unselected package libxrender1:amd64. 259s Preparing to unpack .../116-libxrender1_1%3a0.9.12-1_amd64.deb ... 259s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 259s Selecting previously unselected package libqt5gui5t64:amd64. 259s Preparing to unpack .../117-libqt5gui5t64_5.15.17+dfsg-1ubuntu1_amd64.deb ... 259s Unpacking libqt5gui5t64:amd64 (5.15.17+dfsg-1ubuntu1) ... 259s Selecting previously unselected package libqt5widgets5t64:amd64. 259s Preparing to unpack .../118-libqt5widgets5t64_5.15.17+dfsg-1ubuntu1_amd64.deb ... 259s Unpacking libqt5widgets5t64:amd64 (5.15.17+dfsg-1ubuntu1) ... 259s Selecting previously unselected package libost-gui2.9. 259s Preparing to unpack .../119-libost-gui2.9_2.9.3-2build1_amd64.deb ... 259s Unpacking libost-gui2.9 (2.9.3-2build1) ... 259s Selecting previously unselected package libost-gui-dev. 259s Preparing to unpack .../120-libost-gui-dev_2.9.3-2build1_amd64.deb ... 259s Unpacking libost-gui-dev (2.9.3-2build1) ... 259s Selecting previously unselected package libost-img-alg-dev. 259s Preparing to unpack .../121-libost-img-alg-dev_2.9.3-2build1_amd64.deb ... 259s Unpacking libost-img-alg-dev (2.9.3-2build1) ... 259s Selecting previously unselected package libost-img-dev. 259s Preparing to unpack .../122-libost-img-dev_2.9.3-2build1_amd64.deb ... 259s Unpacking libost-img-dev (2.9.3-2build1) ... 259s Selecting previously unselected package libost-info-dev. 259s Preparing to unpack .../123-libost-info-dev_2.9.3-2build1_amd64.deb ... 259s Unpacking libost-info-dev (2.9.3-2build1) ... 259s Selecting previously unselected package libost-io-dev. 259s Preparing to unpack .../124-libost-io-dev_2.9.3-2build1_amd64.deb ... 259s Unpacking libost-io-dev (2.9.3-2build1) ... 259s Selecting previously unselected package libost-mol-alg-dev. 259s Preparing to unpack .../125-libost-mol-alg-dev_2.9.3-2build1_amd64.deb ... 259s Unpacking libost-mol-alg-dev (2.9.3-2build1) ... 259s Selecting previously unselected package libost-mol-dev. 259s Preparing to unpack .../126-libost-mol-dev_2.9.3-2build1_amd64.deb ... 259s Unpacking libost-mol-dev (2.9.3-2build1) ... 259s Selecting previously unselected package libost-mol-mm2.9. 259s Preparing to unpack .../127-libost-mol-mm2.9_2.9.3-2build1_amd64.deb ... 259s Unpacking libost-mol-mm2.9 (2.9.3-2build1) ... 259s Selecting previously unselected package libost-mol-mm-dev. 259s Preparing to unpack .../128-libost-mol-mm-dev_2.9.3-2build1_amd64.deb ... 259s Unpacking libost-mol-mm-dev (2.9.3-2build1) ... 259s Selecting previously unselected package libost-seq-alg-dev. 259s Preparing to unpack .../129-libost-seq-alg-dev_2.9.3-2build1_amd64.deb ... 259s Unpacking libost-seq-alg-dev (2.9.3-2build1) ... 259s Selecting previously unselected package libost-seq-dev. 259s Preparing to unpack .../130-libost-seq-dev_2.9.3-2build1_amd64.deb ... 259s Unpacking libost-seq-dev (2.9.3-2build1) ... 259s Selecting previously unselected package libqhull-r8.0:amd64. 259s Preparing to unpack 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libtk8.6:amd64 (8.6.17-1) ... 260s Selecting previously unselected package libwebpdemux2:amd64. 260s Preparing to unpack .../142-libwebpdemux2_1.5.0-0.1_amd64.deb ... 260s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 260s Selecting previously unselected package libwebpmux3:amd64. 260s Preparing to unpack .../143-libwebpmux3_1.5.0-0.1_amd64.deb ... 260s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 260s Selecting previously unselected package libxslt1.1:amd64. 260s Preparing to unpack .../144-libxslt1.1_1.1.43-0.3_amd64.deb ... 260s Unpacking libxslt1.1:amd64 (1.1.43-0.3) ... 260s Selecting previously unselected package libzopfli1. 260s Preparing to unpack .../145-libzopfli1_1.0.3-3_amd64.deb ... 260s Unpacking libzopfli1 (1.0.3-3) ... 260s Selecting previously unselected package ncbi-data. 260s Preparing to unpack .../146-ncbi-data_6.1.20170106+dfsg2-6_all.deb ... 260s Unpacking ncbi-data (6.1.20170106+dfsg2-6) ... 260s Selecting previously unselected package ncbi-blast+. 260s Preparing to unpack .../147-ncbi-blast+_2.16.0+ds-7_amd64.deb ... 260s Unpacking ncbi-blast+ (2.16.0+ds-7) ... 260s Selecting previously unselected package python-matplotlib-data. 260s Preparing to unpack .../148-python-matplotlib-data_3.10.7+dfsg1-1_all.deb ... 260s Unpacking python-matplotlib-data (3.10.7+dfsg1-1) ... 260s Selecting previously unselected package libopenjp2-7:amd64. 260s Preparing to unpack .../149-libopenjp2-7_2.5.3-2.1_amd64.deb ... 260s Unpacking libopenjp2-7:amd64 (2.5.3-2.1) ... 260s Selecting previously unselected package python3-pil:amd64. 260s Preparing to unpack .../150-python3-pil_12.0.0-1ubuntu1_amd64.deb ... 260s Unpacking python3-pil:amd64 (12.0.0-1ubuntu1) ... 260s Selecting previously unselected package python3.13-tk. 260s Preparing to unpack .../151-python3.13-tk_3.13.9-1_amd64.deb ... 260s Unpacking python3.13-tk (3.13.9-1) ... 260s Selecting previously unselected package python3.14-tk. 260s Preparing to unpack .../152-python3.14-tk_3.14.0-4_amd64.deb ... 260s Unpacking python3.14-tk (3.14.0-4) ... 260s Selecting previously unselected package python3-tk. 260s Preparing to unpack .../153-python3-tk_3.13.9-2_amd64.deb ... 260s Unpacking python3-tk (3.13.9-2) ... 260s Selecting previously unselected package python3-pil.imagetk:amd64. 260s Preparing to unpack .../154-python3-pil.imagetk_12.0.0-1ubuntu1_amd64.deb ... 260s Unpacking python3-pil.imagetk:amd64 (12.0.0-1ubuntu1) ... 260s Selecting previously unselected package python3-contourpy. 260s Preparing to unpack .../155-python3-contourpy_1.3.3-1_amd64.deb ... 260s Unpacking python3-contourpy (1.3.3-1) ... 260s Selecting previously unselected package python3-cycler. 260s Preparing to unpack .../156-python3-cycler_0.12.1-2_all.deb ... 260s Unpacking python3-cycler (0.12.1-2) ... 260s Selecting previously unselected package python3-brotli. 260s Preparing to unpack .../157-python3-brotli_1.1.0-2build6_amd64.deb ... 260s Unpacking python3-brotli (1.1.0-2build6) ... 260s Selecting previously unselected package python3-platformdirs. 260s Preparing to unpack .../158-python3-platformdirs_4.4.0-1_all.deb ... 260s Unpacking python3-platformdirs (4.4.0-1) ... 260s Selecting previously unselected package python3-fs. 260s Preparing to unpack .../159-python3-fs_2.4.16-9ubuntu1_all.deb ... 260s Unpacking python3-fs (2.4.16-9ubuntu1) ... 260s Selecting previously unselected package python3-lxml:amd64. 260s Preparing to unpack .../160-python3-lxml_6.0.2-1_amd64.deb ... 260s Unpacking python3-lxml:amd64 (6.0.2-1) ... 260s Selecting previously unselected package python3-lz4. 260s Preparing to unpack .../161-python3-lz4_4.4.4+dfsg-3_amd64.deb ... 260s Unpacking python3-lz4 (4.4.4+dfsg-3) ... 260s Selecting previously unselected package python3-munkres. 260s Preparing to unpack .../162-python3-munkres_1.1.4-3_all.deb ... 260s Unpacking python3-munkres (1.1.4-3) ... 260s Selecting previously unselected package python3-mpmath. 260s Preparing to unpack .../163-python3-mpmath_1.3.0-2_all.deb 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unselected package python3-fonttools. 261s Preparing to unpack .../169-python3-fonttools_4.57.0-3_amd64.deb ... 261s Unpacking python3-fonttools (4.57.0-3) ... 261s Selecting previously unselected package python3-kiwisolver. 261s Preparing to unpack .../170-python3-kiwisolver_1.4.10~rc0-1_amd64.deb ... 261s Unpacking python3-kiwisolver (1.4.10~rc0-1) ... 261s Selecting previously unselected package python3-matplotlib. 261s Preparing to unpack .../171-python3-matplotlib_3.10.7+dfsg1-1_amd64.deb ... 261s Unpacking python3-matplotlib (3.10.7+dfsg1-1) ... 261s Selecting previously unselected package python3-pyqt5.sip. 261s Preparing to unpack .../172-python3-pyqt5.sip_12.17.1-1_amd64.deb ... 261s Unpacking python3-pyqt5.sip (12.17.1-1) ... 261s Selecting previously unselected package python3-pyqt5. 261s Preparing to unpack .../173-python3-pyqt5_5.15.11+dfsg-3_amd64.deb ... 261s Unpacking python3-pyqt5 (5.15.11+dfsg-3) ... 262s Selecting previously unselected package python3-ost. 262s 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up libdouble-conversion3:amd64 (3.3.1-2) ... 262s Setting up libxcb-xfixes0:amd64 (1.17.0-2build1) ... 262s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 262s Setting up libxcb-xinput0:amd64 (1.17.0-2build1) ... 262s Setting up libxrender1:amd64 (1:0.9.12-1) ... 262s Setting up libparasail8:amd64 (2.6.2+dfsg-2ubuntu2) ... 262s Setting up python3-lz4 (4.4.4+dfsg-3) ... 262s Setting up libxcb-render0:amd64 (1.17.0-2build1) ... 262s Setting up libglvnd0:amd64 (1.7.0-1build2) ... 262s Setting up python3-unicodedata2 (16.0.0+ds-1build1) ... 262s Setting up fonts-lyx (2.4.4-2) ... 262s Setting up libxcb-glx0:amd64 (1.17.0-2build1) ... 262s Setting up libdrm-intel1:amd64 (2.4.127-1ubuntu1) ... 262s Setting up libxcb-keysyms1:amd64 (0.4.1-1) ... 262s Setting up libxcb-shape0:amd64 (1.17.0-2build1) ... 262s Setting up x11-common (1:7.7+24ubuntu1) ... 263s Setting up libdeflate0:amd64 (1.23-2) ... 263s Setting up libboost-thread1.83.0:amd64 (1.83.0-5ubuntu2) ... 263s Setting up libqhull-r8.0:amd64 (2020.2-7) ... 263s Setting up libxcb-render-util0:amd64 (0.3.10-1) ... 263s Setting up libxcb-shm0:amd64 (1.17.0-2build1) ... 263s Setting up libxcb-icccm4:amd64 (0.4.2-1) ... 263s Setting up libboost-filesystem1.83.0:amd64 (1.83.0-5ubuntu2) ... 263s Setting up libgomp1:amd64 (15.2.0-9ubuntu1) ... 263s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 263s Setting up libpcre2-16-0:amd64 (10.46-1) ... 263s Setting up python3-platformdirs (4.4.0-1) ... 263s Setting up libopengl0:amd64 (1.7.0-1build2) ... 263s Setting up libxcb-util1:amd64 (0.4.1-1) ... 263s Setting up libxxf86vm1:amd64 (1:1.1.4-2) ... 263s Setting up libxcb-xkb1:amd64 (1.17.0-2build1) ... 263s Setting up libxcb-image0:amd64 (0.4.0-2build1) ... 263s Setting up python3-fs (2.4.16-9ubuntu1) ... 263s Setting up libxcb-present0:amd64 (1.17.0-2build1) ... 263s Setting up unicode-data (16.0.0-1) ... 263s Setting up libqt5core5t64:amd64 (5.15.17+dfsg-1ubuntu1) ... 263s Setting up libblas3:amd64 (3.12.1-7) ... 263s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 263s Setting up libxcb-xinerama0:amd64 (1.17.0-2build1) ... 263s Setting up libzopfli1 (1.0.3-3) ... 263s Setting up libxcb-sync1:amd64 (1.17.0-2build1) ... 263s Setting up libboost-iostreams1.83.0:amd64 (1.83.0-5ubuntu2) ... 263s Setting up python3-brotli (1.1.0-2build6) ... 263s Setting up libavahi-common-data:amd64 (0.8-16ubuntu3) ... 263s Setting up python3-cycler (0.12.1-2) ... 263s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 263s Setting up libxkbcommon-x11-0:amd64 (1.12.3-1) ... 263s Setting up fonts-dejavu-mono (2.37-8) ... 263s Setting up python3-kiwisolver (1.4.10~rc0-1) ... 263s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 263s Setting up libtcl8.6:amd64 (8.6.17+dfsg-1) ... 263s Setting up fonts-dejavu-core (2.37-8) ... 263s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 263s Setting up libcifpp-data (9.0.5-2) ... 264s Setting up libgfortran5:amd64 (15.2.0-9ubuntu1) ... 264s Setting up libvulkan1:amd64 (1.4.328.1-1) ... 264s Setting up libwebp7:amd64 (1.5.0-0.1) ... 264s Setting up python3-pyqt5.sip (12.17.1-1) ... 264s Setting up libmtdev1t64:amd64 (1.1.7-1) ... 264s Setting up libxshmfence1:amd64 (1.3.3-1) ... 264s Setting up libxcb-randr0:amd64 (1.17.0-2build1) ... 264s Setting up libxslt1.1:amd64 (1.1.43-0.3) ... 264s Setting up python3-munkres (1.1.4-3) ... 264s Setting up libqt5sql5t64:amd64 (5.15.17+dfsg-1ubuntu1) ... 264s Setting up clustalw (2.1+lgpl-7build1) ... 264s Setting up libmd4c0:amd64 (0.5.2-2) ... 264s Setting up libost-base2.9:amd64 (2.9.3-2build1) ... 264s Setting up libopenjp2-7:amd64 (2.5.3-2.1) ... 264s Setting up libharfbuzz0b:amd64 (12.1.0-1) ... 264s Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... 264s Setting up libglu1-mesa:amd64 (9.0.2-1.1build1) ... 264s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 264s Setting up libmbedcrypto16:amd64 (3.6.2-3ubuntu1) ... 264s Setting up python3-mpmath (1.3.0-2) ... 265s Setting up libost-base-dev (2.9.3-2build1) ... 265s Setting up python-matplotlib-data (3.10.7+dfsg1-1) ... 265s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 265s Setting up libopenmm8.1 (8.1.2+dfsg-12) ... 265s Setting up libost-geom2.9:amd64 (2.9.3-2build1) ... 265s Setting up libwacom-common (2.16.1-1) ... 265s Setting up libwayland-client0:amd64 (1.24.0-2) ... 265s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 265s Setting up python3-sympy (1.14.0-2) ... 271s Setting up libice6:amd64 (2:1.1.1-1) ... 271s Setting up mesa-libgallium:amd64 (25.2.7-1ubuntu1) ... 271s Setting up liblapack3:amd64 (3.12.1-7) ... 271s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 271s Setting up libqt5dbus5t64:amd64 (5.15.17+dfsg-1ubuntu1) ... 271s Setting up libfftw3-single3:amd64 (3.3.10-2fakesync1build2) ... 271s Setting up libgbm1:amd64 (25.2.7-1ubuntu1) ... 271s Setting up libwacom9:amd64 (2.16.1-1) ... 271s Setting up libcifpp9:amd64 (9.0.5-2) ... 271s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 272s Setting up voronota (1.29.4415+ds-1) ... 272s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 272s Setting up libgl1-mesa-dri:amd64 (25.2.7-1ubuntu1) ... 272s Setting up libqt5network5t64:amd64 (5.15.17+dfsg-1ubuntu1) ... 272s Setting up libavahi-common3:amd64 (0.8-16ubuntu3) ... 272s Setting up libqt5xml5t64:amd64 (5.15.17+dfsg-1ubuntu1) ... 272s Setting up libqt5test5t64:amd64 (5.15.17+dfsg-1ubuntu1) ... 272s Setting up dssp (4.5.7-1) ... 272s Setting up python3-zopfli (0.4.0-1) ... 272s Setting up libinput-bin (1.30.0-1) ... 272s Setting up libegl-mesa0:amd64 (25.2.7-1ubuntu1) ... 272s Setting up libmbedx509-7:amd64 (3.6.2-3ubuntu1) ... 272s Setting up libraqm0:amd64 (0.10.3-1) ... 272s Setting up libost-mol2.9 (2.9.3-2build1) ... 272s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 274s Setting up libmbedtls21:amd64 (3.6.2-3ubuntu1) ... 274s Setting up python3-lxml:amd64 (6.0.2-1) ... 274s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 274s Setting up libegl1:amd64 (1.7.0-1build2) ... 274s Setting up python3-contourpy (1.3.3-1) ... 274s Setting up libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 274s Setting up libost-geom-dev (2.9.3-2build1) ... 274s Setting up libsm6:amd64 (2:1.2.6-1) ... 274s Setting up libavahi-client3:amd64 (0.8-16ubuntu3) ... 274s Setting up libost-conop2.9 (2.9.3-2build1) ... 274s Setting up libinput10:amd64 (1.30.0-1) ... 274s Setting up fontconfig (2.15.0-2.3ubuntu1) ... 276s Regenerating fonts cache... done. 276s Setting up libxft2:amd64 (2.3.6-1build1) ... 276s Setting up libost-info2.9 (2.9.3-2build1) ... 276s Setting up libglx-mesa0:amd64 (25.2.7-1ubuntu1) ... 276s Setting up libglx0:amd64 (1.7.0-1build2) ... 276s Setting up libost-info-dev (2.9.3-2build1) ... 276s Setting up libost-seq2.9 (2.9.3-2build1) ... 276s Setting up libtk8.6:amd64 (8.6.17-1) ... 276s Setting up libost-mol-dev (2.9.3-2build1) ... 276s Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... 276s Setting up libost-img2.9 (2.9.3-2build1) ... 276s Setting up libost-seq-dev (2.9.3-2build1) ... 276s Setting up python3.13-tk (3.13.9-1) ... 276s Setting up libost-conop-dev (2.9.3-2build1) ... 276s Setting up ncbi-blast+ (2.16.0+ds-7) ... 276s Setting up python3-pil:amd64 (12.0.0-1ubuntu1) ... 277s Setting up libgl1:amd64 (1.7.0-1build2) ... 277s Setting up libost-img-alg2.9 (2.9.3-2build1) ... 277s Setting up libost-seq-alg2.9 (2.9.3-2build1) ... 277s Setting up libost-bindings2.9 (2.9.3-2build1) ... 277s Setting up libost-db2.9 (2.9.3-2build1) ... 277s Setting up libcups2t64:amd64 (2.4.12-0ubuntu3) ... 277s Setting up libost-img-dev (2.9.3-2build1) ... 277s Setting up libost-db-dev (2.9.3-2build1) ... 277s Setting up libost-mol-alg2.9 (2.9.3-2build1) ... 277s Setting up python3.14-tk (3.14.0-4) ... 277s Setting up python3-tk (3.13.9-2) ... 277s Setting up libost-seq-alg-dev (2.9.3-2build1) ... 277s Setting up libost-img-alg-dev (2.9.3-2build1) ... 277s Setting up libost-gfx2.9 (2.9.3-2build1) ... 277s Setting up libqt5gui5t64:amd64 (5.15.17+dfsg-1ubuntu1) ... 277s Setting up python3-pil.imagetk:amd64 (12.0.0-1ubuntu1) ... 277s Setting up libost-bindings-dev (2.9.3-2build1) ... 277s Setting up libost-mol-alg-dev (2.9.3-2build1) ... 277s Setting up libost-io2.9 (2.9.3-2build1) ... 277s Setting up libost-gfx-dev (2.9.3-2build1) ... 277s Setting up libqt5widgets5t64:amd64 (5.15.17+dfsg-1ubuntu1) ... 277s Setting up libost-mol-mm2.9 (2.9.3-2build1) ... 277s Setting up libost-mol-mm-dev (2.9.3-2build1) ... 277s Setting up libqt5help5:amd64 (5.15.17-4) ... 277s Setting up libost-gui2.9 (2.9.3-2build1) ... 277s Setting up libost-io-dev (2.9.3-2build1) ... 277s Setting up libqt5printsupport5t64:amd64 (5.15.17+dfsg-1ubuntu1) ... 277s Setting up libqt5designer5:amd64 (5.15.17-4) ... 277s Setting up libost-gui-dev (2.9.3-2build1) ... 277s Setting up python3-pyqt5 (5.15.11+dfsg-3) ... 277s Setting up python3-fonttools (4.57.0-3) ... 278s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 278s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 280s Setting up python3-ost (2.9.3-2build1) ... 280s Setting up openstructure (2.9.3-2build1) ... 327s Building compounds library, this may take a while... 0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ 327s Processing triggers for man-db (2.13.1-1) ... 327s Processing triggers for udev (257.9-0ubuntu2) ... 328s Processing triggers for libc-bin (2.42-2ubuntu2) ... 337s autopkgtest [07:35:34]: test python: [----------------------- 337s Compound library not available. Some functionality may not work as expected. 337s .... 337s ---------------------------------------------------------------------- 337s Ran 4 tests in 0.000s 337s 337s OK 337s Compound library not available. Some functionality may not work as expected. 337s ...... 337s ---------------------------------------------------------------------- 337s Ran 6 tests in 0.001s 337s 337s OK 337s Compound library not available. Some functionality may not work as expected. 338s ...../usr/lib/python3/dist-packages/ost/table.py:2696: DeprecationWarning: `trapz` is deprecated. Use `trapezoid` instead, or one of the numerical integration functions in `scipy.integrate`. 338s return np.trapz(enr[1], enr[0]) 338s ../usr/lib/python3/dist-packages/ost/table.py:2807: DeprecationWarning: `trapz` is deprecated. Use `trapezoid` instead, or one of the numerical integration functions in `scipy.integrate`. 338s return np.trapz(roc[1], roc[0]) 338s ...................../usr/lib/python3/dist-packages/ost/table.py:2807: DeprecationWarning: `trapz` is deprecated. Use `trapezoid` instead, or one of the numerical integration functions in `scipy.integrate`. 338s return np.trapz(roc[1], roc[0]) 338s ........../usr/lib/python3.13/unittest/case.py:606: ResourceWarning: unclosed file <_io.BufferedReader name='testfiles/enrichment-out.png'> 338s if method() is not None: 338s ResourceWarning: Enable tracemalloc to get the object allocation traceback 339s ../usr/lib/python3/dist-packages/matplotlib/_api/__init__.py:126: ResourceWarning: unclosed file <_io.FileIO name='testfiles/logroc-out.png' mode='rb' closefd=True> 339s if val not in values: 339s ResourceWarning: Enable tracemalloc to get the object allocation traceback 339s /usr/lib/python3.13/unittest/case.py:606: ResourceWarning: unclosed file <_io.BufferedReader name='testfiles/roc-out.png'> 339s if method() is not None: 339s ResourceWarning: Enable tracemalloc to get the object allocation traceback 339s ./usr/lib/python3.13/unittest/case.py:606: ResourceWarning: unclosed file <_io.BufferedReader name='testfiles/roc-same-val-out.png'> 339s if method() is not None: 339s ResourceWarning: Enable tracemalloc to get the object allocation traceback 339s .......................................... 339s ---------------------------------------------------------------------- 339s Ran 83 tests in 1.432s 339s 339s OK 339s Could not find scipy.stats.mstats: ignoring some table class unit tests 339s Could not find scipy.ndimage: ignoring some table class unit tests 339s /tmp/autopkgtest.rsMlrT/build.xov/src/modules/bindings/tests/test_blast.py:81: SyntaxWarning: invalid escape sequence '\d' 339s re_v = re.compile('\d+\.\d+\.\d+') 339s Compound library not available. Some functionality may not work as expected. 340s Could not find /I/do/not/exist 340s ...Could not find /I/do/not/exist 340s ... 340s ---------------------------------------------------------------------- 340s Ran 6 tests in 0.451s 340s 340s OK 340s Compound library not available. Some functionality may not work as expected. 356s s. 356s ---------------------------------------------------------------------- 356s Ran 2 tests in 15.466s 356s 356s OK (skipped=1) 356s Compound library not available. Some functionality may not work as expected. 356s ....... 356s ---------------------------------------------------------------------- 356s Ran 7 tests in 0.612s 356s 356s OK 356s Compound library not available. Some functionality may not work as expected. 357s Could not find DockQ.py, could not test binding... 357s Compound library not available. Some functionality may not work as expected. 357s Could not find hbplus, could not test binding... 357s Compound library not available. Some functionality may not work as expected. 357s No HHblits installation found: skip unit tests 357s Compound library not available. Some functionality may not work as expected. 357s Could not find ialign master perl script: ignoring unit tests 357s . 357s ---------------------------------------------------------------------- 357s Ran 1 test in 0.013s 357s 357s OK 357s Compound library not available. Some functionality may not work as expected. 357s Could not find kClust executable: ignoring unit tests 357s Compound library not available. Some functionality may not work as expected. 357s .Could not find lga executable: ignoring unit tests 357s 357s ---------------------------------------------------------------------- 357s Ran 1 test in 0.016s 357s 357s OK 358s Compound library not available. Some functionality may not work as expected. 358s Could not find msms executable: ignoring unit tests 358s Compound library not available. Some functionality may not work as expected. 358s Could not find NACCESS, could not test binding... 358s Compound library not available. Some functionality may not work as expected. 358s ...Could not find tmalign executable: ignoring unit tests 358s Could not find tmalign executable: ignoring unit tests 358s 358s ---------------------------------------------------------------------- 358s Ran 3 tests in 0.182s 358s 358s OK 358s Compound library not available. Some functionality may not work as expected. 358s No compound library available. Ignoring test_cleanup.py tests. 358s Compound library not available. Some functionality may not work as expected. 358s ../tmp/autopkgtest.rsMlrT/build.xov/src/modules/conop/tests/test_complib.py:71: UserWarning: Compound library not available. Some functionality may not work as expected. 358s warnings.warn("Compound library not available. Some functionality may not work as expected.") 359s ...... 359s ---------------------------------------------------------------------- 359s Ran 8 tests in 0.103s 359s 359s OK 359s Compound library not available. Some functionality may not work as expected. 359s No compound library available. Ignoring test_compound.py tests. 359s Compound library not available. Some functionality may not work as expected. 359s . 359s ---------------------------------------------------------------------- 359s Ran 1 test in 0.000s 359s 359s OK 359s Compound library not available. Some functionality may not work as expected. 359s ... 359s ---------------------------------------------------------------------- 359s Ran 3 tests in 0.001s 359s 359s OK 359s Compound library not available. Some functionality may not work as expected. 359s ........ 359s ---------------------------------------------------------------------- 359s Ran 8 tests in 0.002s 359s 359s OK 359s Traceback (most recent call last): 359s File "/tmp/autopkgtest.rsMlrT/build.xov/src/modules/gfx/tests/test_entity.py", line 1, in 359s eh=io.LoadPDB("1crn",remote=True) 359s ^^ 359s NameError: name 'io' is not defined. Did you mean: 'id'? Or did you forget to import 'io'? 359s Compound library not available. Some functionality may not work as expected. 359s ...... 359s ---------------------------------------------------------------------- 359s Ran 6 tests in 0.001s 359s 359s OK 359s Traceback (most recent call last): 359s File "/tmp/autopkgtest.rsMlrT/build.xov/src/modules/gfx/tests/test_gost_export.py", line 1, in 359s import desost_util as util 359s ModuleNotFoundError: No module named 'desost_util' 360s Traceback (most recent call last): 360s File "/tmp/autopkgtest.rsMlrT/build.xov/src/modules/gfx/tests/test_gost_import.py", line 3, in 360s with open("test.gost","rb") as gf: 360s ~~~~^^^^^^^^^^^^^^^^^^ 360s FileNotFoundError: [Errno 2] No such file or directory: 'test.gost' 360s Compound library not available. Some functionality may not work as expected. 360s .No citation for identifier '1' found. Couldn't set author list. 360s SEQRES requires a valid compound library to handle non standard compounds. Their One letter codes will be set to X. 360s ..SEQRES requires a valid compound library to handle non standard compounds. Their One letter codes will be set to X. 360s .SEQRES requires a valid compound library to handle non standard compounds. Their One letter codes will be set to X. 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 360s .SEQRES requires a valid compound library to handle non standard compounds. Their One letter codes will be set to X. 360s No SEQRES found for chain 'A'. Most likely the entity_poly_seq category was missing from the input file. 360s No SEQRES found for chain 'B'. Most likely the entity_poly_seq category was missing from the input file. 360s No SEQRES found for chain 'C'. Most likely the entity_poly_seq category was missing from the input file. 360s ......s 360s ---------------------------------------------------------------------- 360s Ran 12 tests in 0.646s 360s 360s OK (skipped=1) 360s Compound library not available. Some functionality may not work as expected. 360s No compound library available. Ignoring test_stereochemistry.py tests. 361s Compound library not available. Some functionality may not work as expected. 361s ....s 361s ---------------------------------------------------------------------- 361s Ran 5 tests in 0.003s 361s 361s OK (skipped=1) 361s Compound library not available. Some functionality may not work as expected. 361s ..... 361s ---------------------------------------------------------------------- 361s Ran 5 tests in 0.005s 361s 361s OK 361s Compound library not available. Some functionality may not work as expected. 363s sCould not find NACCESS, could not compare Accessiblity function... 363s . 363s ---------------------------------------------------------------------- 363s Ran 2 tests in 2.165s 363s 363s OK (skipped=1) 363s Compound library not available. Some functionality may not work as expected. 363s Failed to import bb_lddt.py. Happens when numpy or scipy missing. Ignoring qsscore.py tests. 364s Compound library not available. Some functionality may not work as expected. 364s Ignoring struct_ref_seq_dif with missing data item seq_num 364s Ignoring struct_ref_seq_dif with missing data item seq_num 364s SEQRES requires a valid compound library to handle non standard compounds. Their One letter codes will be set to X. 364s unknown residue 'ACE' in SEQRES record. Setting one-letter-code to 'X' 364s . 364s ---------------------------------------------------------------------- 364s Ran 1 test in 0.126s 364s 364s OK 364s Compound library not available. Some functionality may not work as expected. 364s Failed to import chain_mapping.py. Happens when numpy or scipy missing. Ignoring test_chain_mapping.py tests. 364s Compound library not available. Some functionality may not work as expected. 364s Failed to import contact_score.py. Happens when numpy or scipy missing. Ignoring contact_score.py tests. 364s Compound library not available. Some functionality may not work as expected. 365s ......... 365s ---------------------------------------------------------------------- 365s Ran 9 tests in 0.862s 365s 365s OK 365s Compound library not available. Some functionality may not work as expected. 365s .. 365s ---------------------------------------------------------------------- 365s Ran 2 tests in 0.010s 365s 365s OK 365s Compound library not available. Some functionality may not work as expected. 366s Failed to import qsscoring. Happens when numpy or scipy missing. Ignoring test_lddt.py tests. 366s Compound library not available. Some functionality may not work as expected. 366s Failed to import ligand_scoring.py. Happens when numpy, scipy or networkx is missing. Ignoring test_ligand_scoring.py tests. 366s Compound library not available. Some functionality may not work as expected. 366s No compound library available. Ignoring test_nonstandard.py tests. 366s Compound library not available. Some functionality may not work as expected. 366s . 366s ---------------------------------------------------------------------- 366s Ran 1 test in 0.209s 366s 366s OK 366s Compound library not available. Some functionality may not work as expected. 366s ........ 366s ---------------------------------------------------------------------- 366s Ran 8 tests in 0.005s 367s 367s OK 367s Compound library not available. Some functionality may not work as expected. 367s Failed to import qsscore.py. Happens when numpy or scipy missing. Ignoring qsscore.py tests. 367s Compound library not available. Some functionality may not work as expected. 367s Failed to import qsscoring. Happens when numpy or scipy missing. Ignoring test_qsscoring.py tests. 367s Compound library not available. Some functionality may not work as expected. 367s s 367s ---------------------------------------------------------------------- 367s Ran 1 test in 0.000s 367s 367s OK (skipped=1) 367s Compound library not available. Some functionality may not work as expected. 367s No compound library available. Ignoring test_stereochemistry.py tests. 367s Compound library not available. Some functionality may not work as expected. 367s ....... 367s ---------------------------------------------------------------------- 367s Ran 7 tests in 0.002s 367s 367s OK 368s Compound library not available. Some functionality may not work as expected. 368s ... 368s ---------------------------------------------------------------------- 368s Ran 3 tests in 0.016s 368s 368s OK 368s Compound library not available. Some functionality may not work as expected. 368s . 368s ---------------------------------------------------------------------- 368s Ran 1 test in 0.044s 368s 368s OK 368s Compound library not available. Some functionality may not work as expected. 368s . 368s ---------------------------------------------------------------------- 368s Ran 1 test in 0.001s 368s 368s OK 368s Compound library not available. Some functionality may not work as expected. 368s No compound library available. Ignoring test_aligntoseqres.py tests. 368s Compound library not available. Some functionality may not work as expected. 368s ... 368s ---------------------------------------------------------------------- 368s Ran 3 tests in 0.001s 368s 368s OK 368s Compound library not available. Some functionality may not work as expected. 368s ... 368s ---------------------------------------------------------------------- 368s Ran 3 tests in 0.001s 368s 368s OK 369s Compound library not available. Some functionality may not work as expected. 369s ........ 369s ---------------------------------------------------------------------- 369s Ran 8 tests in 0.028s 369s 369s OK 369s Compound library not available. Some functionality may not work as expected. 369s . 369s ---------------------------------------------------------------------- 369s Ran 1 test in 0.001s 369s 369s OK 369s Compound library not available. Some functionality may not work as expected. 369s .. 369s ---------------------------------------------------------------------- 369s Ran 2 tests in 0.000s 369s 369s OK 369s Compound library not available. Some functionality may not work as expected. 369s .............. 369s ---------------------------------------------------------------------- 369s Ran 14 tests in 0.005s 369s 369s OK 370s autopkgtest [07:36:07]: test python: -----------------------] 370s autopkgtest [07:36:07]: test python: - - - - - - - - - - results - - - - - - - - - - 370s python PASS 371s autopkgtest [07:36:08]: @@@@@@@@@@@@@@@@@@@@ summary 371s python PASS