0s autopkgtest [13:41:04]: starting date and time: 2025-03-22 13:41:04+0000 0s autopkgtest [13:41:04]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [13:41:04]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.pg8tq10n/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:cctbx --apt-upgrade cctbx --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=cctbx/2024.10+ds2+~3.22.1+ds1-4build2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-17.secgroup --name adt-plucky-arm64-cctbx-20250322-130601-juju-7f2275-prod-proposed-migration-environment-20-fb72ca39-dc3f-43f5-8d0a-fd0ddc18fa1c --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 130s autopkgtest [13:43:14]: testbed dpkg architecture: arm64 130s autopkgtest [13:43:14]: testbed apt version: 2.9.34 131s autopkgtest [13:43:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 131s autopkgtest [13:43:15]: testbed release detected to be: None 132s autopkgtest [13:43:16]: updating testbed package index (apt update) 132s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 132s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 132s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 132s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 133s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [1232 B] 133s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [12.2 kB] 133s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [292 kB] 133s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [30.7 kB] 133s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [39.1 kB] 133s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1292 B] 133s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 133s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [198 kB] 133s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [11.1 kB] 133s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [3684 B] 133s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [216 B] 135s Fetched 716 kB in 1s (925 kB/s) 136s Reading package lists... 136s autopkgtest [13:43:20]: upgrading testbed (apt dist-upgrade and autopurge) 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 137s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 138s Starting 2 pkgProblemResolver with broken count: 0 138s Done 139s Entering ResolveByKeep 139s 139s Calculating upgrade... 140s The following packages will be upgraded: 140s gcc-15-base libatomic1 libgcc-s1 libstdc++6 140s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s Need to get 879 kB of archives. 140s After this operation, 0 B of additional disk space will be used. 140s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libatomic1 arm64 15-20250319-1ubuntu1 [11.2 kB] 140s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-15-base arm64 15-20250319-1ubuntu1 [53.6 kB] 140s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-s1 arm64 15-20250319-1ubuntu1 [61.1 kB] 140s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++6 arm64 15-20250319-1ubuntu1 [753 kB] 141s Fetched 879 kB in 1s (1615 kB/s) 142s (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 ... 117732 files and directories currently installed.) 142s Preparing to unpack .../libatomic1_15-20250319-1ubuntu1_arm64.deb ... 142s Unpacking libatomic1:arm64 (15-20250319-1ubuntu1) over (15-20250315-1ubuntu1) ... 142s Preparing to unpack .../gcc-15-base_15-20250319-1ubuntu1_arm64.deb ... 142s Unpacking gcc-15-base:arm64 (15-20250319-1ubuntu1) over (15-20250315-1ubuntu1) ... 142s Setting up gcc-15-base:arm64 (15-20250319-1ubuntu1) ... 142s (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 ... 117732 files and directories currently installed.) 142s Preparing to unpack .../libgcc-s1_15-20250319-1ubuntu1_arm64.deb ... 142s Unpacking libgcc-s1:arm64 (15-20250319-1ubuntu1) over (15-20250315-1ubuntu1) ... 142s Setting up libgcc-s1:arm64 (15-20250319-1ubuntu1) ... 142s (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 ... 117732 files and directories currently installed.) 142s Preparing to unpack .../libstdc++6_15-20250319-1ubuntu1_arm64.deb ... 142s Unpacking libstdc++6:arm64 (15-20250319-1ubuntu1) over (15-20250315-1ubuntu1) ... 142s Setting up libstdc++6:arm64 (15-20250319-1ubuntu1) ... 142s Setting up libatomic1:arm64 (15-20250319-1ubuntu1) ... 142s Processing triggers for libc-bin (2.41-1ubuntu2) ... 143s Reading package lists... 143s Building dependency tree... 143s Reading state information... 144s Starting pkgProblemResolver with broken count: 0 144s Starting 2 pkgProblemResolver with broken count: 0 144s Done 145s Solving dependencies... 145s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s autopkgtest [13:43:32]: testbed running kernel: Linux 6.14.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Mon Mar 17 12:19:09 UTC 2025 148s autopkgtest [13:43:32]: @@@@@@@@@@@@@@@@@@@@ apt-source cctbx 152s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe cctbx 2024.10+ds2+~3.22.1+ds1-4build2 (dsc) [4106 B] 152s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe cctbx 2024.10+ds2+~3.22.1+ds1-4build2 (tar) [378 kB] 152s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe cctbx 2024.10+ds2+~3.22.1+ds1-4build2 (tar) [23.9 MB] 152s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe cctbx 2024.10+ds2+~3.22.1+ds1-4build2 (diff) [418 kB] 152s gpgv: Signature made Tue Mar 4 14:45:06 2025 UTC 152s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 152s gpgv: Can't check signature: No public key 152s dpkg-source: warning: cannot verify inline signature for ./cctbx_2024.10+ds2+~3.22.1+ds1-4build2.dsc: no acceptable signature found 155s autopkgtest [13:43:39]: testing package cctbx version 2024.10+ds2+~3.22.1+ds1-4build2 156s autopkgtest [13:43:40]: build not needed 161s autopkgtest [13:43:45]: test cctbx: preparing testbed 161s Reading package lists... 161s Building dependency tree... 161s Reading state information... 162s Starting pkgProblemResolver with broken count: 0 162s Starting 2 pkgProblemResolver with broken count: 0 162s Done 163s The following NEW packages will be installed: 163s adwaita-icon-theme at-spi2-common blt cpp cpp-14 cpp-14-aarch64-linux-gnu 163s cpp-aarch64-linux-gnu dconf-gsettings-backend dconf-service fontconfig 163s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 163s fonts-lato fonts-lyx g++ g++-14 g++-14-aarch64-linux-gnu 163s g++-aarch64-linux-gnu gcc gcc-14 gcc-14-aarch64-linux-gnu 163s gcc-aarch64-linux-gnu gtk-update-icon-cache hicolor-icon-theme libaec0 163s libann-cctbx-dev libann-cctbx0 libantlr3c-3.4-0 libasan8 163s libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 libavahi-client3 163s libavahi-common-data libavahi-common3 libblas3 libboost-numpy1.83.0 163s libboost-python-dev libboost-python1.83-dev libboost-python1.83.0 163s libboost-thread1.83.0 libboost-timer1.83.0 libboost1.83-dev 163s libcairo-gobject2 libcairo2 libcbf1t64 libcc1-0 libccp4-data libccp4-dev 163s libccp4c0t64 libccp4f0t64 libcctbx-dev libcctbx0 libcolord2 libcups2t64 163s libdatrie1 libdconf1 libdeflate0 libdouble-conversion3 libegl-mesa0 libegl1 163s libepoxy0 libexpat1-dev libfontconfig1 libgbm1 libgcc-14-dev 163s libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgl1 163s libgl1-mesa-dri libglew2.2 libglu1-mesa libglut3.12 libglvnd0 libglx-mesa0 163s libglx0 libgomp1 libgraphite2-3 libgtk-3-0t64 libgtk-3-common libharfbuzz0b 163s libhdf5-310 libhdf5-hl-310 libhwasan0 libice6 libimagequant0 libinput-bin 163s libinput10 libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 163s libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 163s liblcms2-2 liblerc4 liblsan0 liblzf1 libmd4c0 libmmdb2-0 libmpc3 163s libmtdev1t64 libnetcdf22 libnotify4 libopengl0 libopenjp2-7 libpango-1.0-0 163s libpangocairo-1.0-0 libpangoft2-1.0-0 libpcre2-16-0 libpcre2-32-0 163s libpixman-1-0 libpython3-dev libpython3.13-dev libqhull-r8.0 libqt5core5t64 163s libqt5dbus5t64 libqt5designer5 libqt5gui5t64 libqt5help5 libqt5network5t64 163s libqt5opengl5t64 libqt5printsupport5t64 libqt5sql5t64 libqt5test5t64 163s libqt5widgets5t64 libqt5xml5t64 libraqm0 libsharpyuv0 libsm6 libssm2 163s libstdc++-14-dev libsz2 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 163s libtsan2 libubsan1 libvulkan1 libwacom-common libwacom9 libwayland-client0 163s libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 163s libwebpmux3 libwxbase3.2-1t64 libwxgtk-gl3.2-1t64 libwxgtk3.2-1t64 163s libx11-xcb1 libxcb-dri3-0 libxcb-glx0 libxcb-icccm4 libxcb-image0 163s libxcb-keysyms1 libxcb-present0 libxcb-randr0 libxcb-render-util0 163s libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-util1 163s libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxcomposite1 163s libxcursor1 libxdamage1 libxfixes3 libxft2 libxi6 libxinerama1 163s libxkbcommon-x11-0 libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1 163s libxtst6 libxxf86vm1 mesa-libgallium pymol-data python-matplotlib-data 163s python3-all python3-brotli python3-cctbx python3-contourpy python3-cycler 163s python3-dateutil python3-decorator python3-dev python3-flexcache 163s python3-flexparser python3-fonttools python3-fs python3-h5py 163s python3-h5py-serial python3-hdf5plugin python3-iniconfig python3-kiwisolver 163s python3-legacy-cgi python3-lxml python3-lz4 python3-matplotlib 163s python3-mpmath python3-mrcfile python3-natsort python3-numpy 163s python3-numpy-dev python3-nxmx python3-opengl python3-ordered-set 163s python3-packaging python3-pil python3-pil.imagetk python3-pint 163s python3-platformdirs python3-pluggy python3-procrunner python3-pycbf 163s python3-pymol python3-pyqt5 python3-pyqt5.qtopengl python3-pyqt5.sip 163s python3-pytest python3-scipy python3-six python3-sympy python3-tk 163s python3-tqdm python3-ufolib2 python3-wxgtk4.0 python3.13-dev python3.13-tk 163s sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data x11-common zlib1g-dev 163s 0 upgraded, 253 newly installed, 0 to remove and 0 not upgraded. 163s Need to get 244 MB of archives. 163s After this operation, 1171 MB of additional disk space will be used. 163s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-lato all 2.015-1 [2781 kB] 164s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 164s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 164s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250319-1ubuntu1 [443 kB] 164s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 164s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 164s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [8004 B] 164s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 164s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 164s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 164s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 164s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 164s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 164s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 164s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 164s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-2 [147 kB] 164s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 gtk-update-icon-cache arm64 4.18.2+ds-1 [52.8 kB] 164s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 hicolor-icon-theme all 0.18-2 [13.3 kB] 164s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 adwaita-icon-theme all 48.0-1 [578 kB] 164s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 at-spi2-common all 2.56.0-2 [9108 B] 164s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 164s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 164s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 164s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2.1ubuntu1 [37.7 kB] 164s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2.1ubuntu1 [144 kB] 164s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 164s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 164s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 164s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 164s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 164s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-8 [624 kB] 164s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-8 [4824 B] 164s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 164s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 164s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-19ubuntu1 [10.6 MB] 164s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-19ubuntu1 [1030 B] 164s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 164s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 164s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libdconf1 arm64 0.40.0-5 [40.0 kB] 164s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 dconf-service arm64 0.40.0-5 [27.1 kB] 164s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 dconf-gsettings-backend arm64 0.40.0-5 [22.3 kB] 164s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2.1ubuntu1 [191 kB] 164s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 164s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.3-1 [171 kB] 164s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250319-1ubuntu1 [44.3 kB] 165s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250319-1ubuntu1 [147 kB] 165s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250319-1ubuntu1 [28.0 kB] 165s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250319-1ubuntu1 [2922 kB] 165s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250319-1ubuntu1 [1318 kB] 165s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250319-1ubuntu1 [2693 kB] 165s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250319-1ubuntu1 [1178 kB] 165s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250319-1ubuntu1 [1641 kB] 165s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-19ubuntu1 [2593 kB] 165s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-19ubuntu1 [20.9 MB] 166s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-19ubuntu1 [528 kB] 166s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 166s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 166s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-19ubuntu1 [2501 kB] 166s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-19ubuntu1 [12.1 MB] 167s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-19ubuntu1 [22.2 kB] 167s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 167s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 167s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 167s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 libann-cctbx0 arm64 1.1.2+doc-9build1 [32.8 kB] 167s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 libann-cctbx-dev arm64 1.1.2+doc-9build1 [45.1 kB] 167s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 libantlr3c-3.4-0 arm64 3.4+dfsg-4build2 [45.7 kB] 167s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 libatk1.0-0t64 arm64 2.56.0-2 [55.4 kB] 167s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 libxi6 arm64 2:1.8.2-1 [32.4 kB] 167s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libatspi2.0-0t64 arm64 2.56.0-2 [84.5 kB] 167s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libatk-bridge2.0-0t64 arm64 2.56.0-2 [66.7 kB] 167s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-common-data arm64 0.8-16ubuntu2 [31.0 kB] 167s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-common3 arm64 0.8-16ubuntu2 [22.9 kB] 167s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-client3 arm64 0.8-16ubuntu2 [26.9 kB] 167s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-python1.83.0 arm64 1.83.0-4.1ubuntu2 [309 kB] 167s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 libboost-numpy1.83.0 arm64 1.83.0-4.1ubuntu2 [242 kB] 167s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost1.83-dev arm64 1.83.0-4.1ubuntu2 [10.7 MB] 167s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libexpat1-dev arm64 2.6.4-1 [129 kB] 167s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 167s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-dev arm64 3.13.2-2 [5399 kB] 167s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-dev arm64 3.13.2-2 [10.7 kB] 167s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-dev arm64 3.13.2-2 [509 kB] 167s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 168s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 168s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 168s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dev arm64 3.13.2-2 [26.7 kB] 168s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 libboost-python1.83-dev arm64 1.83.0-4.1ubuntu2 [336 kB] 168s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 libboost-python-dev arm64 1.83.0.2ubuntu1 [4516 B] 168s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-thread1.83.0 arm64 1.83.0-4.1ubuntu2 [276 kB] 168s Get:89 http://ftpmaster.internal/ubuntu plucky/universe arm64 libboost-timer1.83.0 arm64 1.83.0-4.1ubuntu2 [242 kB] 168s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 168s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 168s Get:92 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 168s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.4-1 [560 kB] 168s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo-gobject2 arm64 1.18.4-1 [127 kB] 168s Get:95 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 168s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-310 arm64 1.14.5+repack-3 [1331 kB] 168s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcbf1t64 arm64 0.9.7+dfsg1-5build1 [356 kB] 168s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 libccp4-data all 8.0.0-4 [65.2 kB] 168s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 libccp4c0t64 arm64 8.0.0-4 [93.5 kB] 168s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmmdb2-0 arm64 2.0.22-1 [347 kB] 168s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 libccp4f0t64 arm64 8.0.0-4 [202 kB] 168s Get:102 http://ftpmaster.internal/ubuntu plucky/universe arm64 libccp4-dev arm64 8.0.0-4 [42.3 kB] 168s Get:103 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 libcctbx0 arm64 2024.10+ds2+~3.22.1+ds1-4build2 [2016 kB] 168s Get:104 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 libcctbx-dev arm64 2024.10+ds2+~3.22.1+ds1-4build2 [1192 kB] 168s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 168s Get:106 http://ftpmaster.internal/ubuntu plucky/main arm64 libcolord2 arm64 1.4.7-3 [151 kB] 168s Get:107 http://ftpmaster.internal/ubuntu plucky/main arm64 libcups2t64 arm64 2.4.11-0ubuntu2 [274 kB] 168s Get:108 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 168s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 libdouble-conversion3 arm64 3.3.1-1 [38.8 kB] 168s Get:110 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-server0 arm64 1.23.1-3 [36.1 kB] 168s Get:111 http://ftpmaster.internal/ubuntu plucky/main arm64 libx11-xcb1 arm64 2:1.8.10-2 [8020 B] 168s Get:112 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-dri3-0 arm64 1.17.0-2 [7606 B] 168s Get:113 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-present0 arm64 1.17.0-2 [6224 B] 169s Get:114 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-randr0 arm64 1.17.0-2 [18.5 kB] 169s Get:115 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-sync1 arm64 1.17.0-2 [9688 B] 169s Get:116 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-xfixes0 arm64 1.17.0-2 [10.6 kB] 169s Get:117 http://ftpmaster.internal/ubuntu plucky/main arm64 libxshmfence1 arm64 1.3-1build5 [4938 B] 169s Get:118 http://ftpmaster.internal/ubuntu plucky/main arm64 mesa-libgallium arm64 25.0.1-2ubuntu2 [9452 kB] 169s Get:119 http://ftpmaster.internal/ubuntu plucky/main arm64 libgbm1 arm64 25.0.1-2ubuntu2 [33.7 kB] 169s Get:120 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-client0 arm64 1.23.1-3 [27.0 kB] 169s Get:121 http://ftpmaster.internal/ubuntu plucky/main arm64 libegl-mesa0 arm64 25.0.1-2ubuntu2 [122 kB] 169s Get:122 http://ftpmaster.internal/ubuntu plucky/main arm64 libepoxy0 arm64 1.5.10-2 [236 kB] 169s Get:123 http://ftpmaster.internal/ubuntu plucky/main arm64 libvulkan1 arm64 1.4.304.0-1 [158 kB] 169s Get:124 http://ftpmaster.internal/ubuntu plucky/main arm64 libgl1-mesa-dri arm64 25.0.1-2ubuntu2 [35.4 kB] 169s Get:125 http://ftpmaster.internal/ubuntu plucky/main arm64 libglvnd0 arm64 1.7.0-1build1 [60.6 kB] 169s Get:126 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-glx0 arm64 1.17.0-2 [25.5 kB] 169s Get:127 http://ftpmaster.internal/ubuntu plucky/main arm64 libxxf86vm1 arm64 1:1.1.4-1build4 [9130 B] 169s Get:128 http://ftpmaster.internal/ubuntu plucky/main arm64 libglx-mesa0 arm64 25.0.1-2ubuntu2 [151 kB] 169s Get:129 http://ftpmaster.internal/ubuntu plucky/main arm64 libglx0 arm64 1.7.0-1build1 [33.2 kB] 169s Get:130 http://ftpmaster.internal/ubuntu plucky/main arm64 libgl1 arm64 1.7.0-1build1 [106 kB] 169s Get:131 http://ftpmaster.internal/ubuntu plucky/universe arm64 libglew2.2 arm64 2.2.0-4build1 [191 kB] 169s Get:132 http://ftpmaster.internal/ubuntu plucky/universe arm64 libglut3.12 arm64 3.4.0-4 [97.1 kB] 169s Get:133 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 169s Get:134 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 169s Get:135 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 169s Get:136 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 169s Get:137 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.3-1 [238 kB] 169s Get:138 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.3-1 [49.8 kB] 169s Get:139 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.3-1 [27.6 kB] 169s Get:140 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-cursor0 arm64 1.23.1-3 [10.8 kB] 169s Get:141 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-egl1 arm64 1.23.1-3 [6180 B] 169s Get:142 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcomposite1 arm64 1:0.4.6-1 [6626 B] 169s Get:143 http://ftpmaster.internal/ubuntu plucky/main arm64 libxfixes3 arm64 1:6.0.0-2build1 [11.2 kB] 169s Get:144 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcursor1 arm64 1:1.2.3-1 [22.2 kB] 169s Get:145 http://ftpmaster.internal/ubuntu plucky/main arm64 libxdamage1 arm64 1:1.1.6-1build1 [6236 B] 169s Get:146 http://ftpmaster.internal/ubuntu plucky/main arm64 libxinerama1 arm64 2:1.1.4-3build1 [6394 B] 169s Get:147 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrandr2 arm64 2:1.5.4-1 [19.6 kB] 169s Get:148 http://ftpmaster.internal/ubuntu plucky/main arm64 libgtk-3-common all 3.24.49-2ubuntu1 [1424 kB] 169s Get:149 http://ftpmaster.internal/ubuntu plucky/main arm64 libgtk-3-0t64 arm64 3.24.49-2ubuntu1 [2918 kB] 169s Get:150 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [59.8 kB] 169s Get:151 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 169s Get:152 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 169s Get:153 http://ftpmaster.internal/ubuntu plucky/main arm64 libwacom-common all 2.14.0-1 [103 kB] 169s Get:154 http://ftpmaster.internal/ubuntu plucky/main arm64 libwacom9 arm64 2.14.0-1 [26.7 kB] 169s Get:155 http://ftpmaster.internal/ubuntu plucky/main arm64 libinput-bin arm64 1.27.1-1 [23.5 kB] 169s Get:156 http://ftpmaster.internal/ubuntu plucky/main arm64 libmtdev1t64 arm64 1.1.7-1 [14.6 kB] 169s Get:157 http://ftpmaster.internal/ubuntu plucky/main arm64 libinput10 arm64 1.27.1-1 [136 kB] 169s Get:158 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 169s Get:159 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 170s Get:160 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 170s Get:161 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmd4c0 arm64 0.5.2-2 [42.4 kB] 170s Get:162 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnetcdf22 arm64 1:4.9.3-1 [504 kB] 170s Get:163 http://ftpmaster.internal/ubuntu plucky/main arm64 libnotify4 arm64 0.8.4-1 [26.5 kB] 170s Get:164 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-16-0 arm64 10.45-1 [222 kB] 170s Get:165 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-32-0 arm64 10.45-1 [210 kB] 170s Get:166 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 170s Get:167 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5core5t64 arm64 5.15.15+dfsg-4ubuntu1 [1999 kB] 170s Get:168 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5dbus5t64 arm64 5.15.15+dfsg-4ubuntu1 [222 kB] 170s Get:169 http://ftpmaster.internal/ubuntu plucky/main arm64 libegl1 arm64 1.7.0-1build1 [29.5 kB] 170s Get:170 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5network5t64 arm64 5.15.15+dfsg-4ubuntu1 [735 kB] 170s Get:171 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 170s Get:172 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-icccm4 arm64 0.4.2-1 [10.9 kB] 170s Get:173 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-util1 arm64 0.4.1-1 [10.9 kB] 170s Get:174 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-image0 arm64 0.4.0-2build1 [10.8 kB] 170s Get:175 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-keysyms1 arm64 0.4.1-1 [8802 B] 170s Get:176 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render-util0 arm64 0.3.10-1 [10.5 kB] 170s Get:177 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shape0 arm64 1.17.0-2 [6246 B] 170s Get:178 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-xinerama0 arm64 1.17.0-2 [5590 B] 170s Get:179 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-xinput0 arm64 1.17.0-2 [34.2 kB] 170s Get:180 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-xkb1 arm64 1.17.0-2 [32.5 kB] 170s Get:181 http://ftpmaster.internal/ubuntu plucky/main arm64 libxkbcommon-x11-0 arm64 1.7.0-2 [13.8 kB] 170s Get:182 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5gui5t64 arm64 5.15.15+dfsg-4ubuntu1 [3680 kB] 170s Get:183 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5widgets5t64 arm64 5.15.15+dfsg-4ubuntu1 [2568 kB] 170s Get:184 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5xml5t64 arm64 5.15.15+dfsg-4ubuntu1 [124 kB] 170s Get:185 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5designer5 arm64 5.15.15-6build1 [2840 kB] 170s Get:186 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5sql5t64 arm64 5.15.15+dfsg-4ubuntu1 [123 kB] 170s Get:187 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5help5 arm64 5.15.15-6build1 [165 kB] 170s Get:188 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5opengl5t64 arm64 5.15.15+dfsg-4ubuntu1 [149 kB] 170s Get:189 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5printsupport5t64 arm64 5.15.15+dfsg-4ubuntu1 [209 kB] 170s Get:190 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5test5t64 arm64 5.15.15+dfsg-4ubuntu1 [144 kB] 170s Get:191 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 170s Get:192 http://ftpmaster.internal/ubuntu plucky/universe arm64 libssm2 arm64 1.4.0-2build1 [83.8 kB] 170s Get:193 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 170s Get:194 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 170s Get:195 http://ftpmaster.internal/ubuntu plucky/universe arm64 libwxbase3.2-1t64 arm64 3.2.6+dfsg-2ubuntu1 [870 kB] 170s Get:196 http://ftpmaster.internal/ubuntu plucky/main arm64 libxtst6 arm64 2:1.2.5-1 [13.2 kB] 170s Get:197 http://ftpmaster.internal/ubuntu plucky/universe arm64 libwxgtk3.2-1t64 arm64 3.2.6+dfsg-2ubuntu1 [4426 kB] 170s Get:198 http://ftpmaster.internal/ubuntu plucky/universe arm64 libwxgtk-gl3.2-1t64 arm64 3.2.6+dfsg-2ubuntu1 [52.8 kB] 170s Get:199 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu4 [168 kB] 170s Get:200 http://ftpmaster.internal/ubuntu plucky/universe arm64 pymol-data all 3.1.0+dfsg-1 [1394 kB] 170s Get:201 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-7build1 [2934 kB] 171s Get:202 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.13.2-2 [886 B] 171s Get:203 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build4 [342 kB] 171s Get:204 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-legacy-cgi all 2.6.2-1 [16.6 kB] 171s Get:205 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pycbf arm64 0.9.7+dfsg1-5build1 [152 kB] 171s Get:206 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.13.0-1 [1126 kB] 171s Get:207 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.13.0-1 [7978 B] 171s Get:208 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-hdf5plugin all 5.0.0-1 [23.1 kB] 171s Get:209 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-4 [80.3 kB] 171s Get:210 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.3-2 [183 kB] 171s Get:211 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 11.1.0-5build1 [463 kB] 171s Get:212 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.2-2 [106 kB] 171s Get:213 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.13.2-1 [9818 B] 171s Get:214 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 11.1.0-5build1 [9892 B] 171s Get:215 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.1-1build1 [182 kB] 171s Get:216 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 171s Get:217 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 171s Get:218 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-7 [90.8 kB] 171s Get:219 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.1-1build1 [1258 kB] 171s Get:220 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.4.0+dfsg-1build1 [27.1 kB] 171s Get:221 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 171s Get:222 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu2 [16.7 MB] 172s Get:223 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 172s Get:224 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-5 [4229 kB] 173s Get:225 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 173s Get:226 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 174s Get:227 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.55.3-2build1 [1466 kB] 174s Get:228 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-3build1 [50.7 kB] 174s Get:229 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 174s Get:230 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-7build1 [17.3 MB] 174s Get:231 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 174s Get:232 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mrcfile all 1.5.4-2 [116 kB] 174s Get:233 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-natsort all 8.0.2-2 [33.8 kB] 174s Get:234 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-flexcache all 0.3-2 [13.4 kB] 174s Get:235 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-flexparser all 0.4-1 [43.8 kB] 174s Get:236 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pint all 0.24.4-1 [203 kB] 174s Get:237 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-nxmx all 0.0.4-1 [16.4 kB] 174s Get:238 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ordered-set all 4.1.0-1 [9778 B] 174s Get:239 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-procrunner all 2.3.3-2 [12.0 kB] 174s Get:240 http://ftpmaster.internal/ubuntu plucky/main arm64 libopengl0 arm64 1.7.0-1build1 [35.1 kB] 174s Get:241 http://ftpmaster.internal/ubuntu plucky/main arm64 libglu1-mesa arm64 9.0.2-1.1build1 [139 kB] 174s Get:242 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-opengl all 3.1.9+dfsg-1syncable1 [631 kB] 174s Get:243 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyqt5.sip arm64 12.17.0-1build1 [67.6 kB] 174s Get:244 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyqt5 arm64 5.15.11+dfsg-2 [2580 kB] 174s Get:245 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyqt5.qtopengl arm64 5.15.11+dfsg-2 [119 kB] 174s Get:246 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pymol arm64 3.1.0+dfsg-1 [3999 kB] 174s Get:247 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.17.0-1 [13.2 kB] 174s Get:248 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tqdm all 4.67.1-2 [92.5 kB] 174s Get:249 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-wxgtk4.0 arm64 4.2.2+dfsg-3build1 [7689 kB] 175s Get:250 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-cctbx arm64 2024.10+ds2+~3.22.1+ds1-4build2 [28.3 MB] 175s Get:251 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 175s Get:252 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 175s Get:253 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.5-1 [252 kB] 176s Fetched 244 MB in 12s (19.5 MB/s) 176s Selecting previously unselected package fonts-lato. 176s (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 ... 117732 files and directories currently installed.) 176s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ... 176s Unpacking fonts-lato (2.015-1) ... 177s Selecting previously unselected package python3-numpy-dev:arm64. 177s Preparing to unpack .../001-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 177s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 177s Selecting previously unselected package libblas3:arm64. 177s Preparing to unpack .../002-libblas3_3.12.1-2_arm64.deb ... 177s Unpacking libblas3:arm64 (3.12.1-2) ... 177s Selecting previously unselected package libgfortran5:arm64. 177s Preparing to unpack .../003-libgfortran5_15-20250319-1ubuntu1_arm64.deb ... 177s Unpacking libgfortran5:arm64 (15-20250319-1ubuntu1) ... 177s Selecting previously unselected package liblapack3:arm64. 177s Preparing to unpack .../004-liblapack3_3.12.1-2_arm64.deb ... 177s Unpacking liblapack3:arm64 (3.12.1-2) ... 177s Selecting previously unselected package python3-numpy. 177s Preparing to unpack .../005-python3-numpy_1%3a2.2.3+ds-5_arm64.deb ... 177s Unpacking python3-numpy (1:2.2.3+ds-5) ... 177s Selecting previously unselected package libgdk-pixbuf2.0-common. 177s Preparing to unpack .../006-libgdk-pixbuf2.0-common_2.42.12+dfsg-2_all.deb ... 177s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... 177s Selecting previously unselected package libjpeg-turbo8:arm64. 177s Preparing to unpack .../007-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 177s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 177s Selecting previously unselected package libjpeg8:arm64. 177s Preparing to unpack .../008-libjpeg8_8c-2ubuntu11_arm64.deb ... 177s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 177s Selecting previously unselected package libdeflate0:arm64. 177s Preparing to unpack .../009-libdeflate0_1.23-1_arm64.deb ... 177s Unpacking libdeflate0:arm64 (1.23-1) ... 177s Selecting previously unselected package libjbig0:arm64. 177s Preparing to unpack .../010-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 177s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 177s Selecting previously unselected package liblerc4:arm64. 177s Preparing to unpack .../011-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 177s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 177s Selecting previously unselected package libsharpyuv0:arm64. 177s Preparing to unpack .../012-libsharpyuv0_1.5.0-0.1_arm64.deb ... 177s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 178s Selecting previously unselected package libwebp7:arm64. 178s Preparing to unpack .../013-libwebp7_1.5.0-0.1_arm64.deb ... 178s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 178s Selecting previously unselected package libtiff6:arm64. 178s Preparing to unpack .../014-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 178s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 178s Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64. 178s Preparing to unpack .../015-libgdk-pixbuf-2.0-0_2.42.12+dfsg-2_arm64.deb ... 178s Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-2) ... 178s Selecting previously unselected package gtk-update-icon-cache. 178s Preparing to unpack .../016-gtk-update-icon-cache_4.18.2+ds-1_arm64.deb ... 178s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 178s 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. 178s Unpacking gtk-update-icon-cache (4.18.2+ds-1) ... 178s Selecting previously unselected package hicolor-icon-theme. 178s Preparing to unpack .../017-hicolor-icon-theme_0.18-2_all.deb ... 178s Unpacking hicolor-icon-theme (0.18-2) ... 178s Selecting previously unselected package adwaita-icon-theme. 178s Preparing to unpack .../018-adwaita-icon-theme_48.0-1_all.deb ... 178s Unpacking adwaita-icon-theme (48.0-1) ... 178s Selecting previously unselected package at-spi2-common. 178s Preparing to unpack .../019-at-spi2-common_2.56.0-2_all.deb ... 178s Unpacking at-spi2-common (2.56.0-2) ... 178s Selecting previously unselected package libtcl8.6:arm64. 178s Preparing to unpack .../020-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 178s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... 178s Selecting previously unselected package fonts-dejavu-mono. 178s Preparing to unpack .../021-fonts-dejavu-mono_2.37-8_all.deb ... 178s Unpacking fonts-dejavu-mono (2.37-8) ... 178s Selecting previously unselected package fonts-dejavu-core. 178s Preparing to unpack .../022-fonts-dejavu-core_2.37-8_all.deb ... 178s Unpacking fonts-dejavu-core (2.37-8) ... 178s Selecting previously unselected package fontconfig-config. 178s Preparing to unpack .../023-fontconfig-config_2.15.0-2.1ubuntu1_arm64.deb ... 179s Unpacking fontconfig-config (2.15.0-2.1ubuntu1) ... 179s Selecting previously unselected package libfontconfig1:arm64. 179s Preparing to unpack .../024-libfontconfig1_2.15.0-2.1ubuntu1_arm64.deb ... 179s Unpacking libfontconfig1:arm64 (2.15.0-2.1ubuntu1) ... 179s Selecting previously unselected package libxrender1:arm64. 179s Preparing to unpack .../025-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 179s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 179s Selecting previously unselected package libxft2:arm64. 179s Preparing to unpack .../026-libxft2_2.3.6-1build1_arm64.deb ... 179s Unpacking libxft2:arm64 (2.3.6-1build1) ... 179s Selecting previously unselected package x11-common. 179s Preparing to unpack .../027-x11-common_1%3a7.7+23ubuntu3_all.deb ... 179s Unpacking x11-common (1:7.7+23ubuntu3) ... 179s Selecting previously unselected package libxss1:arm64. 179s Preparing to unpack .../028-libxss1_1%3a1.2.3-1build3_arm64.deb ... 179s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 179s Selecting previously unselected package libtk8.6:arm64. 179s Preparing to unpack .../029-libtk8.6_8.6.16-1_arm64.deb ... 179s Unpacking libtk8.6:arm64 (8.6.16-1) ... 179s Selecting previously unselected package tk8.6-blt2.5. 179s Preparing to unpack .../030-tk8.6-blt2.5_2.5.3+dfsg-8_arm64.deb ... 179s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 179s Selecting previously unselected package blt. 179s Preparing to unpack .../031-blt_2.5.3+dfsg-8_arm64.deb ... 179s Unpacking blt (2.5.3+dfsg-8) ... 179s Selecting previously unselected package libisl23:arm64. 179s Preparing to unpack .../032-libisl23_0.27-1_arm64.deb ... 179s Unpacking libisl23:arm64 (0.27-1) ... 179s Selecting previously unselected package libmpc3:arm64. 179s Preparing to unpack .../033-libmpc3_1.3.1-1build2_arm64.deb ... 179s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 179s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 179s Preparing to unpack .../034-cpp-14-aarch64-linux-gnu_14.2.0-19ubuntu1_arm64.deb ... 179s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-19ubuntu1) ... 180s Selecting previously unselected package cpp-14. 180s Preparing to unpack .../035-cpp-14_14.2.0-19ubuntu1_arm64.deb ... 180s Unpacking cpp-14 (14.2.0-19ubuntu1) ... 180s Selecting previously unselected package cpp-aarch64-linux-gnu. 180s Preparing to unpack .../036-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 180s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 180s Selecting previously unselected package cpp. 180s Preparing to unpack .../037-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ... 180s Unpacking cpp (4:14.2.0-1ubuntu1) ... 180s Selecting previously unselected package libdconf1:arm64. 180s Preparing to unpack .../038-libdconf1_0.40.0-5_arm64.deb ... 180s Unpacking libdconf1:arm64 (0.40.0-5) ... 180s Selecting previously unselected package dconf-service. 180s Preparing to unpack .../039-dconf-service_0.40.0-5_arm64.deb ... 180s Unpacking dconf-service (0.40.0-5) ... 180s Selecting previously unselected package dconf-gsettings-backend:arm64. 180s Preparing to unpack .../040-dconf-gsettings-backend_0.40.0-5_arm64.deb ... 180s Unpacking dconf-gsettings-backend:arm64 (0.40.0-5) ... 180s Selecting previously unselected package fontconfig. 180s Preparing to unpack .../041-fontconfig_2.15.0-2.1ubuntu1_arm64.deb ... 180s Unpacking fontconfig (2.15.0-2.1ubuntu1) ... 180s Selecting previously unselected package fonts-font-awesome. 180s Preparing to unpack .../042-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 180s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 180s Selecting previously unselected package fonts-lyx. 180s Preparing to unpack .../043-fonts-lyx_2.4.3-1_all.deb ... 180s Unpacking fonts-lyx (2.4.3-1) ... 180s Selecting previously unselected package libcc1-0:arm64. 180s Preparing to unpack .../044-libcc1-0_15-20250319-1ubuntu1_arm64.deb ... 180s Unpacking libcc1-0:arm64 (15-20250319-1ubuntu1) ... 180s Selecting previously unselected package libgomp1:arm64. 180s Preparing to unpack .../045-libgomp1_15-20250319-1ubuntu1_arm64.deb ... 180s Unpacking libgomp1:arm64 (15-20250319-1ubuntu1) ... 180s Selecting previously unselected package libitm1:arm64. 180s Preparing to unpack .../046-libitm1_15-20250319-1ubuntu1_arm64.deb ... 180s Unpacking libitm1:arm64 (15-20250319-1ubuntu1) ... 180s Selecting previously unselected package libasan8:arm64. 180s Preparing to unpack .../047-libasan8_15-20250319-1ubuntu1_arm64.deb ... 180s Unpacking libasan8:arm64 (15-20250319-1ubuntu1) ... 180s Selecting previously unselected package liblsan0:arm64. 181s Preparing to unpack .../048-liblsan0_15-20250319-1ubuntu1_arm64.deb ... 181s Unpacking liblsan0:arm64 (15-20250319-1ubuntu1) ... 181s Selecting previously unselected package libtsan2:arm64. 181s Preparing to unpack .../049-libtsan2_15-20250319-1ubuntu1_arm64.deb ... 181s Unpacking libtsan2:arm64 (15-20250319-1ubuntu1) ... 181s Selecting previously unselected package libubsan1:arm64. 181s Preparing to unpack .../050-libubsan1_15-20250319-1ubuntu1_arm64.deb ... 181s Unpacking libubsan1:arm64 (15-20250319-1ubuntu1) ... 181s Selecting previously unselected package libhwasan0:arm64. 181s Preparing to unpack .../051-libhwasan0_15-20250319-1ubuntu1_arm64.deb ... 181s Unpacking libhwasan0:arm64 (15-20250319-1ubuntu1) ... 181s Selecting previously unselected package libgcc-14-dev:arm64. 181s Preparing to unpack .../052-libgcc-14-dev_14.2.0-19ubuntu1_arm64.deb ... 181s Unpacking libgcc-14-dev:arm64 (14.2.0-19ubuntu1) ... 181s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 181s Preparing to unpack .../053-gcc-14-aarch64-linux-gnu_14.2.0-19ubuntu1_arm64.deb ... 181s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-19ubuntu1) ... 182s Selecting previously unselected package gcc-14. 182s Preparing to unpack .../054-gcc-14_14.2.0-19ubuntu1_arm64.deb ... 182s Unpacking gcc-14 (14.2.0-19ubuntu1) ... 182s Selecting previously unselected package gcc-aarch64-linux-gnu. 182s Preparing to unpack .../055-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 182s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 182s Selecting previously unselected package gcc. 182s Preparing to unpack .../056-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ... 182s Unpacking gcc (4:14.2.0-1ubuntu1) ... 182s Selecting previously unselected package libstdc++-14-dev:arm64. 182s Preparing to unpack .../057-libstdc++-14-dev_14.2.0-19ubuntu1_arm64.deb ... 182s Unpacking libstdc++-14-dev:arm64 (14.2.0-19ubuntu1) ... 182s Selecting previously unselected package g++-14-aarch64-linux-gnu. 182s Preparing to unpack .../058-g++-14-aarch64-linux-gnu_14.2.0-19ubuntu1_arm64.deb ... 182s Unpacking g++-14-aarch64-linux-gnu (14.2.0-19ubuntu1) ... 182s Selecting previously unselected package g++-14. 182s Preparing to unpack .../059-g++-14_14.2.0-19ubuntu1_arm64.deb ... 182s Unpacking g++-14 (14.2.0-19ubuntu1) ... 182s Selecting previously unselected package g++-aarch64-linux-gnu. 182s Preparing to unpack .../060-g++-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 182s Unpacking g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 182s Selecting previously unselected package g++. 182s Preparing to unpack .../061-g++_4%3a14.2.0-1ubuntu1_arm64.deb ... 182s Unpacking g++ (4:14.2.0-1ubuntu1) ... 182s Selecting previously unselected package libaec0:arm64. 182s Preparing to unpack .../062-libaec0_1.1.3-1_arm64.deb ... 182s Unpacking libaec0:arm64 (1.1.3-1) ... 182s Selecting previously unselected package libann-cctbx0. 182s Preparing to unpack .../063-libann-cctbx0_1.1.2+doc-9build1_arm64.deb ... 182s Unpacking libann-cctbx0 (1.1.2+doc-9build1) ... 183s Selecting previously unselected package libann-cctbx-dev. 183s Preparing to unpack .../064-libann-cctbx-dev_1.1.2+doc-9build1_arm64.deb ... 183s Unpacking libann-cctbx-dev (1.1.2+doc-9build1) ... 183s Selecting previously unselected package libantlr3c-3.4-0:arm64. 183s Preparing to unpack .../065-libantlr3c-3.4-0_3.4+dfsg-4build2_arm64.deb ... 183s Unpacking libantlr3c-3.4-0:arm64 (3.4+dfsg-4build2) ... 183s Selecting previously unselected package libatk1.0-0t64:arm64. 183s Preparing to unpack .../066-libatk1.0-0t64_2.56.0-2_arm64.deb ... 183s Unpacking libatk1.0-0t64:arm64 (2.56.0-2) ... 183s Selecting previously unselected package libxi6:arm64. 183s Preparing to unpack .../067-libxi6_2%3a1.8.2-1_arm64.deb ... 183s Unpacking libxi6:arm64 (2:1.8.2-1) ... 183s Selecting previously unselected package libatspi2.0-0t64:arm64. 183s Preparing to unpack .../068-libatspi2.0-0t64_2.56.0-2_arm64.deb ... 183s Unpacking libatspi2.0-0t64:arm64 (2.56.0-2) ... 183s Selecting previously unselected package libatk-bridge2.0-0t64:arm64. 183s Preparing to unpack .../069-libatk-bridge2.0-0t64_2.56.0-2_arm64.deb ... 183s Unpacking libatk-bridge2.0-0t64:arm64 (2.56.0-2) ... 183s Selecting previously unselected package libavahi-common-data:arm64. 183s Preparing to unpack .../070-libavahi-common-data_0.8-16ubuntu2_arm64.deb ... 183s Unpacking libavahi-common-data:arm64 (0.8-16ubuntu2) ... 183s Selecting previously unselected package libavahi-common3:arm64. 183s Preparing to unpack .../071-libavahi-common3_0.8-16ubuntu2_arm64.deb ... 183s Unpacking libavahi-common3:arm64 (0.8-16ubuntu2) ... 183s Selecting previously unselected package libavahi-client3:arm64. 183s Preparing to unpack .../072-libavahi-client3_0.8-16ubuntu2_arm64.deb ... 183s Unpacking libavahi-client3:arm64 (0.8-16ubuntu2) ... 183s Selecting previously unselected package libboost-python1.83.0. 183s Preparing to unpack .../073-libboost-python1.83.0_1.83.0-4.1ubuntu2_arm64.deb ... 183s Unpacking libboost-python1.83.0 (1.83.0-4.1ubuntu2) ... 183s Selecting previously unselected package libboost-numpy1.83.0. 183s Preparing to unpack .../074-libboost-numpy1.83.0_1.83.0-4.1ubuntu2_arm64.deb ... 183s Unpacking libboost-numpy1.83.0 (1.83.0-4.1ubuntu2) ... 183s Selecting previously unselected package libboost1.83-dev:arm64. 183s Preparing to unpack .../075-libboost1.83-dev_1.83.0-4.1ubuntu2_arm64.deb ... 183s Unpacking libboost1.83-dev:arm64 (1.83.0-4.1ubuntu2) ... 185s Selecting previously unselected package libexpat1-dev:arm64. 185s Preparing to unpack .../076-libexpat1-dev_2.6.4-1_arm64.deb ... 185s Unpacking libexpat1-dev:arm64 (2.6.4-1) ... 185s Selecting previously unselected package zlib1g-dev:arm64. 185s Preparing to unpack .../077-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 185s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 185s Selecting previously unselected package libpython3.13-dev:arm64. 185s Preparing to unpack .../078-libpython3.13-dev_3.13.2-2_arm64.deb ... 185s Unpacking libpython3.13-dev:arm64 (3.13.2-2) ... 186s Selecting previously unselected package libpython3-dev:arm64. 186s Preparing to unpack .../079-libpython3-dev_3.13.2-2_arm64.deb ... 186s Unpacking libpython3-dev:arm64 (3.13.2-2) ... 186s Selecting previously unselected package python3.13-dev. 186s Preparing to unpack .../080-python3.13-dev_3.13.2-2_arm64.deb ... 186s Unpacking python3.13-dev (3.13.2-2) ... 186s Selecting previously unselected package libjs-jquery. 186s Preparing to unpack .../081-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 186s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 186s Selecting previously unselected package libjs-underscore. 186s Preparing to unpack .../082-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 186s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 186s Selecting previously unselected package libjs-sphinxdoc. 186s Preparing to unpack .../083-libjs-sphinxdoc_8.1.3-5_all.deb ... 186s Unpacking libjs-sphinxdoc (8.1.3-5) ... 186s Selecting previously unselected package python3-dev. 186s Preparing to unpack .../084-python3-dev_3.13.2-2_arm64.deb ... 186s Unpacking python3-dev (3.13.2-2) ... 186s Selecting previously unselected package libboost-python1.83-dev. 186s Preparing to unpack .../085-libboost-python1.83-dev_1.83.0-4.1ubuntu2_arm64.deb ... 186s Unpacking libboost-python1.83-dev (1.83.0-4.1ubuntu2) ... 186s Selecting previously unselected package libboost-python-dev. 186s Preparing to unpack .../086-libboost-python-dev_1.83.0.2ubuntu1_arm64.deb ... 186s Unpacking libboost-python-dev (1.83.0.2ubuntu1) ... 186s Selecting previously unselected package libboost-thread1.83.0:arm64. 186s Preparing to unpack .../087-libboost-thread1.83.0_1.83.0-4.1ubuntu2_arm64.deb ... 186s Unpacking libboost-thread1.83.0:arm64 (1.83.0-4.1ubuntu2) ... 186s Selecting previously unselected package libboost-timer1.83.0:arm64. 186s Preparing to unpack .../088-libboost-timer1.83.0_1.83.0-4.1ubuntu2_arm64.deb ... 186s Unpacking libboost-timer1.83.0:arm64 (1.83.0-4.1ubuntu2) ... 186s Selecting previously unselected package libpixman-1-0:arm64. 186s Preparing to unpack .../089-libpixman-1-0_0.44.0-3_arm64.deb ... 186s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 186s Selecting previously unselected package libxcb-render0:arm64. 186s Preparing to unpack .../090-libxcb-render0_1.17.0-2_arm64.deb ... 186s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 186s Selecting previously unselected package libxcb-shm0:arm64. 186s Preparing to unpack .../091-libxcb-shm0_1.17.0-2_arm64.deb ... 186s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 186s Selecting previously unselected package libcairo2:arm64. 186s Preparing to unpack .../092-libcairo2_1.18.4-1_arm64.deb ... 186s Unpacking libcairo2:arm64 (1.18.4-1) ... 187s Selecting previously unselected package libcairo-gobject2:arm64. 187s Preparing to unpack .../093-libcairo-gobject2_1.18.4-1_arm64.deb ... 187s Unpacking libcairo-gobject2:arm64 (1.18.4-1) ... 187s Selecting previously unselected package libsz2:arm64. 187s Preparing to unpack .../094-libsz2_1.1.3-1_arm64.deb ... 187s Unpacking libsz2:arm64 (1.1.3-1) ... 187s Selecting previously unselected package libhdf5-310:arm64. 187s Preparing to unpack .../095-libhdf5-310_1.14.5+repack-3_arm64.deb ... 187s Unpacking libhdf5-310:arm64 (1.14.5+repack-3) ... 187s Selecting previously unselected package libcbf1t64:arm64. 187s Preparing to unpack .../096-libcbf1t64_0.9.7+dfsg1-5build1_arm64.deb ... 187s Unpacking libcbf1t64:arm64 (0.9.7+dfsg1-5build1) ... 187s Selecting previously unselected package libccp4-data. 187s Preparing to unpack .../097-libccp4-data_8.0.0-4_all.deb ... 187s Unpacking libccp4-data (8.0.0-4) ... 187s Selecting previously unselected package libccp4c0t64:arm64. 187s Preparing to unpack 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libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4build2) ... 187s Selecting previously unselected package liblcms2-2:arm64. 187s Preparing to unpack .../104-liblcms2-2_2.16-2_arm64.deb ... 187s Unpacking liblcms2-2:arm64 (2.16-2) ... 187s Selecting previously unselected package libcolord2:arm64. 187s Preparing to unpack .../105-libcolord2_1.4.7-3_arm64.deb ... 187s Unpacking libcolord2:arm64 (1.4.7-3) ... 188s Selecting previously unselected package libcups2t64:arm64. 188s Preparing to unpack .../106-libcups2t64_2.4.11-0ubuntu2_arm64.deb ... 188s Unpacking libcups2t64:arm64 (2.4.11-0ubuntu2) ... 188s Selecting previously unselected package libdatrie1:arm64. 188s Preparing to unpack .../107-libdatrie1_0.2.13-3build1_arm64.deb ... 188s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 188s Selecting previously unselected package libdouble-conversion3:arm64. 188s Preparing to unpack .../108-libdouble-conversion3_3.3.1-1_arm64.deb ... 188s Unpacking libdouble-conversion3:arm64 (3.3.1-1) ... 188s Selecting previously unselected package libwayland-server0:arm64. 188s Preparing to unpack .../109-libwayland-server0_1.23.1-3_arm64.deb ... 188s Unpacking libwayland-server0:arm64 (1.23.1-3) ... 188s Selecting previously unselected package libx11-xcb1:arm64. 188s Preparing to unpack .../110-libx11-xcb1_2%3a1.8.10-2_arm64.deb ... 188s Unpacking libx11-xcb1:arm64 (2:1.8.10-2) ... 188s Selecting previously unselected package libxcb-dri3-0:arm64. 188s Preparing to unpack .../111-libxcb-dri3-0_1.17.0-2_arm64.deb ... 188s Unpacking libxcb-dri3-0:arm64 (1.17.0-2) ... 188s Selecting previously unselected package libxcb-present0:arm64. 188s Preparing to unpack .../112-libxcb-present0_1.17.0-2_arm64.deb ... 188s Unpacking libxcb-present0:arm64 (1.17.0-2) ... 188s Selecting previously unselected package libxcb-randr0:arm64. 188s Preparing to unpack .../113-libxcb-randr0_1.17.0-2_arm64.deb ... 188s Unpacking libxcb-randr0:arm64 (1.17.0-2) ... 188s Selecting previously unselected package libxcb-sync1:arm64. 188s Preparing to unpack .../114-libxcb-sync1_1.17.0-2_arm64.deb ... 188s Unpacking libxcb-sync1:arm64 (1.17.0-2) ... 188s Selecting previously unselected package libxcb-xfixes0:arm64. 188s Preparing to unpack .../115-libxcb-xfixes0_1.17.0-2_arm64.deb ... 188s Unpacking libxcb-xfixes0:arm64 (1.17.0-2) ... 188s Selecting previously unselected package libxshmfence1:arm64. 188s Preparing to unpack .../116-libxshmfence1_1.3-1build5_arm64.deb ... 188s Unpacking libxshmfence1:arm64 (1.3-1build5) ... 188s Selecting previously unselected package mesa-libgallium:arm64. 188s Preparing to unpack .../117-mesa-libgallium_25.0.1-2ubuntu2_arm64.deb ... 188s Unpacking mesa-libgallium:arm64 (25.0.1-2ubuntu2) ... 188s Selecting previously unselected package libgbm1:arm64. 189s Preparing to unpack .../118-libgbm1_25.0.1-2ubuntu2_arm64.deb ... 189s Unpacking libgbm1:arm64 (25.0.1-2ubuntu2) ... 189s Selecting previously unselected package libwayland-client0:arm64. 189s Preparing to unpack .../119-libwayland-client0_1.23.1-3_arm64.deb ... 189s Unpacking libwayland-client0:arm64 (1.23.1-3) ... 189s Selecting previously unselected package libegl-mesa0:arm64. 189s Preparing to unpack .../120-libegl-mesa0_25.0.1-2ubuntu2_arm64.deb ... 189s Unpacking libegl-mesa0:arm64 (25.0.1-2ubuntu2) ... 189s Selecting previously unselected package libepoxy0:arm64. 189s Preparing to unpack .../121-libepoxy0_1.5.10-2_arm64.deb ... 189s Unpacking libepoxy0:arm64 (1.5.10-2) ... 189s Selecting previously unselected package libvulkan1:arm64. 189s Preparing to unpack .../122-libvulkan1_1.4.304.0-1_arm64.deb ... 189s Unpacking libvulkan1:arm64 (1.4.304.0-1) ... 189s Selecting previously unselected package libgl1-mesa-dri:arm64. 189s Preparing to unpack .../123-libgl1-mesa-dri_25.0.1-2ubuntu2_arm64.deb ... 189s Unpacking libgl1-mesa-dri:arm64 (25.0.1-2ubuntu2) ... 189s Selecting previously unselected package libglvnd0:arm64. 189s Preparing to unpack .../124-libglvnd0_1.7.0-1build1_arm64.deb ... 189s Unpacking libglvnd0:arm64 (1.7.0-1build1) ... 189s Selecting previously unselected package libxcb-glx0:arm64. 189s Preparing to unpack .../125-libxcb-glx0_1.17.0-2_arm64.deb ... 189s Unpacking libxcb-glx0:arm64 (1.17.0-2) ... 189s Selecting previously unselected package libxxf86vm1:arm64. 189s Preparing to unpack .../126-libxxf86vm1_1%3a1.1.4-1build4_arm64.deb ... 189s Unpacking libxxf86vm1:arm64 (1:1.1.4-1build4) ... 189s Selecting previously unselected package libglx-mesa0:arm64. 189s Preparing to unpack .../127-libglx-mesa0_25.0.1-2ubuntu2_arm64.deb ... 189s Unpacking libglx-mesa0:arm64 (25.0.1-2ubuntu2) ... 189s Selecting previously unselected package libglx0:arm64. 189s Preparing to unpack .../128-libglx0_1.7.0-1build1_arm64.deb ... 189s Unpacking libglx0:arm64 (1.7.0-1build1) ... 189s Selecting previously unselected package libgl1:arm64. 189s Preparing to unpack .../129-libgl1_1.7.0-1build1_arm64.deb ... 189s Unpacking libgl1:arm64 (1.7.0-1build1) ... 189s Selecting previously unselected package libglew2.2:arm64. 189s Preparing to unpack .../130-libglew2.2_2.2.0-4build1_arm64.deb ... 189s Unpacking libglew2.2:arm64 (2.2.0-4build1) ... 189s Selecting previously unselected package libglut3.12:arm64. 189s Preparing to unpack .../131-libglut3.12_3.4.0-4_arm64.deb ... 189s Unpacking libglut3.12:arm64 (3.4.0-4) ... 189s Selecting previously unselected package libgraphite2-3:arm64. 189s Preparing to unpack .../132-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 189s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 189s Selecting previously unselected package libharfbuzz0b:arm64. 189s Preparing to unpack .../133-libharfbuzz0b_10.2.0-1_arm64.deb ... 189s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 189s Selecting previously unselected package libthai-data. 189s Preparing to unpack .../134-libthai-data_0.1.29-2build1_all.deb ... 189s Unpacking libthai-data (0.1.29-2build1) ... 190s Selecting previously unselected package libthai0:arm64. 190s Preparing to unpack .../135-libthai0_0.1.29-2build1_arm64.deb ... 190s Unpacking libthai0:arm64 (0.1.29-2build1) ... 190s Selecting previously unselected package libpango-1.0-0:arm64. 190s Preparing to unpack .../136-libpango-1.0-0_1.56.3-1_arm64.deb ... 190s Unpacking libpango-1.0-0:arm64 (1.56.3-1) ... 190s Selecting previously unselected package libpangoft2-1.0-0:arm64. 190s Preparing to unpack .../137-libpangoft2-1.0-0_1.56.3-1_arm64.deb ... 190s Unpacking libpangoft2-1.0-0:arm64 (1.56.3-1) ... 190s Selecting previously unselected package libpangocairo-1.0-0:arm64. 190s Preparing to unpack .../138-libpangocairo-1.0-0_1.56.3-1_arm64.deb ... 190s Unpacking libpangocairo-1.0-0:arm64 (1.56.3-1) ... 190s Selecting previously unselected package libwayland-cursor0:arm64. 190s Preparing to unpack .../139-libwayland-cursor0_1.23.1-3_arm64.deb ... 190s Unpacking libwayland-cursor0:arm64 (1.23.1-3) ... 190s Selecting previously unselected package libwayland-egl1:arm64. 190s Preparing to unpack .../140-libwayland-egl1_1.23.1-3_arm64.deb ... 190s Unpacking libwayland-egl1:arm64 (1.23.1-3) ... 190s Selecting previously unselected package libxcomposite1:arm64. 190s Preparing to unpack .../141-libxcomposite1_1%3a0.4.6-1_arm64.deb ... 190s Unpacking libxcomposite1:arm64 (1:0.4.6-1) ... 190s Selecting previously unselected package libxfixes3:arm64. 190s Preparing to unpack .../142-libxfixes3_1%3a6.0.0-2build1_arm64.deb ... 190s Unpacking libxfixes3:arm64 (1:6.0.0-2build1) ... 190s Selecting previously unselected package libxcursor1:arm64. 190s Preparing to unpack .../143-libxcursor1_1%3a1.2.3-1_arm64.deb ... 190s Unpacking libxcursor1:arm64 (1:1.2.3-1) ... 190s Selecting previously unselected package libxdamage1:arm64. 190s Preparing to unpack .../144-libxdamage1_1%3a1.1.6-1build1_arm64.deb ... 190s Unpacking libxdamage1:arm64 (1:1.1.6-1build1) ... 190s Selecting previously unselected package libxinerama1:arm64. 190s Preparing to unpack .../145-libxinerama1_2%3a1.1.4-3build1_arm64.deb ... 190s Unpacking libxinerama1:arm64 (2:1.1.4-3build1) ... 190s Selecting previously unselected package libxrandr2:arm64. 190s Preparing to unpack .../146-libxrandr2_2%3a1.5.4-1_arm64.deb ... 190s Unpacking libxrandr2:arm64 (2:1.5.4-1) ... 190s Selecting previously unselected package libgtk-3-common. 190s Preparing to unpack .../147-libgtk-3-common_3.24.49-2ubuntu1_all.deb ... 190s Unpacking libgtk-3-common (3.24.49-2ubuntu1) ... 190s Selecting previously unselected package libgtk-3-0t64:arm64. 190s Preparing to unpack .../148-libgtk-3-0t64_3.24.49-2ubuntu1_arm64.deb ... 190s Unpacking libgtk-3-0t64:arm64 (3.24.49-2ubuntu1) ... 190s Selecting previously unselected package libhdf5-hl-310:arm64. 190s Preparing to unpack .../149-libhdf5-hl-310_1.14.5+repack-3_arm64.deb ... 190s Unpacking libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 190s Selecting previously unselected package libice6:arm64. 191s Preparing to unpack .../150-libice6_2%3a1.1.1-1_arm64.deb ... 191s Unpacking libice6:arm64 (2:1.1.1-1) ... 191s Selecting previously unselected package libimagequant0:arm64. 191s Preparing to unpack .../151-libimagequant0_2.18.0-1build1_arm64.deb ... 191s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 191s Selecting previously unselected package libwacom-common. 191s Preparing to unpack .../152-libwacom-common_2.14.0-1_all.deb ... 191s Unpacking libwacom-common (2.14.0-1) ... 191s Selecting previously unselected package libwacom9:arm64. 191s Preparing to unpack .../153-libwacom9_2.14.0-1_arm64.deb ... 191s Unpacking libwacom9:arm64 (2.14.0-1) ... 191s Selecting previously unselected package libinput-bin. 191s Preparing to unpack .../154-libinput-bin_1.27.1-1_arm64.deb ... 191s Unpacking libinput-bin (1.27.1-1) ... 191s Selecting previously unselected package libmtdev1t64:arm64. 191s Preparing to unpack .../155-libmtdev1t64_1.1.7-1_arm64.deb ... 191s Unpacking libmtdev1t64:arm64 (1.1.7-1) ... 191s Selecting previously unselected package libinput10:arm64. 191s Preparing to unpack .../156-libinput10_1.27.1-1_arm64.deb ... 191s Unpacking libinput10:arm64 (1.27.1-1) ... 191s Selecting previously unselected package libjs-jquery-ui. 191s Preparing to unpack .../157-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 191s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 191s Selecting previously unselected package liblbfgsb0:arm64. 191s Preparing to unpack .../158-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 191s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 191s Selecting previously unselected package liblzf1:arm64. 191s Preparing to unpack .../159-liblzf1_3.6-4_arm64.deb ... 191s Unpacking liblzf1:arm64 (3.6-4) ... 191s Selecting previously unselected package libmd4c0:arm64. 191s Preparing to unpack .../160-libmd4c0_0.5.2-2_arm64.deb ... 191s Unpacking libmd4c0:arm64 (0.5.2-2) ... 191s Selecting previously unselected package libnetcdf22:arm64. 191s Preparing to unpack .../161-libnetcdf22_1%3a4.9.3-1_arm64.deb ... 191s Unpacking libnetcdf22:arm64 (1:4.9.3-1) ... 191s Selecting previously unselected package libnotify4:arm64. 191s Preparing to unpack .../162-libnotify4_0.8.4-1_arm64.deb ... 191s Unpacking libnotify4:arm64 (0.8.4-1) ... 191s Selecting previously unselected package libpcre2-16-0:arm64. 191s Preparing to unpack .../163-libpcre2-16-0_10.45-1_arm64.deb ... 191s Unpacking libpcre2-16-0:arm64 (10.45-1) ... 191s Selecting previously unselected package libpcre2-32-0:arm64. 191s Preparing to unpack .../164-libpcre2-32-0_10.45-1_arm64.deb ... 191s Unpacking libpcre2-32-0:arm64 (10.45-1) ... 191s Selecting previously unselected package libqhull-r8.0:arm64. 191s Preparing to unpack .../165-libqhull-r8.0_2020.2-6build1_arm64.deb ... 191s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 192s Selecting previously unselected package libqt5core5t64:arm64. 192s Preparing to unpack .../166-libqt5core5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ... 192s Unpacking libqt5core5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 192s Selecting previously unselected package libqt5dbus5t64:arm64. 192s Preparing to unpack .../167-libqt5dbus5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ... 192s Unpacking libqt5dbus5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 192s Selecting previously unselected package libegl1:arm64. 192s Preparing to unpack .../168-libegl1_1.7.0-1build1_arm64.deb ... 192s Unpacking libegl1:arm64 (1.7.0-1build1) ... 192s Selecting previously unselected package libqt5network5t64:arm64. 192s Preparing to unpack .../169-libqt5network5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ... 192s Unpacking libqt5network5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 192s Selecting previously unselected package libsm6:arm64. 192s Preparing to unpack .../170-libsm6_2%3a1.2.4-1_arm64.deb ... 192s Unpacking libsm6:arm64 (2:1.2.4-1) ... 192s Selecting previously unselected package libxcb-icccm4:arm64. 192s Preparing to unpack .../171-libxcb-icccm4_0.4.2-1_arm64.deb ... 192s Unpacking libxcb-icccm4:arm64 (0.4.2-1) ... 192s Selecting previously unselected package libxcb-util1:arm64. 192s Preparing to unpack .../172-libxcb-util1_0.4.1-1_arm64.deb ... 192s Unpacking libxcb-util1:arm64 (0.4.1-1) ... 192s Selecting previously unselected package libxcb-image0:arm64. 192s Preparing to unpack .../173-libxcb-image0_0.4.0-2build1_arm64.deb ... 192s Unpacking libxcb-image0:arm64 (0.4.0-2build1) ... 192s Selecting previously unselected package libxcb-keysyms1:arm64. 192s Preparing to unpack .../174-libxcb-keysyms1_0.4.1-1_arm64.deb ... 192s Unpacking libxcb-keysyms1:arm64 (0.4.1-1) ... 192s Selecting previously unselected package libxcb-render-util0:arm64. 192s Preparing to unpack .../175-libxcb-render-util0_0.3.10-1_arm64.deb ... 192s Unpacking libxcb-render-util0:arm64 (0.3.10-1) ... 192s Selecting previously unselected package libxcb-shape0:arm64. 192s Preparing to unpack .../176-libxcb-shape0_1.17.0-2_arm64.deb ... 192s Unpacking libxcb-shape0:arm64 (1.17.0-2) ... 192s Selecting previously unselected package libxcb-xinerama0:arm64. 192s Preparing to unpack .../177-libxcb-xinerama0_1.17.0-2_arm64.deb ... 192s Unpacking libxcb-xinerama0:arm64 (1.17.0-2) ... 192s Selecting previously unselected package libxcb-xinput0:arm64. 192s Preparing to unpack .../178-libxcb-xinput0_1.17.0-2_arm64.deb ... 192s Unpacking libxcb-xinput0:arm64 (1.17.0-2) ... 192s Selecting previously unselected package libxcb-xkb1:arm64. 192s Preparing to unpack .../179-libxcb-xkb1_1.17.0-2_arm64.deb ... 192s Unpacking libxcb-xkb1:arm64 (1.17.0-2) ... 192s Selecting previously unselected package libxkbcommon-x11-0:arm64. 192s Preparing to unpack .../180-libxkbcommon-x11-0_1.7.0-2_arm64.deb ... 192s Unpacking libxkbcommon-x11-0:arm64 (1.7.0-2) ... 192s Selecting previously unselected package libqt5gui5t64:arm64. 192s Preparing to unpack .../181-libqt5gui5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ... 192s Unpacking libqt5gui5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 193s Selecting previously unselected package libqt5widgets5t64:arm64. 193s Preparing to unpack .../182-libqt5widgets5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ... 193s Unpacking libqt5widgets5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 193s Selecting previously unselected package libqt5xml5t64:arm64. 193s Preparing to unpack .../183-libqt5xml5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ... 193s Unpacking libqt5xml5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 193s Selecting previously unselected package libqt5designer5:arm64. 193s Preparing to unpack .../184-libqt5designer5_5.15.15-6build1_arm64.deb ... 193s Unpacking libqt5designer5:arm64 (5.15.15-6build1) ... 193s Selecting previously unselected package libqt5sql5t64:arm64. 193s Preparing to unpack .../185-libqt5sql5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ... 193s Unpacking libqt5sql5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 193s Selecting previously unselected package libqt5help5:arm64. 193s Preparing to unpack .../186-libqt5help5_5.15.15-6build1_arm64.deb ... 193s Unpacking libqt5help5:arm64 (5.15.15-6build1) ... 193s Selecting previously unselected package libqt5opengl5t64:arm64. 193s Preparing to unpack .../187-libqt5opengl5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ... 193s Unpacking libqt5opengl5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 193s Selecting previously unselected package libqt5printsupport5t64:arm64. 193s Preparing to unpack .../188-libqt5printsupport5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ... 193s Unpacking libqt5printsupport5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 193s Selecting previously unselected package libqt5test5t64:arm64. 193s Preparing to unpack .../189-libqt5test5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ... 193s Unpacking libqt5test5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 193s Selecting previously unselected package libraqm0:arm64. 193s Preparing to unpack .../190-libraqm0_0.10.2-1_arm64.deb ... 193s Unpacking libraqm0:arm64 (0.10.2-1) ... 193s Selecting previously unselected package libssm2:arm64. 193s Preparing to unpack .../191-libssm2_1.4.0-2build1_arm64.deb ... 193s Unpacking libssm2:arm64 (1.4.0-2build1) ... 193s Selecting previously unselected package libwebpdemux2:arm64. 193s Preparing to unpack .../192-libwebpdemux2_1.5.0-0.1_arm64.deb ... 193s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 193s Selecting previously unselected package libwebpmux3:arm64. 193s Preparing to unpack .../193-libwebpmux3_1.5.0-0.1_arm64.deb ... 193s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 193s Selecting previously unselected package libwxbase3.2-1t64:arm64. 193s Preparing to unpack .../194-libwxbase3.2-1t64_3.2.6+dfsg-2ubuntu1_arm64.deb ... 193s Unpacking libwxbase3.2-1t64:arm64 (3.2.6+dfsg-2ubuntu1) ... 193s Selecting previously unselected package libxtst6:arm64. 193s Preparing to unpack .../195-libxtst6_2%3a1.2.5-1_arm64.deb ... 193s Unpacking libxtst6:arm64 (2:1.2.5-1) ... 193s Selecting previously unselected package libwxgtk3.2-1t64:arm64. 193s Preparing to unpack .../196-libwxgtk3.2-1t64_3.2.6+dfsg-2ubuntu1_arm64.deb ... 193s Unpacking libwxgtk3.2-1t64:arm64 (3.2.6+dfsg-2ubuntu1) ... 194s Selecting previously unselected package libwxgtk-gl3.2-1t64:arm64. 194s Preparing to unpack .../197-libwxgtk-gl3.2-1t64_3.2.6+dfsg-2ubuntu1_arm64.deb ... 194s Unpacking libwxgtk-gl3.2-1t64:arm64 (3.2.6+dfsg-2ubuntu1) ... 194s Selecting previously unselected package libxslt1.1:arm64. 194s Preparing to unpack .../198-libxslt1.1_1.1.39-0exp1ubuntu4_arm64.deb ... 194s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu4) ... 194s Selecting previously unselected package pymol-data. 194s Preparing to unpack .../199-pymol-data_3.1.0+dfsg-1_all.deb ... 194s Unpacking pymol-data (3.1.0+dfsg-1) ... 194s Selecting previously unselected package python-matplotlib-data. 194s Preparing to unpack .../200-python-matplotlib-data_3.8.3-7build1_all.deb ... 194s Unpacking python-matplotlib-data (3.8.3-7build1) ... 194s Selecting previously unselected package python3-all. 194s Preparing to unpack .../201-python3-all_3.13.2-2_arm64.deb ... 194s Unpacking python3-all (3.13.2-2) ... 194s Selecting previously unselected package python3-brotli. 194s Preparing to unpack .../202-python3-brotli_1.1.0-2build4_arm64.deb ... 194s Unpacking python3-brotli (1.1.0-2build4) ... 194s Selecting previously unselected package python3-legacy-cgi. 194s Preparing to unpack .../203-python3-legacy-cgi_2.6.2-1_all.deb ... 194s Unpacking python3-legacy-cgi (2.6.2-1) ... 194s Selecting previously unselected package python3-pycbf. 194s Preparing to unpack .../204-python3-pycbf_0.9.7+dfsg1-5build1_arm64.deb ... 194s Unpacking python3-pycbf (0.9.7+dfsg1-5build1) ... 194s Selecting previously unselected package python3-h5py-serial. 194s Preparing to unpack .../205-python3-h5py-serial_3.13.0-1_arm64.deb ... 194s Unpacking python3-h5py-serial (3.13.0-1) ... 194s Selecting previously unselected package python3-h5py. 194s Preparing to unpack .../206-python3-h5py_3.13.0-1_all.deb ... 194s Unpacking python3-h5py (3.13.0-1) ... 194s Selecting previously unselected package python3-hdf5plugin. 194s Preparing to unpack .../207-python3-hdf5plugin_5.0.0-1_all.deb ... 194s Unpacking python3-hdf5plugin (5.0.0-1) ... 194s Selecting previously unselected package python3-dateutil. 194s Preparing to unpack .../208-python3-dateutil_2.9.0-4_all.deb ... 194s Unpacking python3-dateutil (2.9.0-4) ... 194s Selecting previously unselected package libopenjp2-7:arm64. 194s Preparing to unpack .../209-libopenjp2-7_2.5.3-2_arm64.deb ... 194s Unpacking libopenjp2-7:arm64 (2.5.3-2) ... 195s Selecting previously unselected package python3-pil:arm64. 195s Preparing to unpack .../210-python3-pil_11.1.0-5build1_arm64.deb ... 195s Unpacking python3-pil:arm64 (11.1.0-5build1) ... 195s Selecting previously unselected package python3.13-tk. 195s Preparing to unpack .../211-python3.13-tk_3.13.2-2_arm64.deb ... 195s Unpacking python3.13-tk (3.13.2-2) ... 195s Selecting previously unselected package python3-tk:arm64. 195s Preparing to unpack .../212-python3-tk_3.13.2-1_arm64.deb ... 195s Unpacking python3-tk:arm64 (3.13.2-1) ... 195s Selecting previously unselected package python3-pil.imagetk:arm64. 195s Preparing to unpack .../213-python3-pil.imagetk_11.1.0-5build1_arm64.deb ... 195s Unpacking python3-pil.imagetk:arm64 (11.1.0-5build1) ... 195s Selecting previously unselected package python3-contourpy. 195s Preparing to unpack .../214-python3-contourpy_1.3.1-1build1_arm64.deb ... 195s Unpacking python3-contourpy (1.3.1-1build1) ... 195s Selecting previously unselected package python3-cycler. 195s Preparing to unpack .../215-python3-cycler_0.12.1-1_all.deb ... 195s Unpacking python3-cycler (0.12.1-1) ... 195s Selecting previously unselected package python3-platformdirs. 195s Preparing to unpack .../216-python3-platformdirs_4.3.6-1_all.deb ... 195s Unpacking python3-platformdirs (4.3.6-1) ... 195s Selecting previously unselected package python3-fs. 195s Preparing to unpack .../217-python3-fs_2.4.16-7_all.deb ... 195s Unpacking python3-fs (2.4.16-7) ... 195s Selecting previously unselected package python3-lxml:arm64. 195s Preparing to unpack .../218-python3-lxml_5.3.1-1build1_arm64.deb ... 195s Unpacking python3-lxml:arm64 (5.3.1-1build1) ... 195s Selecting previously unselected package python3-lz4. 195s Preparing to unpack .../219-python3-lz4_4.4.0+dfsg-1build1_arm64.deb ... 195s Unpacking python3-lz4 (4.4.0+dfsg-1build1) ... 195s Selecting previously unselected package python3-decorator. 195s Preparing to unpack .../220-python3-decorator_5.1.1-5_all.deb ... 195s Unpacking python3-decorator (5.1.1-5) ... 195s Selecting previously unselected package python3-scipy. 195s Preparing to unpack .../221-python3-scipy_1.14.1-4ubuntu2_arm64.deb ... 195s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 196s Selecting previously unselected package python3-mpmath. 196s Preparing to unpack .../222-python3-mpmath_1.3.0-1_all.deb ... 196s Unpacking python3-mpmath (1.3.0-1) ... 196s Selecting previously unselected package python3-sympy. 196s Preparing to unpack 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python3-packaging (24.2-1) ... 197s Selecting previously unselected package python3-matplotlib. 197s Preparing to unpack .../229-python3-matplotlib_3.8.3-7build1_arm64.deb ... 197s Unpacking python3-matplotlib (3.8.3-7build1) ... 198s Selecting previously unselected package sphinx-rtd-theme-common. 198s Preparing to unpack .../230-sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb ... 198s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 198s Selecting previously unselected package python3-mrcfile. 198s Preparing to unpack .../231-python3-mrcfile_1.5.4-2_all.deb ... 198s Unpacking python3-mrcfile (1.5.4-2) ... 198s Selecting previously unselected package python3-natsort. 198s Preparing to unpack .../232-python3-natsort_8.0.2-2_all.deb ... 198s Unpacking python3-natsort (8.0.2-2) ... 198s Selecting previously unselected package python3-flexcache. 198s Preparing to unpack .../233-python3-flexcache_0.3-2_all.deb ... 198s Unpacking python3-flexcache (0.3-2) ... 198s Selecting previously 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up libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... 202s Setting up libxcb-keysyms1:arm64 (0.4.1-1) ... 202s Setting up libxcb-shape0:arm64 (1.17.0-2) ... 202s Setting up x11-common (1:7.7+23ubuntu3) ... 202s Setting up libdeflate0:arm64 (1.23-1) ... 202s Setting up libboost-thread1.83.0:arm64 (1.83.0-4.1ubuntu2) ... 202s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 202s Setting up libxcb-render-util0:arm64 (0.3.10-1) ... 202s Setting up python3-all (3.13.2-2) ... 202s Setting up python3-ordered-set (4.1.0-1) ... 203s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 203s Setting up libxcb-icccm4:arm64 (0.4.2-1) ... 203s Setting up libccp4-data (8.0.0-4) ... 203s Setting up libgomp1:arm64 (15-20250319-1ubuntu1) ... 203s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 203s Setting up libpcre2-16-0:arm64 (10.45-1) ... 203s Setting up libaec0:arm64 (1.1.3-1) ... 203s Setting up libcolord2:arm64 (1.4.7-3) ... 203s Setting up python3-platformdirs (4.3.6-1) ... 203s Setting up libopengl0:arm64 (1.7.0-1build1) ... 203s Setting up python3-natsort (8.0.2-2) ... 203s Setting up libxcb-util1:arm64 (0.4.1-1) ... 203s Setting up libxxf86vm1:arm64 (1:1.1.4-1build4) ... 203s Setting up libxcb-xkb1:arm64 (1.17.0-2) ... 203s Setting up libxcb-image0:arm64 (0.4.0-2build1) ... 203s Setting up python3-fs (2.4.16-7) ... 203s Setting up libxcb-present0:arm64 (1.17.0-2) ... 203s Setting up libdconf1:arm64 (0.40.0-5) ... 203s Setting up unicode-data (15.1.0-1) ... 203s Setting up python3-six (1.17.0-1) ... 203s Setting up libqt5core5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 203s Setting up python3-decorator (5.1.1-5) ... 203s Setting up libboost-numpy1.83.0 (1.83.0-4.1ubuntu2) ... 203s Setting up libpcre2-32-0:arm64 (10.45-1) ... 203s Setting up libblas3:arm64 (3.12.1-2) ... 203s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 203s Setting up python3-packaging (24.2-1) ... 203s 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python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 204s Setting up libxrandr2:arm64 (2:1.5.4-1) ... 204s Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ... 204s Setting up fonts-dejavu-core (2.37-8) ... 204s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 204s Setting up libgfortran5:arm64 (15-20250319-1ubuntu1) ... 204s Setting up libvulkan1:arm64 (1.4.304.0-1) ... 204s Setting up python3-pluggy (1.5.0-1) ... 204s Setting up libwebp7:arm64 (1.5.0-0.1) ... 204s Setting up libubsan1:arm64 (15-20250319-1ubuntu1) ... 204s Setting up python3-legacy-cgi (2.6.2-1) ... 204s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 204s Setting up python3-pyqt5.sip (12.17.0-1build1) ... 204s Setting up libmtdev1t64:arm64 (1.1.7-1) ... 204s Setting up libxshmfence1:arm64 (1.3-1build5) ... 204s Setting up libhwasan0:arm64 (15-20250319-1ubuntu1) ... 204s Setting up at-spi2-common (2.56.0-2) ... 204s Setting up libccp4c0t64:arm64 (8.0.0-4) ... 204s Setting up libxcb-randr0:arm64 (1.17.0-2) ... 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(5.15.15+dfsg-4ubuntu1) ... 211s Setting up libccp4f0t64:arm64 (8.0.0-4) ... 211s Setting up libinput-bin (1.27.1-1) ... 211s Setting up python3-pint (0.24.4-1) ... 212s Setting up libthai0:arm64 (0.1.29-2build1) ... 212s Setting up libegl-mesa0:arm64 (25.0.1-2ubuntu2) ... 212s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 212s Setting up libraqm0:arm64 (0.10.2-1) ... 212s Setting up libpython3.13-dev:arm64 (3.13.2-2) ... 212s Setting up python3-numpy (1:2.2.3+ds-5) ... 213s Setting up libjs-sphinxdoc (8.1.3-5) ... 213s Setting up libhdf5-310:arm64 (1.14.5+repack-3) ... 213s Setting up cpp-14-aarch64-linux-gnu (14.2.0-19ubuntu1) ... 213s Setting up python3-lxml:arm64 (5.3.1-1build1) ... 213s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 213s Setting up libwayland-cursor0:arm64 (1.23.1-3) ... 213s Setting up libegl1:arm64 (1.7.0-1build1) ... 213s Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-2) ... 213s Setting up python3-contourpy (1.3.1-1build1) ... 214s Setting up libfontconfig1:arm64 (2.15.0-2.1ubuntu1) ... 214s Setting up libgcc-14-dev:arm64 (14.2.0-19ubuntu1) ... 214s Setting up libstdc++-14-dev:arm64 (14.2.0-19ubuntu1) ... 214s Setting up libsm6:arm64 (2:1.2.4-1) ... 214s Setting up libavahi-client3:arm64 (0.8-16ubuntu2) ... 214s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 214s Setting up python3-mrcfile (1.5.4-2) ... 214s Setting up libatk-bridge2.0-0t64:arm64 (2.56.0-2) ... 214s Setting up libinput10:arm64 (1.27.1-1) ... 214s Setting up gtk-update-icon-cache (4.18.2+ds-1) ... 214s Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 214s Setting up fontconfig (2.15.0-2.1ubuntu1) ... 216s Regenerating fonts cache... done. 216s Setting up libxft2:arm64 (2.3.6-1build1) ... 216s Setting up libboost1.83-dev:arm64 (1.83.0-4.1ubuntu2) ... 216s Setting up libglx-mesa0:arm64 (25.0.1-2ubuntu2) ... 216s Setting up python3-scipy (1.14.1-4ubuntu2) ... 219s Setting up libpython3-dev:arm64 (3.13.2-2) ... 219s Setting up libcbf1t64:arm64 (0.9.7+dfsg1-5build1) ... 219s Setting up libglx0:arm64 (1.7.0-1build1) ... 219s Setting up dconf-gsettings-backend:arm64 (0.40.0-5) ... 219s Setting up libccp4-dev:arm64 (8.0.0-4) ... 219s Setting up python3.13-dev (3.13.2-2) ... 219s Setting up libtk8.6:arm64 (8.6.16-1) ... 219s Setting up libpango-1.0-0:arm64 (1.56.3-1) ... 219s Setting up libnetcdf22:arm64 (1:4.9.3-1) ... 219s Setting up python3-h5py-serial (3.13.0-1) ... 219s Setting up libcairo2:arm64 (1.18.4-1) ... 219s Setting up python3.13-tk (3.13.2-2) ... 219s Setting up python3-pil:arm64 (11.1.0-5build1) ... 220s Setting up cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 220s Setting up libgl1:arm64 (1.7.0-1build1) ... 220s Setting up adwaita-icon-theme (48.0-1) ... 220s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 220s Setting up libglut3.12:arm64 (3.4.0-4) ... 220s Setting up libnotify4:arm64 (0.8.4-1) ... 220s Setting up python3-dev (3.13.2-2) ... 220s Setting up libboost-python1.83-dev (1.83.0-4.1ubuntu2) ... 220s Setting up python3-pycbf (0.9.7+dfsg1-5build1) ... 220s Setting up python3-h5py (3.13.0-1) ... 220s Setting up libglew2.2:arm64 (2.2.0-4build1) ... 220s Setting up python3-hdf5plugin (5.0.0-1) ... 220s Setting up cpp-14 (14.2.0-19ubuntu1) ... 220s Setting up cpp (4:14.2.0-1ubuntu1) ... 220s Setting up libcairo-gobject2:arm64 (1.18.4-1) ... 220s Setting up gcc-14-aarch64-linux-gnu (14.2.0-19ubuntu1) ... 220s Setting up libpangoft2-1.0-0:arm64 (1.56.3-1) ... 220s Setting up python3-nxmx (0.0.4-1) ... 220s Setting up libcups2t64:arm64 (2.4.11-0ubuntu2) ... 220s Setting up libgtk-3-common (3.24.49-2ubuntu1) ... 220s Setting up libpangocairo-1.0-0:arm64 (1.56.3-1) ... 220s Setting up libcctbx0 (2024.10+ds2+~3.22.1+ds1-4build2) ... 220s Setting up gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 220s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 220s Setting up g++-14-aarch64-linux-gnu (14.2.0-19ubuntu1) ... 220s Setting up blt (2.5.3+dfsg-8) ... 220s Setting up python3-tk:arm64 (3.13.2-1) ... 220s Setting up python3-opengl (3.1.9+dfsg-1syncable1) ... 220s /usr/lib/python3/dist-packages/OpenGL/GL/AMD/vertex_shader_tessellator.py:30: SyntaxWarning: invalid escape sequence '\ ' 220s |\ |\ 222s Setting up gcc-14 (14.2.0-19ubuntu1) ... 222s Setting up libboost-python-dev (1.83.0.2ubuntu1) ... 222s Setting up libqt5gui5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 222s Setting up python3-pil.imagetk:arm64 (11.1.0-5build1) ... 222s Setting up g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 222s Setting up g++-14 (14.2.0-19ubuntu1) ... 222s Setting up libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4build2) ... 222s Setting up libqt5widgets5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 222s Setting up libqt5help5:arm64 (5.15.15-6build1) ... 222s Setting up gcc (4:14.2.0-1ubuntu1) ... 222s Setting up g++ (4:14.2.0-1ubuntu1) ... 222s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 222s Setting up libqt5opengl5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 222s Setting up libqt5printsupport5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 222s Setting up libqt5designer5:arm64 (5.15.15-6build1) ... 222s Setting up python3-pyqt5 (5.15.11+dfsg-2) ... 222s Setting up python3-pyqt5.qtopengl (5.15.11+dfsg-2) ... 222s Setting up python3-pymol (3.1.0+dfsg-1) ... 223s Setting up python3-fonttools (4.55.3-2build1) ... 223s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 224s Setting up python3-matplotlib (3.8.3-7build1) ... 225s Processing triggers for libc-bin (2.41-1ubuntu2) ... 225s Processing triggers for man-db (2.13.0-1) ... 227s Processing triggers for libglib2.0-0t64:arm64 (2.84.0-1) ... 227s Setting up libgtk-3-0t64:arm64 (3.24.49-2ubuntu1) ... 227s Processing triggers for udev (257.4-1ubuntu1) ... 227s Setting up libwxgtk3.2-1t64:arm64 (3.2.6+dfsg-2ubuntu1) ... 227s Setting up libwxgtk-gl3.2-1t64:arm64 (3.2.6+dfsg-2ubuntu1) ... 227s Setting up python3-wxgtk4.0 (4.2.2+dfsg-3build1) ... 229s Setting up python3-cctbx (2024.10+ds2+~3.22.1+ds1-4build2) ... 231s /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:18: SyntaxWarning: invalid escape sequence '\{' 231s []_,.;:"&<>()/\{}'`~!@#$%*|+- 231s /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:46: SyntaxWarning: invalid escape sequence '\/' 231s special_characters = """[]_,.;:"&<>()\/\{}'`~!@#$%*|+-""" 241s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:724: SyntaxWarning: invalid escape sequence '\o' 241s width=pairwise_differences_db, label='$\omega_{hkl}$' 241s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:739: SyntaxWarning: invalid escape sequence '\o' 241s axes[0].set_ylabel('Distribution of $\omega_{hbk}$') 241s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:740: SyntaxWarning: invalid escape sequence '\o' 241s axes[0].set_xlabel('Normalized PD ($\omega_{hbk}$)') 241s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:759: SyntaxWarning: invalid escape sequence '\o' 241s axes[1].set_xlabel('Sorted Normalized PD ($\omega_{hbk}$)') 241s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:778: SyntaxWarning: invalid escape sequence '\s' 241s axes[2].set_ylabel('Standard Deviation of $I_{hbk}/\sigma_{hbk}$') 241s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:807: SyntaxWarning: invalid escape sequence '\m' 241s axes_sadd.set_ylabel('$s_{\mathrm{fac}}^2 \\times s_{\mathrm{add}}^2$') 241s Processing triggers for libc-bin (2.41-1ubuntu2) ... 242s autopkgtest [13:45:06]: test cctbx: [----------------------- 242s Testing cctbx with python3.13: 243s Running 546 tests on 2 processors: 243s libtbx.python "/usr/lib/python3/dist-packages/annlib_adaptbx/annlib_adaptbx/sample.py" 243s libtbx.python "/usr/lib/python3/dist-packages/annlib_adaptbx/annlib_adaptbx/self_match.py" 243s "/usr/lib/cctbx/python3.13/boost_adaptbx/tests/tst_optional_copy" 243s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_libc_backtrace.py" 243s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_rational.py" 243s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_optional.py" 243s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_std_pair.py" 243s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_tuple.py" 243s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_stdout.py" 243s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_stderr_stdout.py" 243s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_deprecation_tools.py" 243s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_python_streambuf.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sf_low_res_accuracy.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_double_step_filtration.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_is_periodic.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_reindexing.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_map_to_asu_isym.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_data_manipulation.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_bfgs.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_dev.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry/tests/tst_geometry.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/covariance/tests/tst_covariance.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_goodness_of_symmetry.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_from_map.py" P312 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_aniso_restraints.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/math/boost_python/tst_math.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_targets_fd.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_xray.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray.py" I41/acd 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_r1.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_shelxl_wght_ls.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_f_model.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/array_family/boost_python/tst_flex.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_uctbx.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_crystal_orientation.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_sgtbx.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_N_fold_rot.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_ext.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_distance_based_connectivity.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_super_cell.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adptbx/boost_python/tst_adptbx.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/boost_python/tst_miller.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_chemical_elements.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_xray_scattering.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_henke.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_icsd_radii.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_covalent_radii.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_neutron.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_sasaki.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_tiny_pse.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_wavelengths.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_formula.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_attenuation_coefficient.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/boost_python/tst_maptbx.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_bcr.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_loft.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/dmtbx/boost_python/tst_dmtbx.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/translation_search/boost_python/tst_translation_search.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_ext.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_proxy_registry.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_nonbonded_overlaps.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_process_nonbonded_proxies.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_angle_derivs.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_motif.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adp_restraints/tst_ext.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_math_module.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_krivy_gruber.py" --Quick 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_itvb_2001_table_a1427_hall_symbols.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_space_group_type_tidy_cb_op_t.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_denominators.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_subgroups.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_lattice_symmetry.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints.py" P3 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints_cartesian.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_site_constraints.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reflection_statistics.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_harker.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_special_op_simplifier.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_twin_target.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/symbol_confidence.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/bravais_types.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_lookup_utils.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal.py" I41/acd 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_direct_space_asu.py" I41/acd 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pair_asu_table.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_asu_clusters.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_coordination_sequences.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_close_packing.py" R-3mr 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fourier_transform_real_part_at_x.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem_2.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reciprocal_space_asu.py" P312 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_triplet_generator.py" P41 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_emma.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_expand_to_p1.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_change_basis.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wilson_plot.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_derivatives.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_fast_gradients.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F_sq P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_structure_factors.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_weights_for_symmetry_summation.py" Pmmm 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_real_space_refinement_simple.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation_2.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_loc_res.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_target_and_gradients.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_merge_equivalents.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grouped_data.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_fft_map.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sampled_model_density.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fast_nv1995.py" F222 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_lbfgs.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_2.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grm_pickling.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_french_wilson.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/make_cns_input.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/tst_cns_epsilon.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/tst_cns_hl.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/run_shelx76.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pointgroup_tools.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/sub_lattice_tools.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/rational_matrices_point_groups.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/cosets.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_pg_tools.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_twin_laws.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_find_best_cell.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_amplitude_normalisation.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_statistics_graphs.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_web_change_basis.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/direct_space_asu/proto/tst_asu.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_tidy_pickling.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/masks/tests/tst_flood_fill.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_r_free_utils.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/observations/tst_observations.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_ccp.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_mask.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_map_peak_3d_as_2d.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_asymmetric_map.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_peak_volume_estimate.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_resolution_from_map_and_model.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_curves.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_radius_as_central_peak_width.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_get_percentile_cutoffs.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_box.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_create_models_or_maps.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sphericity.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_statistics.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/merging/brehm_diederichs.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/multipolar/regression/tst_multipolar.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity_allsym.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grm_modifications.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_prepare_map_for_docking.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wavelength_units.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fcalc_fft_stability.py" 243s libtbx.python "/usr/lib/python3/dist-packages/cma_es/tst_cma_es.py" 243s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_ext.py" 243s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_equivalence.py" 243s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_read.py" 243s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_cout.py" 243s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_show_calls.py" 243s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_command_line.py" 243s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_separate_files.py" 243s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_cout_compile.py" stop 243s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_io.py" 243s libtbx.python "/usr/lib/python3/dist-packages/gltbx/tst_ellipsoids.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mrc_io.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_wildcard.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/gui_tools/tst.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_parser.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phil.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_cif_inputs.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_manager.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager_wrapping.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_2.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_3.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_4.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_model_sharpening_5.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_model_sharpening_5_cif.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_call_consistency.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_external_sharpening_7.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_half_map_sharpening_6.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_tls_from_map_8.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_cif.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry_cif.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_local_resolution_10.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_tools.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_patterson.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_restraints_merge.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_atom_selections_10k.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/ranges.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_crystal_symmetry_from_any.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_poscar.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/kriber/tst_strudat.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_geometry.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_lex_parse_build.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_restraints.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_parser.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_citations.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model_builder.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_lex_parse_build.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_hklf.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_writer.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_fvar_encoding.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_pdb.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy_2.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_tls.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/hybrid_36.py" exercise 243s "/usr/lib/cctbx/python3.13/iotbx/pdb/hybrid_36_fem" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy_atom_sort.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy_flip_symmetric.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_selected_hierarchy_flip.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_ext.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_rna_dna_atom_names.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_name_interpretation.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_extract_rfactors_resolutions_sigma.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/modified_aa_names.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/modified_rna_dna_names.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_sheet.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation_long.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/secondary_structure.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection_string.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_secondary_structure.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_utils.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_secondary_structure_2.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/remediation/tst_remediator.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_to_map_simple.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_truncate_to_ala/tst.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_tardy_conf_sampling_simple.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_examples.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/space_group_symbols.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/tst_cns.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_merge.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/no_merge_original_index.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/ccp4_map/tst.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_ext.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_extract_from_symmetry_lib.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_dano.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_miller_dict.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_unmerged.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/tst_mtz_free_flipper.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_utils.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_adsc.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_detectors.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xplor/tst_xplormap.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phases.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdbx_mmcif_tutorial.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_statistics.py" Fdd2 P31m 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_plots.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_csv_utils.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_file_reader.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_bioinformatics.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_segids.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_input.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_forward_compatible_pdb.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_multimodel.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_add_conformations.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_symmetry.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reindex.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_editor.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_as_fasta.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_link_records.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_merging_statistics.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_map_coefficients.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_xparm.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_xds_inp.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_integrate_hkl.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_spots_xds.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_as_cif.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_no_merge_original_index.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_export_scalepack_unmerged.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/dsn6/tst.py" P31 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_mtrix_biomt_cmdl.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_mmcif_biomt_reduction_output.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_ligs.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_broken_chain.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_shortcut_1.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_groups_preprocessing.py" 243s libtbx.python 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"/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_ebi_wu_blast_xml.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_ncbi_blast_xml.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/pdb_info.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_as_pdb_1atom.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_1.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_all_chain_ids.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_extract_xtal_data.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cli_parser.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mtz_as_cif.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_group_rounding.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_occupancies_rounding.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_merge_atoms_at_end_to_residues.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_chain_ids_1.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_1.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_2.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_3.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_4.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_copy_select.py" 243s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_id_str.py" 243s libtbx.python 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"/usr/lib/python3/dist-packages/libtbx/tst_representation.py" 243s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_find_unused_imports.py" 243s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_program_template.py" 243s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_version.py" 243s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp_multicore.py" 243s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_runtime_utils.py" 243s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_xmlrpc_utils.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_smoothing.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_genetic_algorithm_with_mp.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_basic.py" 243s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_1" 243s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_2" 243s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_3" 243s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_4" 243s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_5" 243s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_vec3" 243s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_unsigned_float_arithmetic" 243s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_mat3" 243s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_sym_mat3" 243s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_ref_matrix_facet" 243s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_accessors" 243s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_optional_copy" 243s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_rectangular_full_packed" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex_argument_passing.py" 243s "/usr/lib/cctbx/python3.13/scitbx/serialization/tst_base_256" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_minimum_covering_ellipsoid.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian_fit_1d_analytical.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_cubic_equation.py" 243s "/usr/lib/cctbx/python3.13/scitbx/math/tests/tst" 243s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_givens" 243s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_householder" 243s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_svd" 243s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_cholesky" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/tests/tst_row_echelon.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/tests/tst_householder.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_matrix.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_cholesky.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_svd.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_eigensystem.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_svd.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_dsyev.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/error/tst_error.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_map.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_set.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_vector.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/regression_test.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_numpy_bridge.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_smart_selection.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_shared.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_integer_offsets_vs_pointers.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_cost_of_m_handle_in_af_shared.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_cubicle_neighbors.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_r3_utils.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_regular_grid_on_unit_sphere.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/__init__.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_random_transform.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_graph.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_robust.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/superpose.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/spe.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/incremental_SO3_sampling.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_curve_fitting.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_weighted_correlation.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_similarity_indices.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_exp_functions.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_fit_quadratic_function.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gcd.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_math.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_r3_rotation.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_resample.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_line_search.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_quadrature.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_bessel.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_halton.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_euler_angles.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_superpose.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_uniform_rotation_matrix.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike_mom.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/sieve_of_eratosthenes.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/besselk.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/scale_curves.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_fit_peak.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_clustering.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_orthonormal_basis.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_g_function.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_angle_derivative.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_periodogram.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_error_propagation_matrix_inverse.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_tetrahedron.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_undirected_graph.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_so3_lie_algebra.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/minpack/tst.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_ext.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_curvatures.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_func_free_line_search.py" 243s "/usr/lib/cctbx/python3.13/scitbx/lbfgs/tst_lbfgs" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgsb/boost_python/tst_lbfgsb.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/fftpack/boost_python/tst_fftpack.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_grid.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_array_loops.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/principal_axes_of_inertia.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_recipe.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_linear_least_squares_fit.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/chebyshev_lsq_example.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/immoptibox_ports.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/rigid_body_refinement_core.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/integrating_a_weighted_sinc_function.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/minimizer_comparisons.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_utils.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/rigidity.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_rigidity.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/rigidity_matrix_symbolic.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree_find_paths.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/test_cases_tardy_pdb.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_basic.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_tardy.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_energy_plots.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/tst.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/free_motion_reference_impl.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_featherstone.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion_hard.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_joint_lib.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_singular.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_spherical_refinement.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_molecules.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_sparse.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_lu_factorization.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/iso_surface/tst_iso_surface.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/simplex.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/differential_evolution.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/golden_section_search.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/direct_search_simulated_annealing.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/random/tests/tst_random.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/tst_normal_equations.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/test_problems.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/glmtbx/tests/tst.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_basic.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_booth.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_twisted.py" 243s libtbx.python "/usr/lib/python3/dist-packages/scitbx/suffixtree/test/tst_single.py" 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/absolute_structure/tests/tst_absolute_structure.py" --fix_random_seeds 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/ab_initio/tests/tst_ab_initio_ext.py" 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/ab_initio/tests/tst_charge_flipping.py" --fix_seed --on=E "hall: P 1" "hall: P 3" "hall: -P 2ybc" 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/masks/tests/tst_masks.py" 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/structure_factors/direct/tests/tst_standard_xray.py" 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_weighting_schemes.py" --fix_random_seeds 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_lbfgs.py" 243s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_reparametrisation" 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_occupancies.py" 243s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens" 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_same_group.py" 243s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_special_position" 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_reparametrisation.py" 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=naive 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_disorder.py" 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=levenberg-marquardt 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_rigid.py" 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_direction.py" 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_adp_restraints.py" 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_manager.py" 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_restraints.py" --verbose --scatterers=5 --resolution=0.2 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_refine.py" 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py" 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/tests/tst_utils.py" 243s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_least_squares.py" 243s libtbx.python "/usr/lib/python3/dist-packages/rstbx/dps_core/tst_iotbx_converter.py" 243s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_predict.py" 243s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_ewald_sphere.py" 243s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_partial_derivatives.py" 243s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/fastbragg/tst_bragg_minimal.py" 243s libtbx.python "/usr/lib/python3/dist-packages/rstbx/sublattice_support/tst_sublattice.py" 243s libtbx.python -c "from rstbx.run_tests import run; run()" 243s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/core_toolbox/boost_python/tst_small_image.py" 243s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/diffraction/geometry.py" 243s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/math_support/sphere_formulae.py" 243s 243s libtbx.python "/usr/lib/python3/dist-packages/annlib_adaptbx/annlib_adaptbx/self_match.py" [OK] 0.3s 243s Time: 0.28 243s Return code: 0 243s OKs: 1 243s Standard out: 243s OK 243s "/usr/lib/cctbx/python3.13/boost_adaptbx/tests/tst_optional_copy" [OK] 0.0s 243s Time: 0.01 243s Return code: 0 243s OKs: 1 243s Standard out: 243s OK 243s Standard error: 243s show_stack(1): /usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_libc_backtrace.py(9) run 243s show_stack(2): /usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_libc_backtrace.py(15) 243s libc backtrace (20 frames, most recent call last): 243s /usr/bin/python3.13(_start+0x30) [0x5c0970] 243s /lib/aarch64-linux-gnu/libc.so.6(__libc_start_main+0x9c) [0xea2215ba23bc] 243s /lib/aarch64-linux-gnu/libc.so.6(+0x222dc) [0xea2215ba22dc] 243s /usr/bin/python3.13(Py_BytesMain+0x28) [0x5c1de8] 243s /usr/bin/python3.13(Py_RunMain+0x2b8) [0x629658] 243s /usr/bin/python3.13() [0x62baec] 243s /usr/bin/python3.13() [0x62bd54] 243s /usr/bin/python3.13() [0x62c62c] 243s /usr/bin/python3.13() [0x5fe194] 243s /usr/bin/python3.13() [0x603f1c] 243s /usr/bin/python3.13(PyEval_EvalCode+0xc0) [0x5d814c] 243s /usr/bin/python3.13(_PyEval_EvalFrameDefault+0x2b60) [0x4c5640] 243s /usr/bin/python3.13(_PyObject_MakeTpCall+0x278) [0x4a7600] 243s /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0(+0x219c0) [0xea22151f19c0] 243s /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0(boost::python::handle_exception_impl(boost::function0)+0xa8) [0xea22151f16c8] 243s /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0(+0x26140) [0xea22151f6140] 243s /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0(boost::python::objects::function::call(_object*, _object*) const+0x108) [0xea22151ebc14] 243s /usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-313-aarch64-linux-gnu.so(+0x18c04) [0xea2215248c04] 243s /usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-313-aarch64-linux-gnu.so(+0x23794) [0xea2215253794] 243s /usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-313-aarch64-linux-gnu.so(+0x232ac) [0xea22152532ac] 243s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_libc_backtrace.py" [OK] 0.1s 243s Time: 0.07 243s Return code: 0 243s OKs: 1 243s Standard out: 243s OK 243s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_rational.py" [OK] 0.1s 243s Time: 0.14 243s Return code: 0 243s OKs: 1 243s Standard out: 243s OK 243s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_optional.py" [OK] 0.1s 243s Time: 0.11 243s Return code: 0 243s OKs: 1 243s Standard out: 243s exercise_wstring: 243s OK 243s libtbx.python "/usr/lib/python3/dist-packages/annlib_adaptbx/annlib_adaptbx/sample.py" [OK] 0.6s 243s Time: 0.62 243s Return code: 0 243s OKs: 1 243s Standard out: 243s OK 243s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_tuple.py" [OK] 0.1s 243s Time: 0.07 243s Return code: 0 243s OKs: 1 243s Standard out: 243s OK 244s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_std_pair.py" [OK] 0.1s 244s Time: 0.12 244s Return code: 0 244s OKs: 1 244s Standard out: 244s OK 244s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_stderr_stdout.py" [OK] 0.1s 244s Time: 0.07 244s Return code: 0 244s OKs: 1 244s Standard out: 244s OK 244s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_stdout.py" [OK] 0.1s 244s Time: 0.14 244s Return code: 0 244s OKs: 1 244s Standard out: 244s OK 244s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_deprecation_tools.py" [OK] 0.1s 244s Time: 0.07 244s Return code: 0 244s OKs: 1 244s Standard out: 244s OK 248s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 248s 1 248s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 248s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_python_streambuf.py" [EXPECTED FAIL] 3.9s 248s Time: 3.92 248s Return code: 1 248s OKs: 0 248s Standard error: 248s Traceback (most recent call last): 248s File "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_python_streambuf.py", line 7, in 248s import StringIO 248s ModuleNotFoundError: No module named 'StringIO' 248s Standard error: 248s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 248s 139 248s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 248s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sf_low_res_accuracy.py" [FAIL] 4.8s 248s Time: 4.80 248s Return code: 139 248s OKs: 0 248s Segmentation fault (core dumped) 252s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 252s 139 252s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 252s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_double_step_filtration.py" [FAIL] 4.3s 252s Standard error: 252s Segmentation fault (core dumped) 252s Time: 4.31 252s Return code: 139 252s OKs: 0 255s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 255s 139 255s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 255s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_is_periodic.py" [FAIL] 6.9s 255s Time: 6.89 255s Return code: 139 255s OKs: 0 255s Standard error: 255s Segmentation fault (core dumped) 256s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_map_to_asu_isym.py" [OK] 0.4s 256s Time: 0.43 256s Return code: 0 256s OKs: 1 256s Standard out: 256s OK 259s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 259s 139 259s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 259s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_reindexing.py" [FAIL] 7.0s 259s Time: 6.97 259s Return code: 139 259s OKs: 0 259s Standard error: 259s Segmentation fault (core dumped) 262s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 262s 139 262s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 262s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_data_manipulation.py" [FAIL] 6.2s 262s Time: 6.25 262s Return code: 139 262s OKs: 0 262s Standard error: 262s Segmentation fault (core dumped) 265s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 265s 139 265s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 265s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_bfgs.py" [FAIL] 6.6s 265s Time: 6.56 265s Return code: 139 265s OKs: 0 265s Standard error: 265s Segmentation fault (core dumped) 269s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 269s 139 269s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 269s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_dev.py" P31 [FAIL] 6.6s 269s Time: 6.55 269s Return code: 139 269s OKs: 0 269s Standard error: 269s Segmentation fault (core dumped) 272s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 272s 139 272s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 272s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry/tests/tst_geometry.py" [FAIL] 6.4s 272s Standard error: 272s Segmentation fault (core dumped) 272s Time: 6.37 272s Return code: 139 272s OKs: 0 275s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 275s 139 275s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 275s libtbx.python "/usr/lib/python3/dist-packages/cctbx/covariance/tests/tst_covariance.py" [FAIL] 6.7s 275s Time: 6.68 275s Return code: 139 275s OKs: 0 275s Standard error: 275s Segmentation fault (core dumped) 279s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 279s 139 279s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 279s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_goodness_of_symmetry.py" [FAIL] 7.1s 279s Time: 7.15 279s Return code: 139 279s OKs: 0 279s Standard error: 279s Segmentation fault (core dumped) 279s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_aniso_restraints.py" [OK] 0.3s 279s Time: 0.27 279s Return code: 0 279s OKs: 1 279s Standard out: 279s Skipping exercise(): chem_data directory not available 279s OK 279s libtbx.python "/usr/lib/python3/dist-packages/cctbx/math/boost_python/tst_math.py" [OK] 0.1s 279s Time: 0.11 279s Return code: 0 279s OKs: 1 279s Standard out: 279s OK 280s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_targets_fd.py" [OK] 0.4s 280s Time: 0.43 280s Return code: 0 280s OKs: 1 280s Standard out: 280s OK 282s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 282s 139 282s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 282s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_from_map.py" P312 [FAIL] 6.9s 282s Time: 6.86 282s Return code: 139 282s OKs: 0 282s Standard error: 282s Segmentation fault (core dumped) 286s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 286s 139 286s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 286s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_xray.py" [FAIL] 6.0s 286s Time: 5.99 286s Return code: 139 286s OKs: 0 286s Standard error: 286s Segmentation fault (core dumped) 289s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 289s 139 289s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 289s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray.py" I41/acd [FAIL] 7.2s 289s Time: 7.20 289s Return code: 139 289s OKs: 0 289s Standard error: 289s Segmentation fault (core dumped) 293s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 293s 139 293s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 293s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_r1.py" [FAIL] 6.8s 293s Standard error: 293s Segmentation fault (core dumped) 293s Time: 6.83 293s Return code: 139 293s OKs: 0 296s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 296s 139 296s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 296s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_shelxl_wght_ls.py" [FAIL] 6.6s 296s Time: 6.56 296s Return code: 139 296s OKs: 0 296s Standard error: 296s Segmentation fault (core dumped) 299s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 299s 139 299s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 299s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_f_model.py" [FAIL] 6.7s 299s Time: 6.69 299s Return code: 139 299s OKs: 0 299s Standard error: 299s Segmentation fault (core dumped) 303s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 303s 139 303s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 303s libtbx.python "/usr/lib/python3/dist-packages/cctbx/array_family/boost_python/tst_flex.py" [FAIL] 6.7s 303s Time: 6.66 303s Return code: 139 303s OKs: 0 303s Standard error: 303s Segmentation fault (core dumped) 306s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 306s 139 306s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 306s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_uctbx.py" [FAIL] 6.7s 306s Time: 6.73 306s Return code: 139 306s OKs: 0 306s Standard error: 306s Segmentation fault (core dumped) 309s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 309s 139 309s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 309s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_crystal_orientation.py" [FAIL] 6.6s 309s Time: 6.61 309s Return code: 139 309s OKs: 0 309s Standard error: 309s Segmentation fault (core dumped) 309s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_N_fold_rot.py" [OK] 0.2s 309s Time: 0.23 309s Return code: 0 309s OKs: 1 309s Standard out: 309s OK 313s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 313s 139 313s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 313s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_sgtbx.py" [FAIL] 6.9s 313s Time: 6.87 313s Return code: 139 313s OKs: 0 313s Standard error: 313s Segmentation fault (core dumped) 317s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 317s 139 317s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 317s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_ext.py" [FAIL] 7.7s 317s Time: 7.72 317s Return code: 139 317s OKs: 0 317s Standard error: 317s Segmentation fault (core dumped) 320s Standard error: 320s Segmentation fault (core dumped) 320s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 320s 139 320s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 320s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_distance_based_connectivity.py" [FAIL] 7.5s 320s Time: 7.51 320s Return code: 139 320s OKs: 0 325s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 325s 139 325s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 325s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_super_cell.py" [FAIL] 7.7s 325s Time: 7.65 325s Return code: 139 325s OKs: 0 325s Standard error: 325s Segmentation fault (core dumped) 328s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 328s 139 328s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 328s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adptbx/boost_python/tst_adptbx.py" [FAIL] 7.9s 328s Time: 7.88 328s Return code: 139 328s OKs: 0 328s Standard error: 328s Segmentation fault (core dumped) 328s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_chemical_elements.py" [OK] 0.1s 328s Time: 0.10 328s Return code: 0 328s OKs: 1 328s Standard out: 328s OK 332s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 332s 139 332s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 332s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/boost_python/tst_miller.py" [FAIL] 6.8s 332s Time: 6.83 332s Return code: 139 332s OKs: 0 332s Standard error: 332s Segmentation fault (core dumped) 332s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_henke.py" [OK] 0.1s 332s Time: 0.11 332s Return code: 0 332s OKs: 1 332s Standard out: 332s OK 332s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_icsd_radii.py" [OK] 0.1s 332s Time: 0.11 332s Return code: 0 332s OKs: 1 332s Standard out: 332s OK 332s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_covalent_radii.py" [OK] 0.1s 332s Time: 0.10 332s Return code: 0 332s OKs: 1 332s Standard out: 332s OK 332s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_neutron.py" [OK] 0.1s 332s Time: 0.11 332s Return code: 0 332s OKs: 1 332s Standard out: 332s OK 332s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_sasaki.py" [OK] 0.1s 332s Time: 0.11 332s Return code: 0 332s OKs: 1 332s Standard out: 332s OK 332s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_tiny_pse.py" [OK] 0.1s 332s Time: 0.11 332s Return code: 0 332s OKs: 1 332s Standard out: 332s OK 332s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_wavelengths.py" [OK] 0.1s 332s Time: 0.11 332s Return code: 0 332s OKs: 1 332s Standard out: 332s OK 335s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 335s 139 335s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 335s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_xray_scattering.py" [FAIL] 6.4s 335s Standard error: 335s Segmentation fault (core dumped) 335s Time: 6.43 335s Return code: 139 335s OKs: 0 338s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 338s 139 338s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 338s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_formula.py" [FAIL] 5.6s 338s Time: 5.64 338s Return code: 139 338s OKs: 0 338s Standard error: 338s Segmentation fault (core dumped) 341s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 341s 139 341s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 341s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_attenuation_coefficient.py" [FAIL] 6.5s 341s Time: 6.47 341s Return code: 139 341s OKs: 0 341s Standard error: 341s Segmentation fault (core dumped) 345s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 345s 139 345s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 345s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/boost_python/tst_maptbx.py" [FAIL] 6.5s 345s Time: 6.55 345s Return code: 139 345s OKs: 0 345s Standard error: 345s Segmentation fault (core dumped) 349s Standard error: 349s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 349s 139 349s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 349s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_bcr.py" [FAIL] 7.3s 349s Time: 7.35 349s Return code: 139 349s OKs: 0 349s Segmentation fault (core dumped) 352s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 352s 139 352s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 352s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_loft.py" [FAIL] 7.3s 352s Time: 7.32 352s Return code: 139 352s OKs: 0 352s Standard error: 352s Segmentation fault (core dumped) 355s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 355s 139 355s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 355s libtbx.python "/usr/lib/python3/dist-packages/cctbx/dmtbx/boost_python/tst_dmtbx.py" [FAIL] 6.5s 355s Standard error: 355s Time: 6.46 355s Return code: 139 355s OKs: 0 355s Segmentation fault (core dumped) 358s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 358s 139 358s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 358s libtbx.python "/usr/lib/python3/dist-packages/cctbx/translation_search/boost_python/tst_translation_search.py" [FAIL] 6.5s 358s Time: 6.45 358s Return code: 139 358s OKs: 0 358s Standard error: 358s Segmentation fault (core dumped) 359s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_proxy_registry.py" [OK] 0.2s 359s Time: 0.25 359s Return code: 0 359s OKs: 1 359s Standard out: 359s OK 359s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_nonbonded_overlaps.py" [OK] 0.7s 359s Time: 0.74 359s Return code: 0 359s OKs: 0 359s Standard out: 359s chem_data not present, skipping 360s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_process_nonbonded_proxies.py" [OK] 0.8s 360s Time: 0.76 360s Return code: 0 360s OKs: 0 360s Standard out: 360s Test skipped, need monomer library 362s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 362s 139 362s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 362s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_ext.py" [FAIL] 6.8s 362s Time: 6.75 362s Return code: 139 362s OKs: 0 362s Standard error: 362s Segmentation fault (core dumped) 362s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_motif.py" [OK] 0.3s 362s Time: 0.27 362s Return code: 0 362s OKs: 0 362s Standard out: 362s u+s,u,s: 0.21 0.17 0.04 365s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 365s 139 365s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 365s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_angle_derivs.py" [FAIL] 4.8s 365s Time: 4.83 365s Return code: 139 365s OKs: 0 365s Standard error: 365s Segmentation fault (core dumped) 365s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_math_module.py" [OK] 0.1s 365s Time: 0.11 365s Return code: 0 365s OKs: 1 365s Standard out: 365s OK 368s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 368s 139 368s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 368s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adp_restraints/tst_ext.py" [FAIL] 6.3s 368s Time: 6.27 368s Return code: 139 368s OKs: 0 368s Standard error: 368s Segmentation fault (core dumped) 372s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 372s 139 372s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 372s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_krivy_gruber.py" --Quick [FAIL] 6.8s 372s Time: 6.84 372s Return code: 139 372s OKs: 0 372s Standard error: 372s Segmentation fault (core dumped) 372s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_itvb_2001_table_a1427_hall_symbols.py" [OK] 0.2s 372s Time: 0.22 372s Return code: 0 372s OKs: 1 372s Standard out: 372s Skipping exercise(): input file not available 372s OK 375s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 375s 139 375s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 375s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx.py" [FAIL] 6.6s 375s Time: 6.60 375s Return code: 139 375s OKs: 0 375s Standard error: 375s Segmentation fault (core dumped) 378s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 378s 139 378s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 378s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_space_group_type_tidy_cb_op_t.py" [FAIL] 6.3s 378s Time: 6.29 378s Return code: 139 378s OKs: 0 378s Standard error: 378s Segmentation fault (core dumped) 382s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 382s 139 382s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_denominators.py" P31 [FAIL] 6.7s 382s Time: 6.72 382s Return code: 139 382s OKs: 0 382s Standard error: 382s Segmentation fault (core dumped) 385s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 385s 139 385s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 385s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_subgroups.py" [FAIL] 6.4s 385s Time: 6.45 385s Return code: 139 385s OKs: 0 385s Standard error: 385s Segmentation fault (core dumped) 388s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 388s 139 388s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 388s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_lattice_symmetry.py" [FAIL] 6.2s 388s Time: 6.15 388s Return code: 139 388s OKs: 0 388s Standard error: 388s Segmentation fault (core dumped) 391s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 391s 139 391s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 391s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints.py" P3 [FAIL] 6.2s 391s Time: 6.25 391s Return code: 139 391s OKs: 0 391s Standard error: 391s Segmentation fault (core dumped) 391s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_site_constraints.py" [OK] 0.4s 391s Time: 0.43 391s Return code: 0 391s OKs: 0 391s Standard out: 391s Skipping process_zeolite_atlas(): input file not available 391s u+s,u,s: 0.34 0.30 0.04 394s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 394s 139 394s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 394s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints_cartesian.py" [FAIL] 6.5s 394s Time: 6.47 394s Return code: 139 394s OKs: 0 394s Standard error: 394s Segmentation fault (core dumped) 398s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 398s 139 398s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 398s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reflection_statistics.py" [FAIL] 6.0s 398s Time: 6.01 398s Return code: 139 398s OKs: 0 398s Standard error: 398s Segmentation fault (core dumped) 401s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 401s 139 401s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 401s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_harker.py" [FAIL] 6.2s 401s Time: 6.25 401s Return code: 139 401s OKs: 0 401s Standard error: 401s Segmentation fault (core dumped) 404s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 404s 139 404s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 404s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_special_op_simplifier.py" [FAIL] 6.2s 404s Time: 6.21 404s Return code: 139 404s OKs: 0 404s Standard error: 404s Segmentation fault (core dumped) 407s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 407s 139 407s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 407s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_twin_target.py" [FAIL] 6.5s 407s Standard error: 407s Segmentation fault (core dumped) 407s Time: 6.49 407s Return code: 139 407s OKs: 0 410s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 410s 139 410s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 410s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/symbol_confidence.py" [FAIL] 6.4s 410s Time: 6.37 410s Return code: 139 410s OKs: 0 410s Standard error: 410s Segmentation fault (core dumped) 413s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 413s 139 413s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 413s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/bravais_types.py" [FAIL] 6.3s 413s Time: 6.27 413s Return code: 139 413s OKs: 0 413s Standard error: 413s Segmentation fault (core dumped) 417s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 417s 139 417s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 417s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_lookup_utils.py" [FAIL] 6.6s 417s Time: 6.64 417s Return code: 139 417s OKs: 0 417s Standard error: 417s Segmentation fault (core dumped) 420s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 420s 139 420s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 420s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal.py" I41/acd [FAIL] 6.9s 420s Time: 6.88 420s Return code: 139 420s OKs: 0 420s Standard error: 420s Segmentation fault (core dumped) 423s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 423s 139 423s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 423s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_direct_space_asu.py" I41/acd [FAIL] 6.8s 423s Time: 6.78 423s Return code: 139 423s OKs: 0 423s Standard error: 423s Segmentation fault (core dumped) 427s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 427s 139 427s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 427s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pair_asu_table.py" [FAIL] 6.7s 427s Time: 6.65 427s Return code: 139 427s OKs: 0 427s Standard error: 427s Segmentation fault (core dumped) 427s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_coordination_sequences.py" [OK] 0.4s 427s Time: 0.40 427s Return code: 0 427s OKs: 1 427s Standard out: 427s Skipping exercise(): input file not available 427s OK 430s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 430s 139 430s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 430s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_asu_clusters.py" [FAIL] 6.6s 430s Time: 6.65 430s Return code: 139 430s OKs: 0 430s Standard error: 430s Segmentation fault (core dumped) 434s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 434s 139 434s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 434s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_close_packing.py" R-3mr [FAIL] 6.5s 434s Time: 6.45 434s Return code: 139 434s OKs: 0 434s Standard error: 434s Segmentation fault (core dumped) 437s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 437s 139 437s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 437s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fourier_transform_real_part_at_x.py" P31 [FAIL] 6.5s 437s Time: 6.53 437s Return code: 139 437s OKs: 0 437s Standard error: 437s Segmentation fault (core dumped) 440s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 440s 139 440s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 440s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller.py" P31 [FAIL] 6.5s 440s Time: 6.48 440s Return code: 139 440s OKs: 0 440s Standard error: 440s Segmentation fault (core dumped) 440s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem_2.py" [OK] 0.3s 440s Time: 0.30 440s Return code: 0 440s OKs: 0 440s Standard out: 440s Skipping test: phenix not available 443s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 443s 139 443s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 443s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem.py" [FAIL] 6.8s 443s Time: 6.79 443s Return code: 139 443s OKs: 0 443s Standard error: 443s Segmentation fault (core dumped) 447s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 447s 139 447s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 447s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reciprocal_space_asu.py" P312 [FAIL] 6.2s 447s Time: 6.16 447s Return code: 139 447s OKs: 0 447s Standard error: 447s Segmentation fault (core dumped) 450s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 450s 139 450s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 450s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_triplet_generator.py" P41 [FAIL] 6.4s 450s Time: 6.37 450s Return code: 139 450s OKs: 0 450s Standard error: 450s Segmentation fault (core dumped) 453s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 453s 139 453s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 453s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_emma.py" P31 [FAIL] 6.8s 453s Time: 6.77 453s Return code: 139 453s OKs: 0 453s Standard error: 453s Segmentation fault (core dumped) 457s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 457s 139 457s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 457s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_expand_to_p1.py" P31 [FAIL] 7.0s 457s Time: 6.97 457s Return code: 139 457s OKs: 0 457s Standard error: 457s Segmentation fault (core dumped) 460s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 460s 139 460s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 460s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_change_basis.py" P31 [FAIL] 6.6s 460s Standard error: 460s Segmentation fault (core dumped) 460s Time: 6.62 460s Return code: 139 460s OKs: 0 463s Standard error: 463s Segmentation fault (core dumped) 463s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 463s 139 463s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 463s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wilson_plot.py" P31 [FAIL] 6.4s 463s Time: 6.43 463s Return code: 139 463s OKs: 0 467s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 467s 139 467s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 467s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_derivatives.py" P31 [FAIL] 6.6s 467s Time: 6.65 467s Return code: 139 467s OKs: 0 467s Standard error: 467s Segmentation fault (core dumped) 470s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 470s 139 470s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 470s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_fast_gradients.py" P31 [FAIL] 6.8s 470s Standard error: 470s Segmentation fault (core dumped) 470s Time: 6.81 470s Return code: 139 470s OKs: 0 474s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 474s 139 474s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 474s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F P31 [FAIL] 7.1s 474s Time: 7.12 474s Return code: 139 474s OKs: 0 474s Standard error: 474s Segmentation fault (core dumped) 474s Standard error: 474s Segmentation fault (core dumped) 474s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 474s 139 474s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 474s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F_sq P31 [FAIL] 3.8s 474s Time: 3.77 474s Return code: 139 474s OKs: 0 477s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 477s 139 477s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 477s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_weights_for_symmetry_summation.py" Pmmm [FAIL] 3.6s 477s Time: 3.63 477s Return code: 139 477s OKs: 0 477s Standard error: 477s Segmentation fault (core dumped) 481s Standard error: 481s Segmentation fault (core dumped) 481s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 481s 139 481s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 481s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_structure_factors.py" P31 [FAIL] 7.1s 481s Time: 7.06 481s Return code: 139 481s OKs: 0 484s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 484s 139 484s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 484s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_real_space_refinement_simple.py" [FAIL] 6.6s 484s Time: 6.64 484s Return code: 139 484s OKs: 0 484s Standard error: 484s Segmentation fault (core dumped) 487s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 487s 139 487s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 487s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation.py" [FAIL] 6.4s 487s Time: 6.37 487s Return code: 139 487s OKs: 0 487s Standard error: 487s Segmentation fault (core dumped) 491s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 491s 139 491s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 491s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation_2.py" [FAIL] 7.2s 491s Time: 7.21 491s Return code: 139 491s OKs: 0 491s Standard error: 491s Segmentation fault (core dumped) 497s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 497s 139 497s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 497s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_loc_res.py" [FAIL] 10.2s 497s Time: 10.19 497s Return code: 139 497s OKs: 0 497s Standard error: 497s Segmentation fault (core dumped) 501s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 501s 139 501s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 501s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_target_and_gradients.py" [FAIL] 9.4s 501s Time: 9.43 501s Return code: 139 501s OKs: 0 501s Standard error: 501s Segmentation fault (core dumped) 504s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 504s 139 504s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 504s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_merge_equivalents.py" P31 [FAIL] 6.6s 504s Time: 6.63 504s Return code: 139 504s OKs: 0 504s Standard error: 504s Segmentation fault (core dumped) 508s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 508s 139 508s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 508s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grouped_data.py" P31 [FAIL] 6.8s 508s Standard error: 508s Segmentation fault (core dumped) 508s Time: 6.79 508s Return code: 139 508s OKs: 0 511s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 511s 139 511s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 511s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_fft_map.py" P31 [FAIL] 6.9s 511s Time: 6.91 511s Return code: 139 511s OKs: 0 511s Standard error: 511s Segmentation fault (core dumped) 514s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 514s 139 514s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 514s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sampled_model_density.py" P31 [FAIL] 6.9s 514s Time: 6.86 514s Return code: 139 514s OKs: 0 514s Standard error: 514s Segmentation fault (core dumped) 515s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints.py" [OK] 0.7s 515s Time: 0.67 515s Return code: 0 515s OKs: 1 515s Standard out: 515s OK 518s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 518s 139 518s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 518s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fast_nv1995.py" F222 [FAIL] 6.7s 518s Time: 6.69 518s Return code: 139 518s OKs: 0 518s Standard error: 518s Segmentation fault (core dumped) 521s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 521s 139 521s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 521s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_lbfgs.py" [FAIL] 5.8s 521s Time: 5.78 521s Return code: 139 521s OKs: 0 521s Standard error: 521s Segmentation fault (core dumped) 521s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grm_pickling.py" [OK] 0.4s 521s Time: 0.44 521s Return code: 0 521s OKs: 0 521s Standard out: 521s Can not initialize monomer_library, skipping test. 524s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 524s 139 524s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 524s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_2.py" [FAIL] 6.7s 524s Time: 6.69 524s Return code: 139 524s OKs: 0 524s Standard error: 524s Segmentation fault (core dumped) 528s Standard error: 528s Segmentation fault (core dumped) 528s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 528s 139 528s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 528s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_french_wilson.py" [FAIL] 6.3s 528s Time: 6.26 528s Return code: 139 528s OKs: 0 528s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/tst_cns_epsilon.py" P31 [OK] 0.3s 528s Time: 0.27 528s Return code: 0 528s OKs: 0 528s Standard out: 528s Skipping tests: cns not available. 528s u+s,u,s: 0.20 0.18 0.02 528s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/tst_cns_hl.py" P31 [OK] 0.3s 528s Time: 0.27 528s Return code: 0 528s OKs: 0 528s Standard out: 528s Skipping tests: cns not available. 528s u+s,u,s: 0.20 0.17 0.03 528s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/run_shelx76.py" P31 [OK] 0.3s 528s Time: 0.29 528s Return code: 0 528s OKs: 0 528s Standard out: 528s shelx76 not available. 531s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 531s 139 531s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 531s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/make_cns_input.py" P31 [FAIL] 6.3s 531s Time: 6.32 531s Return code: 139 531s OKs: 0 531s Standard error: 531s Segmentation fault (core dumped) 534s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 534s 139 534s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 534s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pointgroup_tools.py" [FAIL] 5.8s 534s Time: 5.79 534s Return code: 139 534s OKs: 0 534s Standard error: 534s Segmentation fault (core dumped) 538s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 538s 139 538s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 538s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/sub_lattice_tools.py" [FAIL] 7.4s 538s Time: 7.41 538s Return code: 139 538s OKs: 0 538s Standard error: 538s Segmentation fault (core dumped) 541s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 541s 139 541s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 541s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/rational_matrices_point_groups.py" [FAIL] 7.3s 541s Time: 7.27 541s Return code: 139 541s OKs: 0 541s Standard error: 541s Segmentation fault (core dumped) 545s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 545s 139 545s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 545s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/cosets.py" [FAIL] 6.8s 545s Time: 6.81 545s Return code: 139 545s OKs: 0 545s Standard error: 545s Segmentation fault (core dumped) 548s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 548s 139 548s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 548s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_pg_tools.py" [FAIL] 7.0s 548s Time: 7.02 548s Return code: 139 548s OKs: 0 548s Standard error: 548s Segmentation fault (core dumped) 552s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 552s 139 552s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 552s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_twin_laws.py" [FAIL] 6.9s 552s Time: 6.91 552s Return code: 139 552s OKs: 0 552s Standard error: 552s Segmentation fault (core dumped) 555s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 555s 139 555s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 555s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_find_best_cell.py" [FAIL] 6.6s 555s Time: 6.57 555s Return code: 139 555s OKs: 0 555s Standard error: 555s Segmentation fault (core dumped) 558s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 558s 139 558s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 558s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_amplitude_normalisation.py" [FAIL] 6.6s 558s Time: 6.62 558s Return code: 139 558s OKs: 0 558s Standard error: 558s Segmentation fault (core dumped) 562s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 562s 139 562s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 562s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_statistics_graphs.py" [FAIL] 7.3s 562s Time: 7.27 562s Return code: 139 562s OKs: 0 562s Standard error: 562s Segmentation fault (core dumped) 566s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 566s 139 566s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 566s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_web_change_basis.py" [FAIL] 7.3s 566s Time: 7.27 566s Return code: 139 566s OKs: 0 566s Standard error: 566s Segmentation fault (core dumped) 569s Standard error: 569s Segmentation fault (core dumped) 569s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 569s 139 569s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 569s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/direct_space_asu/proto/tst_asu.py" [FAIL] 7.0s 569s Time: 6.96 569s Return code: 139 569s OKs: 0 573s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 573s 139 573s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 573s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_tidy_pickling.py" [FAIL] 7.1s 573s Time: 7.13 573s Return code: 139 573s OKs: 0 573s Standard error: 573s Segmentation fault (core dumped) 576s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 576s 139 576s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 576s libtbx.python "/usr/lib/python3/dist-packages/cctbx/masks/tests/tst_flood_fill.py" [FAIL] 6.9s 576s Time: 6.86 576s Return code: 139 576s OKs: 0 576s Standard error: 576s Segmentation fault (core dumped) 576s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/observations/tst_observations.py" [OK] 0.3s 576s Time: 0.31 576s Return code: 0 576s OKs: 1 576s Standard out: 576s OK 580s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 580s 139 580s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 580s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_r_free_utils.py" [FAIL] 7.2s 580s Standard error: 580s Segmentation fault (core dumped) 580s Time: 7.17 580s Return code: 139 580s OKs: 0 584s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 584s 139 584s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 584s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_ccp.py" [FAIL] 7.0s 584s Time: 7.03 584s Return code: 139 584s OKs: 0 584s Standard error: 584s Segmentation fault (core dumped) 587s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 587s 139 587s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 587s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_mask.py" [FAIL] 7.0s 587s Time: 7.04 587s Return code: 139 587s OKs: 0 587s Standard error: 587s Segmentation fault (core dumped) 591s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 591s 139 591s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 591s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_map_peak_3d_as_2d.py" [FAIL] 7.3s 591s Standard error: 591s Segmentation fault (core dumped) 591s Time: 7.33 591s Return code: 139 591s OKs: 0 594s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 594s 139 594s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 594s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_asymmetric_map.py" [FAIL] 7.1s 594s Time: 7.13 594s Return code: 139 594s OKs: 0 594s Standard error: 594s Segmentation fault (core dumped) 598s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 598s 139 598s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 598s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_peak_volume_estimate.py" [FAIL] 6.8s 598s Time: 6.78 598s Return code: 139 598s OKs: 0 598s Standard error: 598s Segmentation fault (core dumped) 601s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 601s 139 601s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 601s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_resolution_from_map_and_model.py" [FAIL] 6.8s 601s Time: 6.81 601s Return code: 139 601s OKs: 0 601s Standard error: 601s Segmentation fault (core dumped) 604s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 604s 139 604s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 604s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_curves.py" [FAIL] 6.6s 604s Time: 6.60 604s Return code: 139 604s OKs: 0 604s Standard error: 604s Segmentation fault (core dumped) 608s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 608s 139 608s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 608s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_radius_as_central_peak_width.py" [FAIL] 6.7s 608s Time: 6.69 608s Return code: 139 608s OKs: 0 608s Standard error: 608s Segmentation fault (core dumped) 608s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_box.py" [OK] 0.8s 608s Time: 0.80 608s Return code: 0 608s OKs: 0 608s Standard out: 608s phenix is not available, skipping test 609s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_create_models_or_maps.py" [OK] 0.8s 609s Time: 0.85 609s Return code: 0 609s OKs: 1 609s Standard out: 609s Skipping exercise(): chem_data directory not available 609s OK 611s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 611s 139 611s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 611s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_get_percentile_cutoffs.py" [FAIL] 7.0s 611s Time: 6.97 611s Return code: 139 611s OKs: 0 611s Standard error: 611s Segmentation fault (core dumped) 615s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 615s 139 615s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 615s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sphericity.py" [FAIL] 5.5s 615s Time: 5.51 615s Return code: 139 615s OKs: 0 615s Standard error: 615s Segmentation fault (core dumped) 615s libtbx.python "/usr/lib/python3/dist-packages/cctbx/merging/brehm_diederichs.py" [OK] 0.3s 615s Time: 0.29 615s Return code: 0 615s OKs: 1 615s Standard out: 615s OK 615s libtbx.python "/usr/lib/python3/dist-packages/cctbx/multipolar/regression/tst_multipolar.py" [OK] 0.2s 615s Time: 0.22 615s Return code: 0 615s OKs: 3 615s Standard out: 615s OK 615s 0 615s 1 615s 2 615s OK 615s Skipping exercise(): chem_data directory not available 615s OK 618s Standard error: 618s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 618s 139 618s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 618s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_statistics.py" [FAIL] 6.9s 618s Time: 6.91 618s Return code: 139 618s OKs: 0 618s Segmentation fault (core dumped) 622s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 622s 139 622s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 622s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity.py" [FAIL] 6.3s 622s Standard error: 622s Time: 6.29 622s Return code: 139 622s OKs: 0 622s Segmentation fault (core dumped) 625s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 625s 139 625s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 625s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity_allsym.py" [FAIL] 6.7s 625s Standard error: 625s Segmentation fault (core dumped) 625s Time: 6.66 625s Return code: 139 625s OKs: 0 626s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grm_modifications.py" [OK] 0.7s 626s Time: 0.74 626s Return code: 0 626s OKs: 1 626s Standard out: 626s Can not initialize monomer_library, skipping test. 626s OK 631s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 631s 1 631s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 631s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py" [FAIL] 9.4s 631s Time: 9.40 631s Return code: 1 631s OKs: 0 631s Standard error: 631s Segmentation fault (core dumped) 631s Traceback (most recent call last): 631s File "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py", line 140, in 631s exercise() 631s ~~~~~~~~^^ 631s File "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py", line 126, in exercise 631s assert not easy_run.call(cmd) 631s ^^^^^^^^^^^^^^^^^^^^^^ 631s AssertionError 633s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 633s 139 633s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 633s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_prepare_map_for_docking.py" [FAIL] 7.4s 633s Time: 7.42 633s Return code: 139 633s OKs: 0 633s Standard error: 633s Segmentation fault (core dumped) 634s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wavelength_units.py" [OK] 2.8s 634s Time: 2.85 634s Return code: 0 634s OKs: 1 634s Standard out: 634s OK 637s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 637s 139 637s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 637s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fcalc_fft_stability.py" [EXPECTED UNSTABLE] 4.0s 637s Time: 3.98 637s Return code: 139 637s OKs: 0 637s Standard error: 637s Segmentation fault (core dumped) 637s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_ext.py" [OK] 0.1s 637s Time: 0.15 637s Return code: 0 637s OKs: 1 637s Standard out: 637s OK 637s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_equivalence.py" [OK] 0.1s 637s Time: 0.12 637s Return code: 0 637s OKs: 1 637s Standard out: 637s OK 638s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_read.py" [OK] 0.6s 638s Time: 0.58 638s Return code: 0 638s OKs: 1 638s Standard out: 638s OK 638s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_cout.py" [OK] 0.5s 638s Time: 0.45 638s Return code: 0 638s OKs: 1 638s Standard out: 638s OK 639s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_show_calls.py" [OK] 0.4s 639s Time: 0.36 639s Return code: 0 639s OKs: 1 639s Standard out: 639s OK 640s Standard error: 640s Segmentation fault (core dumped) 640s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 640s 139 640s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 640s libtbx.python "/usr/lib/python3/dist-packages/cma_es/tst_cma_es.py" [FAIL] 6.6s 640s Time: 6.56 640s Return code: 139 640s OKs: 0 646s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_command_line.py" [OK] 7.6s 646s Time: 7.61 646s Return code: 0 646s OKs: 1 646s Standard out: 646s fable.split "/usr/lib/python3/dist-packages/fable/test/valid/subroutine_1.f" 646s fable.read --each "/usr/lib/python3/dist-packages/fable/test/valid/write_star.f" 646s fable.read --warnings "/usr/lib/python3/dist-packages/fable/test/valid/equivalence_mixed.f" 646s fable.show_calls --write-graphviz-dot=tmp.dot --top-procedure=sub "/usr/lib/python3/dist-packages/fable/test/valid/external_arg_layers.f" 646s fable.show_calls "/usr/lib/python3/dist-packages/fable/test/valid/dependency_cycle.f" 646s fable.fem_include_search_paths --with-quotes 646s fable.cout --each "/usr/lib/python3/dist-packages/fable/test/valid/write_star.f" 646s fable.cout "/usr/lib/python3/dist-packages/fable/test/valid/common_variants.f" 646s fable.cout "/usr/lib/python3/dist-packages/fable/test/valid/subroutine_3.f" --top-procedure=sub3 --fortran-file-comments 646s fable.cout --compile "/usr/lib/python3/dist-packages/fable/test/valid/write_star.f" 646s fable.cout --namespace=test --run "/usr/lib/python3/dist-packages/fable/test/valid/write_star.f" 646s fable.cout --example 646s fable.cout /usr/lib/python3/dist-packages/fable/test/valid/sf.f --namespace example --run 646s fable.cout "/usr/lib/python3/dist-packages/fable/test/valid/dynamic_parameters_1.f" --dynamic-parameter="int root_size=1" 646s OK 651s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_cout_compile.py" stop [OK] 4.7s 651s Time: 4.66 651s Return code: 0 651s OKs: 1 651s Standard out: 651s g++ -o "stop_bare_fem" -Wall -Wno-sign-compare -Winvalid-pch -Wno-deprecated-declarations -g -O0 -I"/usr/lib/python3/dist-packages/fable" -I"/usr/lib/python3/dist-packages" "stop_bare_fem.cpp" 651s g++ -o "stop_integer_fem" -Wall -Wno-sign-compare -Winvalid-pch -Wno-deprecated-declarations -g -O0 -I"/usr/lib/python3/dist-packages/fable" -I"/usr/lib/python3/dist-packages" "stop_integer_fem.cpp" 651s g++ -o "stop_string_fem" -Wall -Wno-sign-compare -Winvalid-pch -Wno-deprecated-declarations -g -O0 -I"/usr/lib/python3/dist-packages/fable" -I"/usr/lib/python3/dist-packages" "stop_string_fem.cpp" 651s OK 651s usr+sys time: 0.13 seconds 651s wall clock time: 4.60 seconds 655s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_separate_files.py" [OK] 14.8s 655s Time: 14.76 655s Return code: 0 655s OKs: 1 655s Standard out: 655s g++ -o "top.o" -c -Wall -Wno-sign-compare -Winvalid-pch -Wno-deprecated-declarations -g -O0 -I"/usr/lib/python3/dist-packages/fable" -I"/usr/lib/python3/dist-packages" "top.cpp" 655s g++ -o "functions.o" -c -Wall -Wno-sign-compare -Winvalid-pch -Wno-deprecated-declarations -g -O0 -I"/usr/lib/python3/dist-packages/fable" -I"/usr/lib/python3/dist-packages" "functions.cpp" 655s g++ -o "tst_separate_files" -Wall -Wno-sign-compare -Winvalid-pch -Wno-deprecated-declarations -g -O0 -I"/usr/lib/python3/dist-packages/fable" -I"/usr/lib/python3/dist-packages" "top.o" "functions.o" 655s g++ -o "top.o" -c -Wall -Wno-sign-compare -Winvalid-pch -Wno-deprecated-declarations -g -O0 -I"/usr/lib/python3/dist-packages/fable" -I"/usr/lib/python3/dist-packages" "top.cpp" 655s g++ -o "subs.o" -c -Wall -Wno-sign-compare -Winvalid-pch -Wno-deprecated-declarations -g -O0 -I"/usr/lib/python3/dist-packages/fable" -I"/usr/lib/python3/dist-packages" "subs.cpp" 655s g++ -o "tst_separate_files" -Wall -Wno-sign-compare -Winvalid-pch -Wno-deprecated-declarations -g -O0 -I"/usr/lib/python3/dist-packages/fable" -I"/usr/lib/python3/dist-packages" "top.o" "subs.o" 655s g++ -o "top.o" -c -Wall -Wno-sign-compare -Winvalid-pch -Wno-deprecated-declarations -g -O0 -I"/usr/lib/python3/dist-packages/fable" -I"/usr/lib/python3/dist-packages" "top.cpp" 655s g++ -o "subs.o" -c -Wall -Wno-sign-compare -Winvalid-pch -Wno-deprecated-declarations -g -O0 -I"/usr/lib/python3/dist-packages/fable" -I"/usr/lib/python3/dist-packages" "subs.cpp" 655s g++ -o "functions.o" -c -Wall -Wno-sign-compare -Winvalid-pch -Wno-deprecated-declarations -g -O0 -I"/usr/lib/python3/dist-packages/fable" -I"/usr/lib/python3/dist-packages" "functions.cpp" 655s g++ -o "tst_separate_files" -Wall -Wno-sign-compare -Winvalid-pch -Wno-deprecated-declarations -g -O0 -I"/usr/lib/python3/dist-packages/fable" -I"/usr/lib/python3/dist-packages" "top.o" "subs.o" "functions.o" 655s g++ -o "top.o" -c -Wall -Wno-sign-compare -Winvalid-pch -Wno-deprecated-declarations -g -O0 -I"/usr/lib/python3/dist-packages/fable" -I"/usr/lib/python3/dist-packages" "top.cpp" 655s g++ -o "subs.o" -c -Wall -Wno-sign-compare -Winvalid-pch -Wno-deprecated-declarations -g -O0 -I"/usr/lib/python3/dist-packages/fable" -I"/usr/lib/python3/dist-packages" "subs.cpp" 655s g++ -o "tst_separate_files" -Wall -Wno-sign-compare -Winvalid-pch -Wno-deprecated-declarations -g -O0 -I"/usr/lib/python3/dist-packages/fable" -I"/usr/lib/python3/dist-packages" "top.o" "subs.o" 655s g++ -o "top.o" -c -Wall -Wno-sign-compare -Winvalid-pch -Wno-deprecated-declarations -g -O0 -I"/usr/lib/python3/dist-packages/fable" -I"/usr/lib/python3/dist-packages" "top.cpp" 655s g++ -o "subs.o" -c -Wall -Wno-sign-compare -Winvalid-pch -Wno-deprecated-declarations -g -O0 -I"/usr/lib/python3/dist-packages/fable" -I"/usr/lib/python3/dist-packages" "subs.cpp" 655s g++ -o "functions.o" -c -Wall -Wno-sign-compare -Winvalid-pch -Wno-deprecated-declarations -g -O0 -I"/usr/lib/python3/dist-packages/fable" -I"/usr/lib/python3/dist-packages" "functions.cpp" 655s g++ -o "tst_separate_files" -Wall -Wno-sign-compare -Winvalid-pch -Wno-deprecated-declarations -g -O0 -I"/usr/lib/python3/dist-packages/fable" -I"/usr/lib/python3/dist-packages" "top.o" "subs.o" "functions.o" 655s OK 655s usr+sys time: 0.30 seconds 655s wall clock time: 14.71 seconds 656s libtbx.python "/usr/lib/python3/dist-packages/gltbx/tst_ellipsoids.py" [OK] 0.4s 656s Time: 0.39 656s Return code: 0 656s OKs: 1 656s Standard out: 656s OK 660s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 660s 139 660s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 660s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mrc_io.py" [FAIL] 4.1s 660s Time: 4.07 660s Return code: 139 660s OKs: 0 660s Standard error: 660s Segmentation fault (core dumped) 660s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_wildcard.py" [OK] 0.1s 660s Time: 0.11 660s Return code: 0 660s OKs: 1 660s Standard out: 660s OK 661s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_io.py" [OK] 10.3s 661s Time: 10.27 661s Return code: 0 661s OKs: 1 661s Standard out: 661s OK 661s usr+sys time: 0.23 seconds 661s wall clock time: 10.21 seconds 661s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_parser.py" [OK] 0.1s 661s Time: 0.10 661s Return code: 0 661s OKs: 1 661s Standard out: 661s OK 664s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 664s 139 664s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 664s libtbx.python "/usr/lib/python3/dist-packages/iotbx/gui_tools/tst.py" [FAIL] 4.2s 664s Time: 4.15 664s Return code: 139 664s OKs: 0 664s Standard error: 664s Segmentation fault (core dumped) 664s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_cif_inputs.py" [OK] 0.3s 664s Time: 0.29 664s Return code: 0 664s OKs: 1 664s Standard out: 664s OK 667s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 667s 139 667s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 667s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phil.py" [FAIL] 5.9s 667s Time: 5.92 667s Return code: 139 667s OKs: 0 667s Standard error: 667s Segmentation fault (core dumped) 672s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 672s 139 672s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 672s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_manager.py" [FAIL] 7.5s 672s Time: 7.47 672s Return code: 139 672s OKs: 0 672s Standard error: 672s Segmentation fault (core dumped) 675s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 675s 139 675s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 675s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager_wrapping.py" [FAIL] 7.9s 675s Time: 7.92 675s Return code: 139 675s OKs: 0 675s Standard error: 675s Segmentation fault (core dumped) 676s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager.py" [OK] 0.7s 676s Time: 0.73 676s Return code: 0 676s OKs: 1 676s Standard out: 676s Skip test_01, chem_data not available 676s OK 677s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_2.py" [OK] 0.8s 677s Time: 0.78 677s Return code: 0 677s OKs: 0 677s Standard out: 677s chem_data is not available, skipping 677s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_3.py" [OK] 0.8s 677s Time: 0.76 677s Return code: 0 677s OKs: 1 677s Standard out: 677s Skipped: Requires phenix module 677s OK 678s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_4.py" [OK] 0.2s 678s Time: 0.21 678s Return code: 0 678s OKs: 1 678s Standard out: 678s Skipping tst_map_model_manager_4 tests becuase Phenix is not available. 678s OK 678s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_model_sharpening_5.py" [OK] 0.7s 678s Time: 0.73 678s Return code: 0 678s OKs: 1 678s Standard out: 678s Skip test_01, chem_data not available 678s OK 679s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 679s 139 679s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 679s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager.py" [FAIL] 7.2s 679s Time: 7.24 679s Return code: 139 679s OKs: 0 679s Standard error: 679s Segmentation fault (core dumped) 679s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_model_sharpening_5_cif.py" [OK] 0.7s 679s Time: 0.74 679s Return code: 0 679s OKs: 1 679s Standard out: 679s Skip test_01, chem_data not available 679s OK 680s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_call_consistency.py" [OK] 0.7s 680s Time: 0.72 680s Return code: 0 680s OKs: 1 680s Standard out: 680s 680s Expected and actual args in calls for with_bounds 680s 680s box.with_bounds.__init__ : 680s Expected :['log', 'lower_bounds', 'map_manager', 'model', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'upper_bounds', 'use_cubic_boxing', 'wrapping'] 680s Found : ['log', 'lower_bounds', 'map_manager', 'model', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'upper_bounds', 'use_cubic_boxing', 'wrapping'] 680s 680s box_all_maps_with_bounds_and_shift_origin : 680s Expected :['extract_box', 'lower_bounds', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'upper_bounds', 'use_cubic_boxing'] 680s Found : ['boundary_to_smoothing_ratio', 'extract_box', 'lower_bounds', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'soft_mask_around_edges', 'soft_mask_radius', 'stay_inside_current_map', 'upper_bounds', 'use_cubic_boxing'] 680s 680s extract_all_maps_with_bounds : 680s Expected :['lower_bounds', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'upper_bounds', 'use_cubic_boxing'] 680s Found : ['boundary_to_smoothing_ratio', 'lower_bounds', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'soft_mask_around_edges', 'soft_mask_radius', 'stay_inside_current_map', 'upper_bounds', 'use_cubic_boxing'] 680s 680s Expected and actual args in calls for around_model 680s 680s box.around_model.__init__ : 680s Expected :['box_cushion', 'log', 'map_manager', 'model', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'use_cubic_boxing', 'wrapping'] 680s Found : ['box_cushion', 'log', 'map_manager', 'model', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'use_cubic_boxing', 'wrapping'] 680s 680s box_all_maps_around_model_and_shift_origin : 680s Expected :['box_cushion', 'extract_box', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'select_unique_by_ncs', 'selection', 'selection_string', 'self', 'stay_inside_current_map', 'use_cubic_boxing'] 680s Found : ['boundary_to_smoothing_ratio', 'box_cushion', 'extract_box', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'select_unique_by_ncs', 'selection', 'selection_string', 'self', 'soft_mask_around_edges', 'soft_mask_radius', 'stay_inside_current_map', 'use_cubic_boxing'] 680s 680s extract_all_maps_around_model : 680s Expected :['box_cushion', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'select_unique_by_ncs', 'selection', 'selection_string', 'self', 'stay_inside_current_map', 'use_cubic_boxing'] 680s Found : ['boundary_to_smoothing_ratio', 'box_cushion', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'select_unique_by_ncs', 'selection', 'selection_string', 'self', 'soft_mask_around_edges', 'soft_mask_radius', 'stay_inside_current_map', 'use_cubic_boxing'] 680s 680s Expected and actual args in calls for around_density 680s 680s box.around_density.__init__ : 680s Expected :['box_cushion', 'get_half_height_width', 'log', 'map_manager', 'model', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'threshold', 'use_cubic_boxing', 'wrapping'] 680s Found : ['box_cushion', 'get_half_height_width', 'log', 'map_manager', 'model', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'threshold', 'use_cubic_boxing', 'wrapping'] 680s 680s box_all_maps_around_density_and_shift_origin : 680s Expected :['box_cushion', 'extract_box', 'get_half_height_width', 'map_id', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'threshold', 'use_cubic_boxing'] 680s Found : ['boundary_to_smoothing_ratio', 'box_cushion', 'extract_box', 'get_half_height_width', 'map_id', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'soft_mask_around_edges', 'soft_mask_radius', 'stay_inside_current_map', 'threshold', 'use_cubic_boxing'] 680s 680s extract_all_maps_around_density : 680s Expected :['box_cushion', 'get_half_height_width', 'map_id', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'threshold', 'use_cubic_boxing'] 680s Found : ['boundary_to_smoothing_ratio', 'box_cushion', 'get_half_height_width', 'map_id', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'soft_mask_around_edges', 'soft_mask_radius', 'stay_inside_current_map', 'threshold', 'use_cubic_boxing'] 680s 680s Expected and actual args in calls for around_mask 680s 680s box.around_mask.__init__ : 680s Expected :['box_cushion', 'log', 'map_manager', 'mask_as_map_manager', 'model', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'use_cubic_boxing', 'wrapping'] 680s Found : ['box_cushion', 'log', 'map_manager', 'mask_as_map_manager', 'model', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'use_cubic_boxing', 'wrapping'] 680s 680s box_all_maps_around_mask_and_shift_origin : 680s Expected :['box_cushion', 'extract_box', 'mask_id', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'use_cubic_boxing'] 680s Found : ['boundary_to_smoothing_ratio', 'box_cushion', 'extract_box', 'mask_id', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'soft_mask_around_edges', 'soft_mask_radius', 'stay_inside_current_map', 'use_cubic_boxing'] 680s 680s extract_all_maps_around_mask : 680s Expected :['box_cushion', 'mask_id', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'use_cubic_boxing'] 680s Found : ['boundary_to_smoothing_ratio', 'box_cushion', 'mask_id', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'soft_mask_around_edges', 'soft_mask_radius', 'stay_inside_current_map', 'use_cubic_boxing'] 680s 680s Expected and actual args in calls for around_unique 680s 680s box.around_unique.__init__ : 680s Expected :['box_cushion', 'chain_type', 'keep_low_density', 'keep_this_region_only', 'log', 'map_manager', 'mask_expand_ratio', 'model', 'molecular_mass', 'regions_to_keep', 'require_match_unit_cell_crystal_symmetry', 'residues_per_region', 'resolution', 'self', 'sequence', 'soft_mask', 'solvent_content', 'stay_inside_current_map', 'symmetry', 'target_ncs_au_model', 'use_cubic_boxing', 'use_symmetry_in_extract_unique', 'wrapping'] 680s Found : ['box_cushion', 'chain_type', 'keep_low_density', 'keep_this_region_only', 'log', 'map_manager', 'mask_expand_ratio', 'model', 'molecular_mass', 'regions_to_keep', 'require_match_unit_cell_crystal_symmetry', 'residues_per_region', 'resolution', 'self', 'sequence', 'soft_mask', 'solvent_content', 'stay_inside_current_map', 'symmetry', 'target_ncs_au_model', 'use_cubic_boxing', 'use_symmetry_in_extract_unique', 'wrapping'] 680s 680s box_all_maps_around_unique_and_shift_origin : 680s Expected :['box_cushion', 'chain_type', 'extract_box', 'keep_low_density', 'keep_this_region_only', 'mask_expand_ratio', 'molecular_mass', 'regions_to_keep', 'require_match_unit_cell_crystal_symmetry', 'residues_per_region', 'resolution', 'self', 'sequence', 'soft_mask', 'solvent_content', 'stay_inside_current_map', 'symmetry', 'target_ncs_au_model', 'use_cubic_boxing', 'use_symmetry_in_extract_unique'] 680s Found : ['boundary_to_smoothing_ratio', 'box_cushion', 'chain_type', 'extract_box', 'keep_low_density', 'keep_this_region_only', 'mask_expand_ratio', 'molecular_mass', 'regions_to_keep', 'require_match_unit_cell_crystal_symmetry', 'residues_per_region', 'resolution', 'self', 'sequence', 'soft_mask', 'soft_mask_around_edges', 'soft_mask_radius', 'solvent_content', 'stay_inside_current_map', 'symmetry', 'target_ncs_au_model', 'use_cubic_boxing', 'use_symmetry_in_extract_unique'] 680s 680s extract_all_maps_around_unique : 680s Expected :['box_cushion', 'chain_type', 'keep_low_density', 'keep_this_region_only', 'mask_expand_ratio', 'molecular_mass', 'regions_to_keep', 'require_match_unit_cell_crystal_symmetry', 'residues_per_region', 'resolution', 'self', 'sequence', 'soft_mask', 'solvent_content', 'stay_inside_current_map', 'symmetry', 'target_ncs_au_model', 'use_cubic_boxing', 'use_symmetry_in_extract_unique'] 680s Found : ['boundary_to_smoothing_ratio', 'box_cushion', 'chain_type', 'keep_low_density', 'keep_this_region_only', 'mask_expand_ratio', 'molecular_mass', 'regions_to_keep', 'require_match_unit_cell_crystal_symmetry', 'residues_per_region', 'resolution', 'self', 'sequence', 'soft_mask', 'soft_mask_around_edges', 'soft_mask_radius', 'solvent_content', 'stay_inside_current_map', 'symmetry', 'target_ncs_au_model', 'use_cubic_boxing', 'use_symmetry_in_extract_unique'] 680s 680s Expected and actual args in calls for around_atoms 680s 680s cctbx.maptbx.mask.create_mask_around_atoms.__init__ : 680s Expected :['invert_mask', 'map_manager', 'mask_atoms_atom_radius', 'model', 'n_real', 'self', 'wrapping', 'xray_structure'] 680s Found : ['invert_mask', 'map_manager', 'mask_atoms_atom_radius', 'model', 'n_real', 'self', 'wrapping', 'xray_structure'] 680s 680s map_model_manager.create_mask_around_atoms : 680s Expected :['invert_mask', 'mask_atoms_atom_radius', 'mask_id', 'model', 'self', 'soft_mask', 'soft_mask_radius'] 680s Found : ['invert_mask', 'mask_atoms_atom_radius', 'mask_id', 'model', 'self', 'soft_mask', 'soft_mask_radius'] 680s 680s Expected and actual args in calls for around_edges 680s 680s cctbx.maptbx.mask.create_mask_around_edges.__init__ : 680s Expected :['boundary_radius', 'map_manager', 'self'] 680s Found : ['boundary_radius', 'map_manager', 'self'] 680s 680s map_model_manager.create_mask_around_edges : 680s Expected :['boundary_radius', 'mask_id', 'self'] 680s Found : ['boundary_radius', 'boundary_to_smoothing_ratio', 'mask_id', 'self', 'soft_mask_radius'] 680s 680s Expected and actual args in calls for around_density 680s 680s cctbx.maptbx.mask.create_mask_around_density.__init__ : 680s Expected :['map_manager', 'molecular_mass', 'resolution', 'self', 'sequence', 'solvent_content'] 680s Found : ['map_manager', 'molecular_mass', 'resolution', 'self', 'sequence', 'solvent_content'] 680s 680s map_model_manager.create_mask_around_density : 680s Expected :['map_id', 'mask_id', 'resolution', 'self', 'soft_mask', 'soft_mask_radius', 'solvent_content'] 680s Found : ['map_id', 'mask_id', 'resolution', 'self', 'soft_mask', 'soft_mask_radius', 'solvent_content'] 680s OK 680s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_external_sharpening_7.py" [OK] 0.8s 680s Time: 0.78 680s Return code: 0 680s OKs: 1 680s Standard out: 680s Skip test_01, chem_data not available 680s OK 680s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_half_map_sharpening_6.py" [OK] 0.8s 680s Time: 0.77 680s Return code: 0 680s OKs: 1 680s Standard out: 680s Skip test_01, chem_data not available 680s OK 681s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_tls_from_map_8.py" [OK] 0.7s 681s Time: 0.74 681s Return code: 0 681s OKs: 1 681s Standard out: 681s Skip test_01, chem_data not available 681s OK 681s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_cif.py" [OK] 0.8s 681s Time: 0.76 681s Return code: 0 681s OKs: 1 681s Standard out: 681s Skip test_01, chem_data not available 681s OK 685s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 685s 139 685s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 685s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry.py" [FAIL] 4.9s 685s Time: 4.90 685s Return code: 139 685s OKs: 0 685s Standard error: 685s Segmentation fault (core dumped) 686s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_local_resolution_10.py" [OK] 0.8s 686s Time: 0.76 686s Return code: 0 686s OKs: 1 686s Standard out: 686s Skip test_01, chem_data not available 686s OK 690s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 690s 139 690s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 690s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry_cif.py" [FAIL] 8.8s 690s Time: 8.82 690s Return code: 139 690s OKs: 0 690s Standard error: 690s Segmentation fault (core dumped) 690s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_patterson.py" [OK] 0.1s 690s Time: 0.09 690s Return code: 0 690s OKs: 1 690s Standard out: 690s phenix_regression not available, skipping 690s OK 690s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_restraints_merge.py" [OK] 0.3s 690s Time: 0.34 690s Return code: 0 690s OKs: 0 693s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 693s 139 693s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 693s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_tools.py" [FAIL] 7.1s 693s Time: 7.11 693s Return code: 139 693s OKs: 0 693s Standard error: 693s Segmentation fault (core dumped) 693s libtbx.python "/usr/lib/python3/dist-packages/iotbx/ranges.py" [OK] 0.0s 693s Time: 0.04 693s Return code: 0 693s OKs: 1 693s Standard out: 693s OK 697s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 697s 139 697s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 697s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_atom_selections_10k.py" [FAIL] 6.3s 697s Time: 6.31 697s Return code: 139 697s OKs: 0 697s Standard error: 697s Segmentation fault (core dumped) 697s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_poscar.py" [OK] 0.1s 697s Time: 0.10 697s Return code: 0 697s OKs: 1 697s Standard out: 697s Skipping POSCAR tests: input files not available 697s OK 700s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 700s 139 700s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 700s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_crystal_symmetry_from_any.py" [FAIL] 7.0s 700s Time: 7.00 700s Return code: 139 700s OKs: 0 700s Standard error: 700s Segmentation fault (core dumped) 704s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 704s 139 704s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 704s libtbx.python "/usr/lib/python3/dist-packages/iotbx/kriber/tst_strudat.py" [FAIL] 7.1s 704s Time: 7.07 704s Return code: 139 704s OKs: 0 704s Standard error: 704s Segmentation fault (core dumped) 708s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 708s 139 708s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 708s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_geometry.py" [FAIL] 7.3s 708s Time: 7.28 708s Return code: 139 708s OKs: 0 708s Standard error: 708s Segmentation fault (core dumped) 712s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 712s 139 712s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 712s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_lex_parse_build.py" [FAIL] 7.9s 712s Time: 7.87 712s Return code: 139 712s OKs: 0 712s Standard error: 712s Segmentation fault (core dumped) 715s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 715s 139 715s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 715s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model.py" [FAIL] 7.5s 715s Time: 7.52 715s Return code: 139 715s OKs: 0 715s Standard error: 715s Segmentation fault (core dumped) 719s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 719s 1 719s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 719s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py" [FAIL] 3.4s 719s Time: 3.41 719s Return code: 1 719s OKs: 0 719s Standard out: 719s Skipping tst_validation.exercise_smart_load() because of URLError. 719s Standard error: 719s Traceback (most recent call last): 719s File "/usr/lib/python3.13/urllib/request.py", line 1541, in ftp_open 719s fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout) 719s File "/usr/lib/python3.13/urllib/request.py", line 1561, in connect_ftp 719s return ftpwrapper(user, passwd, host, port, dirs, timeout, 719s persistent=False) 719s File "/usr/lib/python3.13/urllib/request.py", line 2409, in __init__ 719s self.init() 719s ~~~~~~~~~^^ 719s File "/usr/lib/python3.13/urllib/request.py", line 2418, in init 719s self.ftp.connect(self.host, self.port, self.timeout) 719s ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 719s File "/usr/lib/python3.13/ftplib.py", line 158, in connect 719s self.sock = socket.create_connection((self.host, self.port), self.timeout, 719s ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 719s source_address=self.source_address) 719s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 719s File "/usr/lib/python3.13/socket.py", line 864, in create_connection 719s raise exceptions[0] 719s File "/usr/lib/python3.13/socket.py", line 849, in create_connection 719s sock.connect(sa) 719s ~~~~~~~~~~~~^^^^ 719s ConnectionRefusedError: [Errno 111] Connection refused 719s 719s The above exception was the direct cause of the following exception: 719s 719s Traceback (most recent call last): 719s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 327, in 719s exercise(sys.argv[1:]) 719s ~~~~~~~~^^^^^^^^^^^^^^ 719s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 26, in exercise 719s exercise_validation() 719s ~~~~~~~~~~~~~~~~~~~^^ 719s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 29, in exercise_validation 719s cd = validation.smart_load_dictionary(name="cif_core.dic") 719s File "/usr/lib/python3/dist-packages/iotbx/cif/validation.py", line 111, in smart_load_dictionary 719s url = locate_dictionary(name, registry_location=registry_location) 719s File "/usr/lib/python3/dist-packages/iotbx/cif/validation.py", line 129, in locate_dictionary 719s cm = cif.reader(file_object=urlopen(registry_location)).model() 719s ~~~~~~~^^^^^^^^^^^^^^^^^^^ 719s File "/usr/lib/python3.13/urllib/request.py", line 189, in urlopen 719s return opener.open(url, data, timeout) 719s ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 719s File "/usr/lib/python3.13/urllib/request.py", line 489, in open 719s response = self._open(req, data) 719s File "/usr/lib/python3.13/urllib/request.py", line 506, in _open 719s result = self._call_chain(self.handle_open, protocol, protocol + 719s '_open', req) 719s File "/usr/lib/python3.13/urllib/request.py", line 466, in _call_chain 719s result = func(*args) 719s File "/usr/lib/python3.13/urllib/request.py", line 1558, in ftp_open 719s raise URLError(exp) from exp 719s urllib.error.URLError: 719s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_parser.py" [OK] 0.3s 719s Time: 0.29 719s Return code: 0 719s OKs: 0 719s Standard out: 719s 1 0 0 719s 1 0 0 719s 1 0 0 719s 1 0 0 719s 1 0 0 719s 1 0 0 719s 1 0 0 719s 1 0 0 719s 1 0 0 719s 0 0 0 719s 0 0 0 719s 1 0 0 719s 0 0 0 719s 0 0 0 719s 1 0 0 719s 1 0 0 719s 1 0 0 719s 1 0 0 719s 1 0 0 719s 1 0 0 719s 1 0 0 719s 1 0 0 719s 1 0 0 719s 1 0 0 719s 1 0 0 719s 1 0 0 719s 0 0 0 719s 1 0 0 719s 1 0 0 719s 1 0 0 719s 1 0 0 719s 1 0 0 719s 0 0 0 719s 0 1 0 719s 0 1 0 719s 0 0 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 0 1 0 719s 1 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s 2 0 0 719s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_citations.py" [OK] 0.4s 719s Time: 0.38 719s Return code: 0 719s OKs: 1 719s Standard out: 719s OK 720s Standard error: 720s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 720s 139 720s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 720s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_restraints.py" [FAIL] 7.7s 720s Time: 7.72 720s Return code: 139 720s OKs: 0 720s Segmentation fault (core dumped) 720s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model_builder.py" [OK] 0.3s 720s Time: 0.30 720s Return code: 0 720s OKs: 0 723s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 723s 139 723s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 723s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_hklf.py" [FAIL] 3.7s 723s Time: 3.69 723s Return code: 139 723s OKs: 0 723s Standard error: 723s Segmentation fault (core dumped) 727s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 727s 139 727s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 727s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_lex_parse_build.py" [FAIL] 7.2s 727s Time: 7.24 727s Return code: 139 727s OKs: 0 727s Standard error: 727s Segmentation fault (core dumped) 731s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 731s 139 731s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 731s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_writer.py" [FAIL] 7.4s 731s Time: 7.36 731s Return code: 139 731s OKs: 0 731s Standard error: 731s Segmentation fault (core dumped) 734s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 734s 139 734s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 734s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_fvar_encoding.py" [FAIL] 7.5s 734s Time: 7.47 734s Return code: 139 734s OKs: 0 734s Standard error: 734s Segmentation fault (core dumped) 735s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif.py" [OK] 0.3s 735s Time: 0.34 735s Return code: 0 735s OKs: 1 735s Standard out: 735s OK 738s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 738s 134 738s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 738s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_pdb.py" [FAIL] 7.1s 738s Time: 7.10 738s Return code: 134 738s OKs: 0 738s Standard error: 738s *** buffer overflow detected ***: terminated 738s Aborted (core dumped) 740s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy_2.py" [OK] 2.1s 740s Time: 2.06 740s Return code: 0 740s OKs: 1 740s Standard out: 740s OK 740s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_tls.py" [OK] 0.7s 740s Time: 0.73 740s Return code: 0 740s OKs: 1 740s Standard out: 740s Skipping exercise_mmcif_tls(): missing phenix_regression directory. 740s OK 741s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/hybrid_36.py" exercise [OK] 0.1s 741s Time: 0.10 741s Return code: 0 741s OKs: 1 741s Standard out: 741s OK 742s "/usr/lib/cctbx/python3.13/iotbx/pdb/hybrid_36_fem" [OK] 1.2s 742s Time: 1.22 742s Return code: 0 742s OKs: 0 742s Standard error: 742s *** buffer overflow detected ***: terminated 742s Aborted (core dumped) 742s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 742s 134 742s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 742s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy.py" [FAIL] 7.2s 742s Time: 7.22 742s Return code: 134 742s OKs: 0 742s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy_atom_sort.py" [OK] 0.3s 742s Time: 0.35 742s Return code: 0 742s OKs: 1 742s Standard out: 742s OK 742s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy_flip_symmetric.py" [OK] 0.3s 742s Time: 0.30 742s Return code: 0 742s OKs: 0 742s Standard out: 742s chem_data is missing, skipping test 743s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_selected_hierarchy_flip.py" [OK] 0.3s 743s Time: 0.32 743s Return code: 0 743s OKs: 0 746s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 746s 139 746s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 746s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy.py" [FAIL] 4.4s 746s Time: 4.37 746s Return code: 139 746s OKs: 0 746s Standard error: 746s Segmentation fault (core dumped) 750s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 750s 139 750s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 750s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_ext.py" [FAIL] 6.8s 750s Time: 6.81 750s Return code: 139 750s OKs: 0 750s Standard error: 750s Segmentation fault (core dumped) 750s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_rna_dna_atom_names.py" [OK] 0.3s 750s Time: 0.31 750s Return code: 0 750s OKs: 1 750s Standard out: 750s OK 750s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_name_interpretation.py" [OK] 0.3s 750s Time: 0.30 750s Return code: 0 750s OKs: 1 750s Standard out: 750s OK 751s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_extract_rfactors_resolutions_sigma.py" [OK] 0.3s 751s Time: 0.30 751s Return code: 0 751s OKs: 1 751s Standard out: 751s OK 751s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/modified_aa_names.py" [OK] 0.0s 751s Time: 0.04 751s Return code: 0 751s OKs: 0 751s Standard out: 751s 2141 751s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/modified_rna_dna_names.py" [OK] 0.0s 751s Time: 0.03 751s Return code: 0 751s OKs: 0 751s Standard out: 751s 792 751s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_sheet.py" [OK] 0.3s 751s Time: 0.31 751s Return code: 0 751s OKs: 1 751s Standard out: 751s OK 751s u+s,u,s: 0.24 0.20 0.04 753s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 753s 139 753s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 753s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection.py" [FAIL] 7.1s 753s Time: 7.08 753s Return code: 139 753s OKs: 0 753s Standard error: 753s Segmentation fault (core dumped) 754s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation_long.py" [OK] 0.3s 754s Time: 0.32 754s Return code: 0 754s OKs: 1 754s Standard out: 754s OK time = 0.013 754s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/secondary_structure.py" [OK] 0.3s 754s Time: 0.34 754s Return code: 0 754s OKs: 0 757s Standard error: 757s Segmentation fault (core dumped) 757s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 757s 139 757s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 757s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation.py" [FAIL] 6.1s 757s Time: 6.09 757s Return code: 139 757s OKs: 0 758s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_secondary_structure.py" [OK] 0.7s 758s Time: 0.73 758s Return code: 0 758s OKs: 5 758s Standard out: 758s OK 758s OK 758s OK 758s OK 758s OK 760s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 760s 139 760s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 760s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection_string.py" [FAIL] 6.5s 760s Time: 6.51 760s Return code: 139 760s OKs: 0 760s Standard error: 760s Segmentation fault (core dumped) 762s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_secondary_structure_2.py" [OK] 1.5s 762s Time: 1.50 762s Return code: 0 762s OKs: 2 762s Standard out: 762s OK 762s OK 763s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/remediation/tst_remediator.py" [OK] 0.8s 763s Time: 0.77 763s Return code: 0 763s OKs: 0 763s Standard out: 763s chem_data is not available for remediator tests, skipping 763s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_to_map_simple.py" [OK] 0.3s 763s Time: 0.34 763s Return code: 0 763s OKs: 0 763s Standard out: 763s Usage: iotbx.python pdb_to_map_simple.py [options] pdb_file... 763s 763s Options: 763s -h, --help show this help message and exit 763s --d_min=FLOAT high-resolution limit for structure-factor calculation 764s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 764s 139 764s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 764s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_utils.py" [FAIL] 6.1s 764s Time: 6.13 764s Return code: 139 764s OKs: 0 764s Standard error: 764s Segmentation fault (core dumped) 764s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_tardy_conf_sampling_simple.py" [OK] 0.3s 764s Time: 0.32 764s Return code: 0 764s OKs: 0 764s Standard out: 764s Time importing extensions: 0.23 764s skipping test: phenix_regression not available. 767s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 767s 134 767s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 767s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_truncate_to_ala/tst.py" [FAIL] 4.4s 767s Time: 4.43 767s Return code: 134 767s OKs: 0 767s Standard error: 767s *** buffer overflow detected ***: terminated 767s Aborted (core dumped) 772s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 772s 139 772s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 772s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_examples.py" [FAIL] 7.5s 772s Time: 7.52 772s Return code: 139 772s OKs: 0 772s Standard error: 772s Segmentation fault (core dumped) 775s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 775s 139 775s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 775s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/space_group_symbols.py" [FAIL] 7.4s 775s Time: 7.37 775s Return code: 139 775s OKs: 0 775s Standard error: 775s Segmentation fault (core dumped) 778s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 778s 139 778s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 778s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/tst_cns.py" [FAIL] 6.8s 778s Standard error: 778s Segmentation fault (core dumped) 778s Time: 6.80 778s Return code: 139 778s OKs: 0 782s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 782s 139 782s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 782s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_merge.py" P31 [FAIL] 7.0s 782s Standard error: 782s Time: 6.97 782s Return code: 139 782s OKs: 0 782s Segmentation fault (core dumped) 785s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 785s 139 785s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 785s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/no_merge_original_index.py" [FAIL] 6.8s 785s Standard error: 785s Segmentation fault (core dumped) 785s Time: 6.80 785s Return code: 139 785s OKs: 0 789s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 789s 139 789s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 789s libtbx.python "/usr/lib/python3/dist-packages/iotbx/ccp4_map/tst.py" [FAIL] 6.8s 789s Time: 6.82 789s Return code: 139 789s OKs: 0 789s Standard error: 789s Segmentation fault (core dumped) 792s Standard error: 792s Segmentation fault (core dumped) 792s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 792s 139 792s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 792s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_ext.py" [FAIL] 7.1s 792s Time: 7.05 792s Return code: 139 792s OKs: 0 796s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 796s 139 796s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 796s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_extract_from_symmetry_lib.py" [FAIL] 7.1s 796s Time: 7.06 796s Return code: 139 796s OKs: 0 796s Standard error: 796s /usr/lib/python3/dist-packages/ccp4io_adaptbx/__init__.py:25: UserWarning: ccp4io_adaptbx: cannot locate syminfo.lib 796s warnings.warn("ccp4io_adaptbx: cannot locate syminfo.lib") 796s Segmentation fault (core dumped) 796s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_miller_dict.py" [OK] 0.3s 796s Time: 0.33 796s Return code: 0 796s OKs: 0 796s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_unmerged.py" [OK] 0.3s 796s Time: 0.33 796s Return code: 0 796s OKs: 0 796s Standard out: 796s Title: . 796s Space group symbol from file: I23 796s Space group number from file: 197 796s Space group from matrices: I 2 3 (No. 197) 796s Point group symbol from file: PG23 796s Number of batches: 45 796s Number of crystals: 2 796s Number of Miller indices: 13 796s Resolution range: 39.0022 31.8451 796s History: 796s From MTZUTILS 21/11/2017 16:26:11 after history: 796s From MOSFLM run on 1/ 7/08 796s From MOSFLM run on 1/ 7/08 796s Crystal 1: 796s Name: HKL_base 796s Project: HKL_base 796s Id: 1 796s Unit cell: (78.0043, 78.0043, 78.0043, 90, 90, 90) 796s Number of datasets: 1 796s Dataset 1: 796s Name: HKL_base 796s Id: 0 796s Wavelength: 0 796s Number of columns: 18 796s label #valid %valid min max type 796s H 13 100.00% 0.00 1.00 H: index h,k,l 796s K 13 100.00% 2.00 2.00 H: index h,k,l 796s L 13 100.00% 0.00 1.00 H: index h,k,l 796s M_ISYM 13 100.00% 6.00 272.00 Y: M/ISYM, packed partial/reject flag and symmetry number 796s BATCH 13 100.00% 16.00 43.00 B: BATCH number 796s I 13 100.00% -19.71 7.39 J: intensity 796s SIGI 13 100.00% 0.41 3.05 Q: standard deviation 796s IPR 13 100.00% -10.84 4.99 J: intensity 796s SIGIPR 13 100.00% 0.41 3.05 Q: standard deviation 796s FRACTIONCALC 13 100.00% 0.07 1.15 R: real 796s XDET 13 100.00% 1099.43 1215.80 R: real 796s YDET 13 100.00% 1110.92 1201.06 R: real 796s ROT 13 100.00% 15.33 41.55 R: real 796s WIDTH 13 100.00% 0.37 2.19 R: real 796s LP 13 100.00% 0.00 0.03 R: real 796s MPART 13 100.00% 0.00 303.00 I: integer 796s FLAG 13 100.00% 0.00 40.00 I: integer 796s BGPKRATIOS 13 100.00% 8.04 10610.05 R: real 796s Crystal 2: 796s Name: DEFAULT 796s Project: AUTOMATIC 796s Id: 2 796s Unit cell: (78.0043, 78.0043, 78.0043, 90, 90, 90) 796s Number of datasets: 1 796s Dataset 1: 796s Name: NATIVE_SWEEP1 796s Id: 1 796s Wavelength: 0.979 796s Number of columns: 0 796s asu: (1, 2, 1) orig: (-1, 1, -2) M/ISYM: 15 796s asu: (1, 2, 1) orig: (1, -1, 2) M/ISYM: 272 796s asu: (1, 2, 1) orig: (1, -1, 2) M/ISYM: 272 796s asu: (1, 2, 1) orig: (-1, 2, 1) M/ISYM: 6 796s asu: (1, 2, 1) orig: (1, -2, -1) M/ISYM: 261 796s asu: (1, 2, 1) orig: (-1, 2, -1) M/ISYM: 263 796s asu: (1, 2, 1) orig: (1, -2, -1) M/ISYM: 261 796s asu: (1, 2, 1) orig: (-1, 2, -1) M/ISYM: 263 796s asu: (1, 2, 1) orig: (1, -2, 1) M/ISYM: 264 796s asu: (1, 2, 1) orig: (1, -2, 1) M/ISYM: 264 796s asu: (0, 2, 0) orig: (0, 0, -2) M/ISYM: 266 796s asu: (0, 2, 0) orig: (0, 0, -2) M/ISYM: 266 796s asu: (0, 2, 0) orig: (0, 0, -2) M/ISYM: 266 799s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 799s 139 799s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 799s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_dano.py" [FAIL] 6.7s 799s Time: 6.70 799s Return code: 139 799s OKs: 0 799s Standard error: 799s Segmentation fault (core dumped) 799s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/tst_mtz_free_flipper.py" [OK] 0.3s 799s Time: 0.32 799s Return code: 0 799s OKs: 0 799s Standard out: 799s Skipping exercise(): input file not available 799s u+s,u,s: 0.25 0.18 0.07 802s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 802s 139 802s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 802s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst.py" P31 [FAIL] 6.1s 802s Time: 6.13 802s Return code: 139 802s OKs: 0 802s Standard error: 802s Segmentation fault (core dumped) 803s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_adsc.py" [OK] 0.2s 803s Time: 0.24 803s Return code: 0 803s OKs: 1 803s Standard out: 803s Skipping exercise_adscread(): input file not available 803s OK 803s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_detectors.py" [OK] 0.1s 803s Time: 0.09 803s Return code: 0 803s OKs: 0 803s Standard out: 803s bpcx_regression not configured, skipping test 807s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 807s 139 807s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 807s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_utils.py" [FAIL] 7.2s 807s Time: 7.18 807s Return code: 139 807s OKs: 0 807s Standard error: 807s Segmentation fault (core dumped) 810s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 810s 139 810s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 810s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xplor/tst_xplormap.py" [FAIL] 7.6s 810s Time: 7.58 810s Return code: 139 810s OKs: 0 810s Standard error: 810s Segmentation fault (core dumped) 810s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdbx_mmcif_tutorial.py" [OK] 0.1s 810s Time: 0.10 810s Return code: 0 810s OKs: 1 810s Standard out: 810s phenix_regression not configured, skipping tst_pdbx_mmcif_tutorial.py 810s OK 814s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 814s 139 814s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 814s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phases.py" P31 [FAIL] 7.3s 814s Time: 7.34 814s Return code: 139 814s OKs: 0 814s Standard error: 814s Segmentation fault (core dumped) 821s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 821s 1 821s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 821s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py" [FAIL] 10.4s 821s Time: 10.35 821s Return code: 1 821s OKs: 0 821s Standard error: 821s Traceback (most recent call last): 821s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 477, in 821s exercise(sys.argv[1:]) 821s ~~~~~~~~^^^^^^^^^^^^^^ 821s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 22, in exercise 821s run_and_compare( 821s ~~~~~~~~~~~~~~~^ 821s ['iotbx.lattice_symmetry' 821s ^^^^^^^^^^^^^^^^^^^^^^^^^ 821s ...<31 lines>... 821s 821s 821s """) 821s ^^^^ 821s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 17, in run_and_compare 821s command=command).raise_if_errors().stdout_lines 821s ~~~~~~~~~~~~~~~^^ 821s File "/usr/lib/python3/dist-packages/libtbx/easy_run.py", line 46, in raise_if_errors 821s raise Error(msg) 821s RuntimeError: child process stderr output: 821s command: 'iotbx.lattice_symmetry --unit_cell="12.7923,12.8923,29.4356,102.846,103.846,22.7475"' 821s Segmentation fault (core dumped) 821s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_plots.py" [OK] 0.1s 821s Time: 0.09 821s Return code: 0 821s OKs: 1 821s Standard out: 821s OK 821s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_csv_utils.py" [OK] 0.2s 821s Time: 0.20 821s Return code: 0 821s OKs: 1 821s Standard out: 821s OK 822s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 822s 139 822s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 822s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_statistics.py" Fdd2 P31m [FAIL] 7.7s 822s Time: 7.68 822s Return code: 139 822s OKs: 0 822s Standard error: 822s Segmentation fault (core dumped) 822s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_bioinformatics.py" [OK] 0.1s 822s Time: 0.13 822s Return code: 0 822s OKs: 3 822s Standard out: 822s Testing guess_chain_types ... OK 822s Testing merge_sequences ... OK 822s testEquality (__main__.test_sequence.testEquality) ... ok 822s testNonEquality (__main__.test_sequence.testNonEquality) ... ok 822s testFormat (__main__.test_fasta_sequence.testFormat) ... ok 822s testStr (__main__.test_fasta_sequence.testStr) ... ok 822s testFormat (__main__.test_pir_sequence.testFormat) ... ok 822s testStr (__main__.test_pir_sequence.testStr) ... ok 822s testConservationCode (__main__.test_midline.testConservationCode) ... ok 822s testMidline (__main__.test_midline.testMidline) ... ok 822s test__str__ (__main__.test_alignment.test__str__) ... ok 822s test_copy (__main__.test_alignment.test_copy) ... ok 822s test_error (__main__.test_alignment.test_error) ... ok 822s test_extend (__main__.test_alignment.test_extend) ... ok 822s test_identity_count (__main__.test_alignment.test_identity_count) ... ok 822s test_identity_fraction (__main__.test_alignment.test_identity_fraction) ... ok 822s test_length (__main__.test_alignment.test_length) ... ok 822s test_multiplicity (__main__.test_alignment.test_multiplicity) ... ok 822s test__str__ (__main__.test_fasta_alignment.test__str__) ... ok 822s test_copy (__main__.test_fasta_alignment.test_copy) ... ok 822s test_error (__main__.test_fasta_alignment.test_error) ... ok 822s test_format (__main__.test_fasta_alignment.test_format) ... ok 822s test__str__ (__main__.test_pir_alignment.test__str__) ... ok 822s test_copy (__main__.test_pir_alignment.test_copy) ... ok 822s test_error (__main__.test_pir_alignment.test_error) ... ok 822s test_format (__main__.test_pir_alignment.test_format) ... ok 822s test__str__ (__main__.test_clustal_alignment.test__str__) ... ok 822s test_copy (__main__.test_clustal_alignment.test_copy) ... ok 822s test_format (__main__.test_clustal_alignment.test_format) ... ok 822s testFasta (__main__.test_sequence_parse.testFasta) ... ok 822s testPir (__main__.test_sequence_parse.testPir) ... ok 822s testSequence (__main__.test_sequence_parse.testSequence) ... ok 822s testTolerantPir (__main__.test_sequence_parse.testTolerantPir) ... ok 822s test_dbfetch_parse (__main__.test_sequence_parse.test_dbfetch_parse) ... ok 822s test_filename_selection (__main__.test_sequence_parse.test_filename_selection) ... ok 822s test_known_formats (__main__.test_sequence_parse.test_known_formats) ... ok 822s test_ls_parse (__main__.test_sequence_parse.test_ls_parse) ... ok 822s test_tf_parse (__main__.test_sequence_parse.test_tf_parse) ... ok 822s testAli (__main__.test_alignment_parse.testAli) ... ok 822s testClustal (__main__.test_alignment_parse.testClustal) ... ok 822s testFasta (__main__.test_alignment_parse.testFasta) ... ok 822s testPir (__main__.test_alignment_parse.testPir) ... ok 822s test_filename_selection (__main__.test_alignment_parse.test_filename_selection) ... ok 822s test_known_formats (__main__.test_alignment_parse.test_known_formats) ... ok 822s test_process_header (__main__.test_hhsearch_parser.test_process_header) ... ok 822s test_process_hits (__main__.test_hhsearch_parser.test_process_hits) ... ok 822s test_process_header (__main__.test_hhalign_parser.test_process_header) ... ok 822s test_process_hits (__main__.test_hhalign_parser.test_process_hits) ... ok 822s 822s ---------------------------------------------------------------------- 822s Ran 46 tests in 0.007s 822s 822s OK 825s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 825s 139 825s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 825s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_file_reader.py" [FAIL] 4.0s 825s Time: 4.01 825s Return code: 139 825s OKs: 0 825s Standard error: 825s Segmentation fault (core dumped) 833s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 833s 1 833s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 833s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py" [FAIL] 10.8s 833s Time: 10.78 833s Return code: 1 833s OKs: 0 833s Standard out: 833s Starting iotbx.pdb.box_around_molecule 833s on Sat Mar 22 13:54:46 2025 by ubuntu 833s =============================================================================== 833s 833s Standard error: 833s *** buffer overflow detected ***: terminated 833s Aborted (core dumped) 833s Traceback (most recent call last): 833s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py", line 138, in 833s exercise() 833s ~~~~~~~~^^ 833s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py", line 48, in exercise 833s assert not easy_run.call("iotbx.pdb.box_around_molecule %s.pdb" % ( 833s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 833s prefix)) 833s ^^^^^^^^ 833s AssertionError 833s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_input.py" [OK] 0.3s 833s Time: 0.33 833s Return code: 0 833s OKs: 0 833s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 833s 134 833s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 833s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_segids.py" [FAIL] 8.3s 833s Standard error: 833s *** buffer overflow detected ***: terminated 833s Aborted (core dumped) 833s Time: 8.28 833s Return code: 134 833s OKs: 0 834s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_multimodel.py" [OK] 0.7s 834s Time: 0.67 834s Return code: 0 834s OKs: 0 834s Standard out: 834s ['_MutableMapping__marker', '__abstractmethods__', '__class__', '__class_getitem__', '__contains__', '__copy__', '__deepcopy__', '__delattr__', '__delitem__', '__dict__', '__dir__', '__doc__', '__eq__', '__firstlineno__', '__format__', '__ge__', '__getattribute__', '__getitem__', '__getstate__', '__gt__', '__hash__', '__init__', '__init_subclass__', '__iter__', '__le__', '__len__', '__lt__', '__module__', '__ne__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__reversed__', '__setattr__', '__setitem__', '__sizeof__', '__slots__', '__static_attributes__', '__str__', '__subclasshook__', '__weakref__', '_abc_impl', '_items', '_set', 'add_data_item', 'add_loop', 'clear', 'copy', 'deepcopy', 'difference', 'get', 'get_loop', 'get_loop_or_row', 'get_loop_with_defaults', 'get_looped_item', 'get_single_item', 'item_keys', 'items', 'iterloops', 'keys', 'keys_lower', 'loop_keys', 'loops', 'pop', 'popitem', 'saves', 'setdefault', 'show', 'sort', 'update', 'validate', 'values'] 834s ['_atom_site.group_PDB', '_atom_site.id', '_atom_site.label_atom_id', '_atom_site.label_alt_id', '_atom_site.label_comp_id', '_atom_site.auth_asym_id', '_atom_site.auth_seq_id', '_atom_site.pdbx_PDB_ins_code', '_atom_site.Cartn_x', '_atom_site.Cartn_y', '_atom_site.Cartn_z', '_atom_site.occupancy', '_atom_site.B_iso_or_equiv', '_atom_site.type_symbol', '_atom_site.pdbx_formal_charge', '_atom_site.label_asym_id', '_atom_site.label_entity_id', '_atom_site.label_seq_id', '_atom_site.pdbx_PDB_model_num', '_chem_comp.id', '_struct_asym.id'] 834s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_add_conformations.py" [OK] 0.3s 834s Time: 0.34 834s Return code: 0 834s OKs: 0 834s Standard out: 834s phenix_regression not available, skipping test. 837s Standard error: 837s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 837s 134 837s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 837s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_forward_compatible_pdb.py" [FAIL] 4.3s 837s Time: 4.26 837s Return code: 134 837s OKs: 0 837s *** buffer overflow detected ***: terminated 837s Aborted (core dumped) 837s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reindex.py" [OK] 0.1s 837s Time: 0.10 837s Return code: 0 837s OKs: 1 837s Standard out: 837s Skipping 837s OK 840s Standard error: 840s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 840s 139 840s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 840s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_symmetry.py" [FAIL] 5.7s 840s Time: 5.75 840s Return code: 139 840s OKs: 0 840s Segmentation fault (core dumped) 843s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 843s 139 843s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 843s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_editor.py" [FAIL] 6.2s 843s Time: 6.23 843s Return code: 139 843s OKs: 0 843s Standard error: 843s Segmentation fault (core dumped) 844s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_as_fasta.py" [OK] 0.3s 844s Time: 0.31 844s Return code: 0 844s OKs: 1 844s Standard out: 844s OK 844s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_link_records.py" [OK] 0.3s 844s Time: 0.35 844s Return code: 0 844s OKs: 0 844s Standard out: 844s Can not initialize monomer_library, skipping test. 844s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_merging_statistics.py" [OK] 0.2s 844s Time: 0.24 844s Return code: 0 844s OKs: 1 844s Standard out: 844s phenix_regression not configured, skipping. 844s OK 849s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 849s 1 849s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 849s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py" [FAIL] 9.3s 849s Time: 9.30 849s Return code: 1 849s OKs: 0 849s Standard error: 849s Traceback (most recent call last): 849s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py", line 60, in 849s exercise() 849s ~~~~~~~~^^ 849s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py", line 48, in exercise 849s assert (len(out.stdout_lines) == 2) and (len(out.stderr_lines) == 0) 849s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 849s AssertionError 850s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 850s 139 850s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 850s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_map_coefficients.py" [FAIL] 5.9s 850s Time: 5.94 850s Return code: 139 850s OKs: 0 850s Standard error: 850s Segmentation fault (core dumped) 850s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_xparm.py" [OK] 0.1s 850s Time: 0.11 850s Return code: 0 850s OKs: 3 850s Standard out: 850s OK 850s OK 850s OK 850s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_xds_inp.py" [OK] 0.1s 850s Time: 0.10 850s Return code: 0 850s OKs: 1 850s Standard out: 850s OK 857s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 857s 1 857s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 857s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py" [FAIL] 7.8s 857s Time: 7.77 857s Return code: 1 857s OKs: 0 857s Standard out: 857s iotbx.pdb.sort_atoms tst_sort_atoms_1.pdb 857s Standard error: 857s Segmentation fault (core dumped) 857s Traceback (most recent call last): 857s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py", line 815, in 857s exercise_1() 857s ~~~~~~~~~~^^ 857s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py", line 806, in exercise_1 857s assert not easy_run.call(cmd) 857s ^^^^^^^^^^^^^^^^^^^^^^ 857s AssertionError 857s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_spots_xds.py" [OK] 0.1s 857s Time: 0.09 857s Return code: 0 857s OKs: 1 857s Standard out: 857s OK 858s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_as_cif.py" [OK] 0.4s 858s Time: 0.43 858s Return code: 0 858s OKs: 1 858s Standard out: 858s Can not initialize monomer_library, skipping tst_pdb_as_cif. 858s OK 858s Standard error: 858s Segmentation fault (core dumped) 858s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 858s 139 858s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 858s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_integrate_hkl.py" [FAIL] 7.9s 858s Time: 7.92 858s Return code: 139 858s OKs: 0 862s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 862s 139 862s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 862s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_no_merge_original_index.py" [FAIL] 3.8s 862s Time: 3.80 862s Return code: 139 862s OKs: 0 862s Standard error: 862s Segmentation fault (core dumped) 865s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 865s 139 865s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 865s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_export_scalepack_unmerged.py" [FAIL] 6.7s 865s Standard error: 865s Segmentation fault (core dumped) 865s Time: 6.73 865s Return code: 139 865s OKs: 0 865s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_mtrix_biomt_cmdl.py" [OK] 0.3s 865s Time: 0.31 865s Return code: 0 865s OKs: 0 865s Standard out: 865s Skipping tests: phenix not found 866s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_mmcif_biomt_reduction_output.py" [OK] 0.7s 866s Time: 0.75 866s Return code: 0 866s OKs: 0 866s Standard out: 866s chem_data is not available, skipping 868s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 868s 139 868s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 868s libtbx.python "/usr/lib/python3/dist-packages/iotbx/dsn6/tst.py" P31 [FAIL] 6.8s 868s Time: 6.77 868s Return code: 139 868s OKs: 0 868s Standard error: 868s Segmentation fault (core dumped) 872s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 872s 139 872s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 872s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_ligs.py" [FAIL] 5.7s 872s Time: 5.73 872s Return code: 139 872s OKs: 0 872s Standard error: 872s Segmentation fault (core dumped) 875s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 875s 139 875s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 875s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_broken_chain.py" [FAIL] 7.1s 875s Time: 7.15 875s Return code: 139 875s OKs: 0 875s Standard error: 875s Segmentation fault (core dumped) 879s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 879s 139 879s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 879s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_shortcut_1.py" [FAIL] 7.2s 879s Time: 7.24 879s Return code: 139 879s OKs: 0 879s Standard error: 879s Segmentation fault (core dumped) 883s Standard error: 883s Segmentation fault (core dumped) 883s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 883s 139 883s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 883s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_groups_preprocessing.py" [FAIL] 7.9s 883s Time: 7.89 883s Return code: 139 883s OKs: 0 887s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 887s 139 887s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 887s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_input.py" [FAIL] 7.6s 887s Time: 7.62 887s Return code: 139 887s OKs: 0 887s Standard error: 887s Segmentation fault (core dumped) 890s Standard error: 890s Segmentation fault (core dumped) 890s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 890s 139 890s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 890s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_user_selections.py" [FAIL] 6.9s 890s Time: 6.91 890s Return code: 139 890s OKs: 0 895s Standard error: 895s Segmentation fault (core dumped) 895s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 895s 139 895s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 895s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs.py" [FAIL] 7.9s 895s Time: 7.89 895s Return code: 139 895s OKs: 0 898s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 898s 139 898s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 898s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_without_validation.py" [FAIL] 8.2s 898s Time: 8.17 898s Return code: 139 898s OKs: 0 898s Standard error: 898s Segmentation fault (core dumped) 903s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 903s 139 903s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 903s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_read_mtrix_records_from_cif.py" [FAIL] 7.9s 903s Time: 7.92 903s Return code: 139 903s OKs: 0 903s Standard error: 903s Segmentation fault (core dumped) 906s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 906s 139 906s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 906s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_show_systematic_absences.py" [FAIL] 7.8s 906s Time: 7.76 906s Return code: 139 906s OKs: 0 906s Standard error: 906s Segmentation fault (core dumped) 907s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_reader.py" [OK] 0.4s 907s Time: 0.43 907s Return code: 0 907s OKs: 1 907s Standard out: 907s OK 910s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 910s 139 910s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 910s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_miller_sort_asu.py" [FAIL] 7.1s 910s Time: 7.09 910s Return code: 139 910s OKs: 0 910s Standard error: 910s Segmentation fault (core dumped) 910s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_alignment_as_hsearch.py" [OK] 0.1s 910s Time: 0.13 910s Return code: 0 910s OKs: 0 910s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_ebi_wu_blast_xml.py" [OK] 0.1s 910s Time: 0.14 910s Return code: 0 910s OKs: 0 910s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_ncbi_blast_xml.py" [OK] 0.1s 910s Time: 0.14 910s Return code: 0 910s OKs: 0 911s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/pdb_info.py" [OK] 1.0s 911s Time: 0.96 911s Return code: 0 911s OKs: 0 914s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 914s 134 914s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 914s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_xray_scale.py" [FAIL] 7.5s 914s Time: 7.51 914s Return code: 134 914s OKs: 0 914s Standard error: 914s *** buffer overflow detected ***: terminated 914s Aborted (core dumped) 918s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 918s 139 918s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 918s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_as_pdb_1atom.py" [FAIL] 7.3s 918s Time: 7.34 918s Return code: 139 918s OKs: 0 918s Standard error: 918s Segmentation fault (core dumped) 923s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 923s 139 923s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 923s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_1.py" [FAIL] 8.4s 923s Time: 8.40 923s Return code: 139 923s OKs: 0 923s Standard error: 923s Segmentation fault (core dumped) 930s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 930s 1 930s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 930s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py" [FAIL] 11.8s 930s Time: 11.83 930s Return code: 1 930s OKs: 0 930s Standard error: 930s Traceback (most recent call last): 930s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py", line 395, in 930s tst_1() 930s ~~~~~^^ 930s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py", line 370, in tst_1 930s assert os.path.isfile('%s.cif_%s_000.mtz' % (prefix, bn)) 930s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 930s AssertionError 932s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 932s 134 932s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 932s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_all_chain_ids.py" [FAIL] 9.1s 932s Time: 9.10 932s Return code: 134 932s OKs: 0 932s Standard error: 932s *** buffer overflow detected ***: terminated 932s Aborted (core dumped) 935s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 935s 139 935s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 935s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_extract_xtal_data.py" [FAIL] 4.9s 935s Time: 4.94 935s Return code: 139 935s OKs: 0 935s Standard error: 935s Segmentation fault (core dumped) 936s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mtz_as_cif.py" [OK] 0.4s 936s Time: 0.43 936s Return code: 0 936s OKs: 1 936s Standard out: 936s Skipping 1akg.mtz test: input file not available 936s Skipping 1zff.mtz test: input file not available 936s Skipping l.mtz test: input file not available 936s Skipping outside_4_exptl_fobs_phases_freeR_flags.mtz test: input file not available 936s Skipping r1wqzsf.mtz test: input file not available 936s Skipping ur0013.sf.mtz test: input file not available 936s Skipping 1aba_test.mtz test: input file not available 936s OK 936s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_group_rounding.py" [OK] 0.3s 936s Time: 0.31 936s Return code: 0 936s OKs: 0 940s Standard error: 940s Segmentation fault (core dumped) 940s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 940s 139 940s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 940s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cli_parser.py" [FAIL] 7.9s 940s Time: 7.92 940s Return code: 139 940s OKs: 0 940s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_merge_atoms_at_end_to_residues.py" [OK] 0.3s 940s Time: 0.33 940s Return code: 0 940s OKs: 1 940s Standard out: 940s [('1', 22), ('3', 17), ('1', 1), ('3', 1)] 940s [('1', 22), ('3', 18), ('1', 1)] 940s OK 941s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_chain_ids_1.py" [OK] 1.2s 941s Time: 1.23 941s Return code: 0 941s OKs: 1 941s Standard out: 941s 941s total number of: 941s models: 1 941s chains: 3 941s alt. conf.: 0 941s residues: 12 941s atoms: 174 941s anisou: 0 941s number of atom element+charge types: 4 941s histogram of atom element+charge frequency: 941s " H " 78 941s " C " 60 941s " O " 21 941s " N " 15 941s residue name classes: 941s "common_amino_acid" 12 941s number of chain ids: 3 941s histogram of chain id frequency: 941s "A" 1 941s "A-2" 1 941s "A-5" 1 941s number of alt. conf. ids: 0 941s number of residue names: 4 941s histogram of residue name frequency: 941s "ASN" 3 941s "PHE" 3 941s "SER" 3 941s "THR" 3 941s Can not initialize monomer_library, skipping test. 941s OK. Time: 0.424 942s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_1.py" [OK] 0.7s 942s Time: 0.72 942s Return code: 0 942s OKs: 1 942s Standard out: 942s OK. Time: 0.383 943s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_2.py" [OK] 0.8s 943s Time: 0.79 943s Return code: 0 943s OKs: 1 943s Standard out: 943s Can not initialize monomer_library, skipping test. 943s OK. Time: 0.017 943s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 943s 134 943s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 943s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_occupancies_rounding.py" [FAIL] 7.2s 943s Time: 7.16 943s Return code: 134 943s OKs: 0 943s Standard error: 943s *** buffer overflow detected ***: terminated 943s Aborted (core dumped) 943s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_3.py" [OK] 0.8s 943s Time: 0.80 943s Return code: 0 943s OKs: 1 943s Standard out: 943s Can not initialize monomer_library, skipping test. 943s OK. Time: 0.016 944s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_copy_select.py" [OK] 0.3s 944s Time: 0.35 944s Return code: 0 944s OKs: 1 944s Standard out: 944s There is no info: pdb=" N " 944s And no parent: None 944s Info is gone: pdb=" N " 944s Info is still here: pdb=" N GLY A 1 " 944s OK. Time: 0.031 944s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_4.py" [OK] 0.8s 944s Time: 0.75 944s Return code: 0 944s OKs: 1 944s Standard out: 944s Can not initialize monomer_library, skipping test. 944s OK. Time: 0.015 944s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_id_str.py" [OK] 0.3s 944s Time: 0.32 944s Return code: 0 944s OKs: 0 944s Standard out: 944s u+s,u,s: 0.24 0.20 0.04 944s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_altlocs.py" [OK] 0.3s 944s Time: 0.31 944s Return code: 0 944s OKs: 1 944s Standard out: 944s OK 948s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 948s 139 948s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 948s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_debug_write.py" [FAIL] 3.6s 948s Time: 3.57 948s Return code: 139 948s OKs: 0 948s Standard error: 948s Segmentation fault (core dumped) 952s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 952s 139 952s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 952s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_reordered_chains.py" [EXPECTED FAIL] 4.3s 952s Standard error: 952s Segmentation fault (core dumped) 952s Time: 4.26 952s Return code: 139 952s OKs: 0 957s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 957s 134 957s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 957s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_to_from_hierarchy.py" [EXPECTED FAIL] 5.5s 957s Time: 5.48 957s Return code: 134 957s OKs: 0 957s Standard error: 957s *** buffer overflow detected ***: terminated 957s Aborted (core dumped) 958s libtbx.python "/usr/lib/python3/dist-packages/libtbx/metric_prefixes.py" [OK] 0.0s 958s Time: 0.03 958s Return code: 0 958s OKs: 1 958s Standard out: 958s OK 962s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_utils.py" [OK] 4.4s 962s Time: 4.36 962s Return code: 0 962s OKs: 0 962s Standard out: 962s Skipping exercise_retrieve_unless_exists 962s ### USER = ubuntu 962s ### PID = 10987 962s multiprocessing problem: None 962s base36_timestamp(): 00m8k9wfr7 now 962s base36_timestamp(): zzydazd000 year 115855 CE 962s get_svn_revision(): None 962s get_build_tag(): None 962s u+s,u,s: 0.12 0.09 0.03 963s libtbx.python "/usr/lib/python3/dist-packages/libtbx/test_utils/__init__.py" [OK] 0.7s 963s Time: 0.70 963s Return code: 0 963s OKs: 1 963s Standard out: 963s OK 963s libtbx.python "/usr/lib/python3/dist-packages/libtbx/queuing_system_utils/pbs_utils.py" [OK] 0.0s 963s Time: 0.03 963s Return code: 0 963s OKs: 1 963s Standard out: 963s *** MY_PBS_ARRAY_SIZE = None 963s *** MY_PBS_ARRAYID_OFFSET = None 963s *** PBS_ARRAYID = None 963s *** OMPI_MCA_ns_nds_num_procs = None 963s *** OMPI_MCA_ns_nds_vpid = None 963s n,i: 1 0 963s OK 963s libtbx.python "/usr/lib/python3/dist-packages/libtbx/queuing_system_utils/sge_utils.py" [OK] 0.0s 963s Time: 0.04 963s Return code: 0 963s OKs: 1 963s Standard out: 963s *** JOB_ID = None 963s *** SGE_ARCH = None 963s *** SGE_TASK_FIRST = None 963s *** SGE_TASK_LAST = None 963s *** SGE_TASK_ID = None 963s OK 963s libtbx.python "/usr/lib/python3/dist-packages/libtbx/introspection.py" [OK] 0.1s 963s Time: 0.06 963s Return code: 0 963s OKs: 1 963s Standard out: 963s number of processors: 2 963s Virtual memory size: 21,209,088 963s Resident set size: 12,308,480 963s Stack size: 139,264 963s Virtual memory size: 21,336,064 exact max: 29,339,648 963s Resident set size: 12,820,480 approx. max: 20,750,336 963s Stack size: 139,264 approx. max: 139,264 963s Memory total: 4,088,070,144 963s Memory free: 133,459,968 963s OK 985s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_thread_utils.py" [OK] 22.3s 985s Time: 22.33 985s Return code: 0 985s OKs: 1 985s Standard out: 985s OK 986s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_fetch.py" [OK] 41.6s 986s Time: 41.62 986s Return code: 0 986s OKs: 1 986s Standard out: 986s data_r1yjpsf 986s # 986s loop_ 986s _audit.revision_id 986s _audit.creation_date 986s _audit.update_record 986s 1_0 2005-06-14 'Initial release' 986s 1_1 2013-05-08 'Status correction and format standardization' 986s # 986s _cell.entry_id 1yjp 986s _cell.length_a 21.937 986s _cell.length_b 4.866 986s _cell.length_c 23.477 986s _cell.angle_alpha 90.000 986s _cell.angle_beta 107.080 986s _cell.angle_gamma 90.000 986s # 986s _diffrn_radiation_wavelength.id 1 986s _diffrn_radiation_wavelength.wavelength 0.97500 986s # 986s _entry.id 1yjp 986s # 986s _exptl_crystal.id 1 986s # 986s _reflns_scale.group_code 1 986s # 986s _symmetry.entry_id 1yjp 986s _symmetry.space_group_name_H-M 'P 1 21 1' 986s # 986s # 986s loop_ 986s _refln.crystal_id 986s _refln.wavelength_id 986s _refln.scale_group_code 986s _refln.index_h 986s _refln.index_k 986s _refln.index_l 986s _refln.status 986s _refln.F_meas_au 986s _refln.F_meas_sigma_au 986s 1 1 1 -12 0 2 o 3.49 2.34 986s 1 1 1 -12 0 3 o 3.31 2.43 986s 1 1 1 -12 0 4 o 7.32 4.25 986s 1 1 1 -12 0 5 o 8.88 5.39 986s 1 1 1 -11 0 1 o 9.46 4.13 986s 1 1 1 -11 0 2 o 4.91 3.21 986s 1 1 1 -11 0 3 o 6.37 3.70 986s 1 1 1 -11 0 4 o 8.50 4.91 986s 1 1 1 -11 0 5 o 17.44 8.06 986s 1 1 1 -11 0 6 o 5.89 3.64 986s 1 1 1 -11 0 8 o 6.39 3.90 986s 1 1 1 -11 1 2 o 5.69 2.18 986s 1 1 1 -11 1 3 o 6.53 2.53 986s 1 1 1 -11 1 5 o 7.26 3.20 986s 1 1 1 -11 1 6 o 11.05 3.47 986s 1 1 1 -10 0 2 o 6.32 3.74 986s 1 1 1 -10 0 3 o 9.36 4.67 986s 1 1 1 -10 0 5 o 7.20 4.12 986s 1 1 1 -10 0 6 o 4.88 3.25 986s 1 1 1 -10 0 7 o 11.84 5.41 986s 1 1 1 -10 0 8 o 14.49 6.53 986s 1 1 1 -10 0 9 o 6.21 3.91 986s 1 1 1 -10 0 10 o 5.55 3.37 986s 1 1 1 -10 1 1 o 4.58 1.49 986s 1 1 1 -10 1 3 o 12.40 3.65 986s 1 1 1 -10 1 4 o 9.07 2.47 986s 1 1 1 -10 1 5 o 17.23 6.02 986s 1 1 1 -10 1 6 o 4.60 2.10 986s 1 1 1 -10 1 7 o 6.34 2.43 986s 1 1 1 -10 1 8 o 9.04 2.92 986s 1 1 1 -9 0 2 o 8.10 3.98 986s 1 1 1 -9 0 3 o 14.22 5.11 986s 1 1 1 -9 0 5 o 6.01 3.78 986s 1 1 1 -9 0 6 o 10.48 4.68 986s 1 1 1 -9 0 7 o 8.79 4.52 986s 1 1 1 -9 0 8 o 6.15 3.63 986s 1 1 1 -9 0 9 o 10.27 4.16 986s 1 1 1 -9 0 10 o 4.38 3.04 986s 1 1 1 -9 0 11 o 7.27 4.16 986s 1 1 1 -9 1 3 o 10.75 2.38 986s 1 1 1 -9 1 4 o 11.86 1.95 986s 1 1 1 -9 1 5 o 10.95 3.27 986s 1 1 1 -9 1 6 o 13.31 2.59 986s 1 1 1 -9 1 7 o 8.06 2.92 986s 1 1 1 -9 1 8 o 14.75 2.87 986s 1 1 1 -9 1 9 o 9.04 2.82 986s 1 1 1 -8 0 2 f 15.88 3.97 986s 1 1 1 -8 0 3 o 26.78 5.79 986s 1 1 1 -8 0 5 o 32.83 7.52 986s 1 1 1 -8 0 7 o 12.74 3.54 986s 1 1 1 -8 0 8 o 29.46 9.29 986s 1 1 1 -8 0 9 f 22.09 3.59 986s 1 1 1 -8 0 10 o 18.81 5.24 986s 1 1 1 -8 0 11 o 12.76 7.11 986s 1 1 1 -8 1 1 o 6.26 2.08 986s 1 1 1 -8 1 2 o 6.97 2.14 986s 1 1 1 -8 1 4 o 19.24 4.18 986s 1 1 1 -8 1 5 o 15.46 2.43 986s 1 1 1 -8 1 6 o 16.87 2.78 986s 1 1 1 -8 1 7 o 15.66 2.34 986s 1 1 1 -8 1 8 o 7.07 2.43 986s 1 1 1 -8 1 9 o 8.81 2.80 986s 1 1 1 -8 1 10 o 8.61 3.09 986s 1 1 1 -8 2 1 o 4.39 1.52 986s 1 1 1 -8 2 2 o 4.20 1.87 986s 1 1 1 -8 2 3 o 6.14 1.87 986s 1 1 1 -8 2 4 o 9.38 2.80 986s 1 1 1 -7 0 3 o 23.46 3.83 986s 1 1 1 -7 0 4 o 37.35 7.40 986s 1 1 1 -7 0 6 o 7.44 3.60 986s 1 1 1 -7 0 7 o 43.94 5.36 986s 1 1 1 -7 0 8 o 18.96 2.98 986s 1 1 1 -7 0 9 o 4.95 3.22 986s 1 1 1 -7 0 10 o 31.73 4.61 986s 1 1 1 -7 0 11 o 6.31 3.82 986s 1 1 1 -7 0 12 o 5.05 3.33 986s 1 1 1 -7 1 1 o 8.89 1.60 986s 1 1 1 -7 1 2 o 13.70 1.71 986s 1 1 1 -7 1 3 o 21.03 2.45 986s 1 1 1 -7 1 4 f 7.57 2.36 986s 1 1 1 -7 1 5 o 11.31 3.34 986s 1 1 1 -7 1 6 o 19.93 3.06 986s 1 1 1 -7 1 7 o 22.86 3.28 986s 1 1 1 -7 1 8 o 10.32 2.58 986s 1 1 1 -7 1 9 f 5.13 2.34 986s 1 1 1 -7 1 10 o 9.91 3.03 986s 1 1 1 -7 1 11 o 5.61 2.33 986s 1 1 1 -7 2 1 o 12.28 3.86 986s 1 1 1 -7 2 2 o 11.29 3.50 986s 1 1 1 -7 2 3 f 7.22 2.40 986s 1 1 1 -7 2 4 o 11.13 2.74 986s 1 1 1 -7 2 5 o 7.86 2.92 986s 1 1 1 -7 2 6 o 5.23 2.15 986s 1 1 1 -6 0 2 o 35.03 5.13 986s 1 1 1 -6 0 3 o 15.64 3.61 986s 1 1 1 -6 0 4 o 12.60 4.22 986s 1 1 1 -6 0 5 o 21.36 2.47 986s 1 1 1 -6 0 6 o 31.19 3.17 986s 1 1 1 -6 0 7 o 33.66 3.99 986s 1 1 1 -6 0 8 o 13.70 4.22 986s 1 1 1 -6 0 9 o 10.99 4.16 986s 1 1 1 -6 0 10 o 24.56 3.98 986s 1 1 1 -6 0 11 o 4.41 3.08 986s 1 1 1 -6 0 12 o 4.07 2.83 986s 1 1 1 -6 1 1 o 10.24 1.40 986s 1 1 1 -6 1 2 o 20.59 2.28 986s 1 1 1 -6 1 3 o 32.14 3.57 986s 1 1 1 -6 1 4 f 11.60 2.18 986s 1 1 1 -6 1 5 o 22.15 2.66 986s 1 1 1 -6 1 6 o 7.68 2.64 986s 1 1 1 -6 1 7 o 6.39 2.58 986s 1 1 1 -6 1 8 o 6.60 2.60 986s 1 1 1 -6 1 9 o 8.21 2.82 986s 1 1 1 -6 1 10 o 13.25 3.07 986s 1 1 1 -6 1 11 o 10.62 3.80 986s 1 1 1 -6 2 1 o 13.78 2.98 986s 1 1 1 -6 2 2 o 5.95 2.11 986s 1 1 1 -6 2 3 o 8.96 3.00 986s 1 1 1 -6 2 4 o 4.88 2.17 986s 1 1 1 -6 2 5 o 7.35 2.58 986s 1 1 1 -6 2 6 o 6.93 2.91 986s 1 1 1 -6 2 7 o 8.14 2.74 986s 1 1 1 -5 0 2 o 44.04 6.46 986s 1 1 1 -5 0 3 o 15.30 3.69 986s 1 1 1 -5 0 4 o 16.95 2.51 986s 1 1 1 -5 0 5 o 14.82 4.54 986s 1 1 1 -5 0 6 o 29.73 3.15 986s 1 1 1 -5 0 7 f 55.71 13.43 986s 1 1 1 -5 0 8 o 15.06 3.67 986s 1 1 1 -5 0 9 o 8.76 4.15 986s 1 1 1 -5 0 10 o 4.69 3.13 986s 1 1 1 -5 0 11 o 16.56 5.19 986s 1 1 1 -5 0 12 o 5.59 3.77 986s 1 1 1 -5 1 1 o 26.70 2.49 986s 1 1 1 -5 1 2 o 38.67 3.63 986s 1 1 1 -5 1 3 o 20.45 2.09 986s 1 1 1 -5 1 4 o 6.46 2.54 986s 1 1 1 -5 1 5 o 20.55 2.58 986s 1 1 1 -5 1 6 o 28.68 2.67 986s 1 1 1 -5 1 7 o 5.68 2.48 986s 1 1 1 -5 1 8 o 6.99 2.70 986s 1 1 1 -5 1 9 o 20.74 2.59 986s 1 1 1 -5 1 10 o 14.70 3.00 986s 1 1 1 -5 1 11 o 8.62 2.89 986s 1 1 1 -5 2 1 o 6.26 2.16 986s 1 1 1 -5 2 2 o 7.93 2.10 986s 1 1 1 -5 2 3 o 19.90 4.18 986s 1 1 1 -5 2 4 o 4.98 2.02 986s 1 1 1 -5 2 5 o 16.85 3.60 986s 1 1 1 -5 2 7 o 8.15 2.74 986s 1 1 1 -5 2 8 o 8.89 2.75 986s 1 1 1 -4 0 2 o 4.55 2.74 986s 1 1 1 -4 0 3 o 23.50 2.52 986s 1 1 1 -4 0 4 o 19.15 3.81 986s 1 1 1 -4 0 7 o 20.06 2.98 986s 1 1 1 -4 0 8 o 28.85 3.55 986s 1 1 1 -4 0 9 o 5.36 3.45 986s 1 1 1 -4 0 10 o 25.68 3.87 986s 1 1 1 -4 0 11 o 23.28 3.81 986s 1 1 1 -4 0 12 o 11.39 4.82 986s 1 1 1 -4 0 13 o 7.07 3.96 986s 1 1 1 -4 1 1 o 31.99 4.35 986s 1 1 1 -4 1 2 o 18.48 1.94 986s 1 1 1 -4 1 3 f 18.93 2.01 986s 1 1 1 -4 1 4 o 38.05 3.65 986s 1 1 1 -4 1 5 o 36.34 3.49 986s 1 1 1 -4 1 6 o 18.08 3.24 986s 1 1 1 -4 1 7 o 20.11 2.29 986s 1 1 1 -4 1 8 o 11.25 2.61 986s 1 1 1 -4 1 9 o 27.09 3.02 986s 1 1 1 -4 1 10 o 17.78 3.55 986s 1 1 1 -4 1 11 o 10.45 3.55 986s 1 1 1 -4 1 12 o 7.42 2.61 986s 1 1 1 -4 2 1 o 7.72 2.01 986s 1 1 1 -4 2 2 o 30.88 3.36 986s 1 1 1 -4 2 3 o 19.14 2.65 986s 1 1 1 -4 2 4 o 4.44 2.00 986s 1 1 1 -4 2 5 f 26.44 8.10 986s 1 1 1 -4 2 6 o 10.83 3.21 986s 1 1 1 -4 2 7 o 6.03 2.73 986s 1 1 1 -4 2 8 o 12.78 2.87 986s 1 1 1 -3 0 2 o 3.40 2.13 986s 1 1 1 -3 0 3 o 5.40 2.78 986s 1 1 1 -3 0 4 o 11.52 2.39 986s 1 1 1 -3 0 5 o 55.13 5.36 986s 1 1 1 -3 0 6 f 31.55 3.22 986s 1 1 1 -3 0 7 o 6.95 4.11 986s 1 1 1 -3 0 8 o 6.00 3.79 986s 1 1 1 -3 0 9 o 23.03 3.41 986s 1 1 1 -3 0 10 o 4.79 3.36 986s 1 1 1 -3 0 11 o 10.46 5.21 986s 1 1 1 -3 0 12 o 11.53 6.07 986s 1 1 1 -3 0 13 o 3.22 2.15 986s 1 1 1 -3 1 1 o 53.95 5.22 986s 1 1 1 -3 1 2 o 21.50 3.03 986s 1 1 1 -3 1 3 o 42.88 4.08 986s 1 1 1 -3 1 4 o 42.70 6.13 986s 1 1 1 -3 1 5 o 41.12 3.18 986s 1 1 1 -3 1 6 o 17.31 2.67 986s 1 1 1 -3 1 7 o 35.59 4.21 986s 1 1 1 -3 1 8 o 18.53 2.36 986s 1 1 1 -3 1 9 o 11.55 2.71 986s 1 1 1 -3 1 10 o 11.41 2.79 986s 1 1 1 -3 1 11 o 6.92 2.69 986s 1 1 1 -3 1 12 o 7.03 2.45 986s 1 1 1 -3 2 1 o 18.65 2.01 986s 1 1 1 -3 2 2 o 16.33 1.93 986s 1 1 1 -3 2 3 o 32.88 5.01 986s 1 1 1 -3 2 4 o 9.99 2.93 986s 1 1 1 -3 2 5 o 20.62 2.93 986s 1 1 1 -3 2 6 o 9.18 3.06 986s 1 1 1 -3 2 7 o 6.90 2.83 986s 1 1 1 -3 2 8 o 5.26 2.23 986s 1 1 1 -2 0 1 o 37.92 5.29 986s 1 1 1 -2 0 2 o 25.98 3.53 986s 1 1 1 -2 0 3 o 20.20 2.27 986s 1 1 1 -2 0 4 o 43.74 4.27 986s 1 1 1 -2 0 5 o 32.34 3.28 986s 1 1 1 -2 0 6 o 61.28 6.06 986s 1 1 1 -2 0 7 o 39.92 3.91 986s 1 1 1 -2 0 8 o 5.73 3.51 986s 1 1 1 -2 0 9 o 34.44 8.22 986s 1 1 1 -2 0 10 o 5.00 3.24 986s 1 1 1 -2 0 11 o 5.95 3.63 986s 1 1 1 -2 0 12 o 7.57 4.58 986s 1 1 1 -2 1 1 o 5.64 1.74 986s 1 1 1 -2 1 2 o 27.80 2.66 986s 1 1 1 -2 1 3 f 58.08 5.70 986s 1 1 1 -2 1 4 o 17.13 2.16 986s 1 1 1 -2 1 5 o 17.82 1.84 986s 1 1 1 -2 1 6 o 38.29 4.36 986s 1 1 1 -2 1 7 o 21.32 2.41 986s 1 1 1 -2 1 8 o 14.24 2.30 986s 1 1 1 -2 1 9 o 23.48 2.71 986s 1 1 1 -2 1 10 f 12.02 2.17 986s 1 1 1 -2 1 11 o 15.91 5.89 986s 1 1 1 -2 1 12 o 7.00 2.53 986s 1 1 1 -2 2 1 o 15.73 2.27 986s 1 1 1 -2 2 2 o 24.74 2.59 986s 1 1 1 -2 2 3 o 16.53 2.59 986s 1 1 1 -2 2 4 o 6.46 2.78 986s 1 1 1 -2 2 5 o 13.27 4.40 986s 1 1 1 -2 2 6 o 5.58 2.29 986s 1 1 1 -2 2 7 o 6.76 2.38 986s 1 1 1 -2 2 8 o 5.29 2.14 986s 1 1 1 -1 0 1 o 28.12 3.79 986s 1 1 1 -1 0 2 o 21.59 2.21 986s 1 1 1 -1 0 3 o 33.14 3.24 986s 1 1 1 -1 0 4 o 43.39 4.18 986s 1 1 1 -1 0 5 f 46.52 4.56 986s 1 1 1 -1 0 6 o 76.28 14.50 986s 1 1 1 -1 0 7 o 5.12 3.18 986s 1 1 1 -1 0 9 o 37.08 8.90 986s 1 1 1 -1 0 10 o 6.65 3.72 986s 1 1 1 -1 0 11 o 6.86 4.45 986s 1 1 1 -1 0 12 o 4.18 2.86 986s 1 1 1 -1 1 1 o 36.99 3.46 986s 1 1 1 -1 1 2 o 40.11 3.76 986s 1 1 1 -1 1 3 o 15.12 3.05 986s 1 1 1 -1 1 4 o 11.44 2.42 986s 1 1 1 -1 1 5 f 7.66 2.37 986s 1 1 1 -1 1 6 o 37.21 3.40 986s 1 1 1 -1 1 7 o 13.99 2.19 986s 1 1 1 -1 1 8 o 23.42 2.40 986s 1 1 1 -1 1 9 o 12.59 2.48 986s 1 1 1 -1 1 10 o 14.84 2.83 986s 1 1 1 -1 1 11 o 13.90 3.02 986s 1 1 1 -1 2 1 o 7.71 2.59 986s 1 1 1 -1 2 2 o 5.95 2.09 986s 1 1 1 -1 2 3 o 25.96 3.59 986s 1 1 1 -1 2 4 o 16.53 2.52 986s 1 1 1 -1 2 5 o 12.51 2.97 986s 1 1 1 -1 2 6 o 12.40 3.34 986s 1 1 1 -1 2 7 o 5.97 2.01 986s 1 1 1 -1 2 8 o 8.24 2.40 986s 1 1 1 0 0 1 o 40.04 3.82 986s 1 1 1 0 0 2 o 58.22 5.69 986s 1 1 1 0 0 3 o 47.47 4.60 986s 1 1 1 0 0 4 o 7.98 2.75 986s 1 1 1 0 0 5 o 50.74 7.60 986s 1 1 1 0 0 6 o 14.87 1.94 986s 1 1 1 0 0 7 o 3.62 2.41 986s 1 1 1 0 0 8 o 36.19 7.98 986s 1 1 1 0 0 9 o 10.11 5.01 986s 1 1 1 0 0 10 o 18.08 3.24 986s 1 1 1 0 0 11 o 12.35 4.26 986s 1 1 1 0 0 12 o 9.41 4.38 986s 1 1 1 0 1 1 o 92.10 11.26 986s 1 1 1 0 1 2 o 47.48 4.50 986s 1 1 1 0 1 3 o 22.08 2.22 986s 1 1 1 0 1 4 o 8.62 2.51 986s 1 1 1 0 1 5 o 24.16 1.98 986s 1 1 1 0 1 6 o 16.72 1.95 986s 1 1 1 0 1 7 o 5.50 2.46 986s 1 1 1 0 1 8 o 21.06 2.19 986s 1 1 1 0 1 9 o 5.99 2.45 986s 1 1 1 0 1 10 o 8.62 3.03 986s 1 1 1 0 1 11 o 9.15 3.06 986s 1 1 1 0 2 0 o 27.82 5.58 986s 1 1 1 0 2 1 o 29.68 4.10 986s 1 1 1 0 2 2 o 37.82 4.30 986s 1 1 1 0 2 3 o 14.42 1.91 986s 1 1 1 0 2 4 o 13.55 2.70 986s 1 1 1 0 2 5 o 8.67 3.07 986s 1 1 1 0 2 6 o 22.77 5.53 986s 1 1 1 0 2 7 o 5.74 2.12 986s 1 1 1 0 2 8 o 9.78 2.64 986s 1 1 1 1 0 1 o 10.19 1.09 986s 1 1 1 1 0 2 o 20.07 1.88 986s 1 1 1 1 0 3 o 28.76 2.81 986s 1 1 1 1 0 4 o 3.16 2.18 986s 1 1 1 1 0 5 o 35.75 3.54 986s 1 1 1 1 0 6 f 52.32 5.12 986s 1 1 1 1 0 7 o 37.09 5.54 986s 1 1 1 1 0 8 o 6.52 3.32 986s 1 1 1 1 0 9 o 3.67 2.45 986s 1 1 1 1 0 10 o 6.03 3.17 986s 1 1 1 1 0 11 o 3.13 2.20 986s 1 1 1 1 0 12 o 4.06 2.74 986s 1 1 1 1 1 0 o 34.97 2.64 986s 1 1 1 1 1 1 o 15.45 1.46 986s 1 1 1 1 1 2 o 27.96 2.66 986s 1 1 1 1 1 3 o 55.14 5.35 986s 1 1 1 1 1 4 o 14.46 1.65 986s 1 1 1 1 1 5 o 7.23 2.19 986s 1 1 1 1 1 6 o 10.31 2.54 986s 1 1 1 1 1 7 o 11.70 2.22 986s 1 1 1 1 1 8 o 11.24 2.14 986s 1 1 1 1 1 9 o 7.60 2.88 986s 1 1 1 1 1 10 o 8.83 2.34 986s 1 1 1 1 1 11 o 12.55 3.17 986s 1 1 1 1 2 0 o 24.36 5.60 986s 1 1 1 1 2 1 o 13.12 2.09 986s 1 1 1 1 2 2 o 10.37 2.52 986s 1 1 1 1 2 3 o 14.39 1.98 986s 1 1 1 1 2 4 o 26.67 8.23 986s 1 1 1 1 2 5 o 22.53 5.20 986s 1 1 1 1 2 6 o 13.94 2.61 986s 1 1 1 1 2 7 o 7.45 2.38 986s 1 1 1 1 2 8 o 4.51 2.05 986s 1 1 1 2 0 1 o 13.06 1.30 986s 1 1 1 2 0 2 o 10.37 1.36 986s 1 1 1 2 0 3 o 20.89 2.04 986s 1 1 1 2 0 4 o 45.12 4.31 986s 1 1 1 2 0 5 o 15.37 1.91 986s 1 1 1 2 0 6 o 28.38 2.79 986s 1 1 1 2 0 7 o 16.02 2.31 986s 1 1 1 2 0 8 o 3.40 2.35 986s 1 1 1 2 0 9 o 4.23 2.72 986s 1 1 1 2 0 10 o 3.89 2.43 986s 1 1 1 2 0 11 o 10.26 3.01 986s 1 1 1 2 1 0 o 34.61 2.64 986s 1 1 1 2 1 1 o 53.93 5.22 986s 1 1 1 2 1 2 o 20.62 2.08 986s 1 1 1 2 1 3 o 44.45 3.37 986s 1 1 1 2 1 4 o 24.41 2.00 986s 1 1 1 2 1 5 o 40.33 4.58 986s 1 1 1 2 1 6 o 41.76 5.03 986s 1 1 1 2 1 7 o 28.20 3.43 986s 1 1 1 2 1 8 o 33.56 3.76 986s 1 1 1 2 1 9 o 4.41 1.97 986s 1 1 1 2 1 10 o 15.24 3.10 986s 1 1 1 2 2 0 o 25.09 3.38 986s 1 1 1 2 2 1 o 9.96 2.30 986s 1 1 1 2 2 2 o 15.79 2.28 986s 1 1 1 2 2 3 f 23.73 2.57 986s 1 1 1 2 2 4 o 31.55 3.47 986s 1 1 1 2 2 5 o 22.42 5.53 986s 1 1 1 2 2 6 o 21.84 3.98 986s 1 1 1 2 2 7 o 11.92 3.24 986s 1 1 1 3 0 1 o 20.22 2.60 986s 1 1 1 3 0 2 o 15.58 1.67 986s 1 1 1 3 0 3 o 43.75 4.24 986s 1 1 1 3 0 4 o 53.24 5.13 986s 1 1 1 3 0 5 o 9.04 2.60 986s 1 1 1 3 0 6 o 16.05 2.16 986s 1 1 1 3 0 7 o 10.18 3.61 986s 1 1 1 3 0 8 f 21.57 2.93 986s 1 1 1 3 0 9 o 5.10 2.75 986s 1 1 1 3 0 10 o 9.06 4.48 986s 1 1 1 3 0 11 o 7.20 4.29 986s 1 1 1 3 1 0 o 6.01 1.35 986s 1 1 1 3 1 1 o 38.17 5.32 986s 1 1 1 3 1 2 o 88.61 10.65 986s 1 1 1 3 1 3 o 46.76 4.49 986s 1 1 1 3 1 4 o 21.38 1.98 986s 1 1 1 3 1 5 o 10.82 1.68 986s 1 1 1 3 1 6 o 9.92 1.96 986s 1 1 1 3 1 7 o 13.79 1.74 986s 1 1 1 3 1 8 o 18.26 2.25 986s 1 1 1 3 1 9 o 10.74 2.36 986s 1 1 1 3 1 10 o 4.53 1.95 986s 1 1 1 3 2 0 o 36.54 6.90 986s 1 1 1 3 2 1 o 7.87 2.79 986s 1 1 1 3 2 2 o 18.30 2.61 986s 1 1 1 3 2 3 o 17.39 2.45 986s 1 1 1 3 2 4 o 17.18 2.74 986s 1 1 1 3 2 5 o 13.02 2.60 986s 1 1 1 3 2 6 o 4.72 1.98 986s 1 1 1 4 0 1 o 3.64 2.08 986s 1 1 1 4 0 2 o 63.80 6.24 986s 1 1 1 4 0 3 o 19.19 1.93 986s 1 1 1 4 0 4 o 63.44 6.28 986s 1 1 1 4 0 5 o 30.78 6.03 986s 1 1 1 4 0 6 o 9.03 2.53 986s 1 1 1 4 0 7 o 18.16 2.40 986s 1 1 1 4 0 8 o 8.94 3.14 986s 1 1 1 4 0 9 o 6.87 3.36 986s 1 1 1 4 0 10 o 9.58 4.40 986s 1 1 1 4 1 0 o 24.37 2.38 986s 1 1 1 4 1 1 o 49.48 4.80 986s 1 1 1 4 1 2 o 10.45 1.03 986s 1 1 1 4 1 3 o 15.01 1.64 986s 1 1 1 4 1 4 o 4.52 1.88 986s 1 1 1 4 1 5 f 35.40 3.27 986s 1 1 1 4 1 6 o 8.15 2.10 986s 1 1 1 4 1 7 o 9.72 1.59 986s 1 1 1 4 1 8 o 5.93 1.88 986s 1 1 1 4 1 9 o 13.31 3.66 986s 1 1 1 4 2 0 o 12.03 2.31 986s 1 1 1 4 2 1 o 13.76 1.98 986s 1 1 1 4 2 2 o 10.87 2.55 986s 1 1 1 4 2 3 o 7.78 2.40 986s 1 1 1 4 2 4 o 19.45 4.53 986s 1 1 1 4 2 5 o 11.32 4.24 986s 1 1 1 4 2 6 o 7.29 3.50 986s 1 1 1 5 0 1 o 67.42 11.14 986s 1 1 1 5 0 2 o 13.50 3.13 986s 1 1 1 5 0 3 o 22.37 2.21 986s 1 1 1 5 0 4 o 56.42 6.72 986s 1 1 1 5 0 5 o 25.46 3.07 986s 1 1 1 5 0 6 o 38.61 4.82 986s 1 1 1 5 0 7 o 14.33 2.65 986s 1 1 1 5 0 8 f 4.56 2.78 986s 1 1 1 5 0 9 o 8.50 3.26 986s 1 1 1 5 1 0 o 21.65 2.85 986s 1 1 1 5 1 1 o 12.29 1.67 986s 1 1 1 5 1 2 o 11.21 3.27 986s 1 1 1 5 1 3 o 9.29 2.49 986s 1 1 1 5 1 4 o 12.76 2.42 986s 1 1 1 5 1 5 o 4.61 0.86 986s 1 1 1 5 1 6 o 21.81 2.38 986s 1 1 1 5 1 7 o 11.05 2.11 986s 1 1 1 5 1 8 o 4.27 1.64 986s 1 1 1 5 2 0 o 17.82 3.76 986s 1 1 1 5 2 1 o 13.94 3.96 986s 1 1 1 5 2 2 o 14.67 2.97 986s 1 1 1 5 2 3 o 12.27 4.35 986s 1 1 1 5 2 4 o 12.90 2.88 986s 1 1 1 5 2 5 o 8.21 2.77 986s 1 1 1 6 0 1 o 4.02 2.51 986s 1 1 1 6 0 2 o 14.11 3.04 986s 1 1 1 6 0 4 o 44.86 5.41 986s 1 1 1 6 0 5 f 22.85 4.74 986s 1 1 1 6 0 6 o 41.69 6.63 986s 1 1 1 6 0 7 o 7.42 2.96 986s 1 1 1 6 0 8 o 13.47 5.61 986s 1 1 1 6 1 0 o 25.42 2.26 986s 1 1 1 6 1 1 o 9.87 3.01 986s 1 1 1 6 1 2 o 28.37 5.85 986s 1 1 1 6 1 3 o 16.66 3.91 986s 1 1 1 6 1 4 o 23.02 5.62 986s 1 1 1 6 1 6 o 26.51 4.88 986s 1 1 1 6 1 7 o 3.67 1.58 986s 1 1 1 6 2 0 o 8.22 2.50 986s 1 1 1 6 2 2 o 9.67 2.35 986s 1 1 1 6 2 3 o 3.73 1.60 986s 1 1 1 7 0 1 o 10.99 3.37 986s 1 1 1 7 0 2 o 17.23 3.99 986s 1 1 1 7 0 3 o 5.15 2.69 986s 1 1 1 7 0 4 o 5.19 3.01 986s 1 1 1 7 0 5 o 23.76 3.00 986s 1 1 1 7 0 6 o 5.48 3.05 986s 1 1 1 7 0 7 o 6.05 3.12 986s 1 1 1 7 0 8 o 7.94 3.69 986s 1 1 1 7 1 0 o 33.08 3.93 986s 1 1 1 7 1 1 o 8.43 3.00 986s 1 1 1 7 1 2 o 10.12 3.61 986s 1 1 1 7 1 3 o 14.66 3.85 986s 1 1 1 7 1 4 o 9.43 3.13 986s 1 1 1 7 1 6 o 14.64 4.20 986s 1 1 1 7 2 0 o 14.80 3.92 986s 1 1 1 7 2 1 o 6.02 2.00 986s 1 1 1 8 0 2 o 29.07 8.06 986s 1 1 1 8 0 3 o 5.29 2.84 986s 1 1 1 8 0 4 o 22.81 5.95 986s 1 1 1 8 0 5 o 4.11 2.70 986s 1 1 1 8 1 0 o 7.24 1.50 986s 1 1 1 8 1 1 o 8.85 3.06 986s 1 1 1 8 1 2 o 6.83 3.09 986s 1 1 1 8 1 3 o 18.14 5.99 986s 1 1 1 9 0 1 o 13.49 3.22 986s 1 1 1 9 0 2 o 11.72 3.95 986s 1 1 1 10 0 2 o 7.39 3.73 986s 1 1 1 10 1 0 o 16.08 6.44 986s #END OF REFLECTIONS 986s 986s Starting iotbx.fetch_pdb 986s on Sat Mar 22 13:56:51 2025 by ubuntu 986s =============================================================================== 986s 986s Processing files: 986s ------------------------------------------------------------------------------- 986s 986s No files found 986s 986s Processing PHIL parameters: 986s ------------------------------------------------------------------------------- 986s 986s Adding command-line PHIL: 986s ------------------------- 986s action=all 986s 986s Final processed PHIL parameters: 986s ------------------------------------------------------------------------------- 986s fetch { 986s pdb_ids = "6yvd" 986s action = model data sequence half_maps *all 986s } 986s 986s 986s Starting job 986s =============================================================================== 986s Validating inputs: 986s 986s Model in PDB format saved to /tmp/autopkgtest.irYrF2/autopkgtest_tmp/python3.13/6yvd.pdb 986s Model in mmCIF format saved to /tmp/autopkgtest.irYrF2/autopkgtest_tmp/python3.13/6yvd.cif 986s Couldn't download sf for 6yvd at https://files.rcsb.org/download/6yvd-sf.cif.gz. 986s Cryo-EM map saved to /tmp/autopkgtest.irYrF2/autopkgtest_tmp/python3.13/emd_10944.map.gz 986s Cryo-EM half map 1 saved to /tmp/autopkgtest.irYrF2/autopkgtest_tmp/python3.13/emd_10944_half_map_1.map.gz 986s Cryo-EM half map 2 saved to /tmp/autopkgtest.irYrF2/autopkgtest_tmp/python3.13/emd_10944_half_map_2.map.gz 986s Sequence saved to /tmp/autopkgtest.irYrF2/autopkgtest_tmp/python3.13/6yvd.fa 986s 986s =============================================================================== 986s Job complete 986s Total CPU time: 0.58 seconds 986s Starting iotbx.fetch_pdb 986s on Sat Mar 22 13:57:03 2025 by ubuntu 986s =============================================================================== 986s 986s Processing files: 986s ------------------------------------------------------------------------------- 986s 986s No files found 986s 986s Processing PHIL parameters: 986s ------------------------------------------------------------------------------- 986s 986s Adding command-line PHIL: 986s ------------------------- 986s action=model 986s 986s Final processed PHIL parameters: 986s ------------------------------------------------------------------------------- 986s fetch { 986s pdb_ids = "6yvd" 986s } 986s 986s 986s Starting job 986s =============================================================================== 986s Validating inputs: 986s 986s Model in PDB format saved to /tmp/autopkgtest.irYrF2/autopkgtest_tmp/python3.13/6yvd.pdb 986s Model in mmCIF format saved to /tmp/autopkgtest.irYrF2/autopkgtest_tmp/python3.13/6yvd.cif 986s 986s =============================================================================== 986s Job complete 986s Total CPU time: 0.49 seconds 986s Starting iotbx.fetch_pdb 986s on Sat Mar 22 13:57:05 2025 by ubuntu 986s =============================================================================== 986s 986s Processing files: 986s ------------------------------------------------------------------------------- 986s 986s No files found 986s 986s Processing PHIL parameters: 986s ------------------------------------------------------------------------------- 986s 986s Adding command-line PHIL: 986s ------------------------- 986s action=model 986s 986s Final processed PHIL parameters: 986s ------------------------------------------------------------------------------- 986s fetch { 986s pdb_ids = "6yvd" 986s } 986s 986s 986s Starting job 986s =============================================================================== 986s Validating inputs: 986s 986s Model in PDB format saved to /tmp/autopkgtest.irYrF2/autopkgtest_tmp/python3.13/6yvd.pdb 986s Model in mmCIF format saved to /tmp/autopkgtest.irYrF2/autopkgtest_tmp/python3.13/6yvd.cif 986s 986s =============================================================================== 986s Job complete 986s Total CPU time: 0.46 seconds 986s Starting iotbx.fetch_pdb 986s on Sat Mar 22 13:57:08 2025 by ubuntu 986s =============================================================================== 986s 986s Processing files: 986s ------------------------------------------------------------------------------- 986s 986s No files found 986s 986s Processing PHIL parameters: 986s ------------------------------------------------------------------------------- 986s 986s Adding command-line PHIL: 986s ------------------------- 986s action=data 986s 986s Final processed PHIL parameters: 986s ------------------------------------------------------------------------------- 986s fetch { 986s pdb_ids = "6yvd" 986s action = model *data sequence half_maps all 986s } 986s 986s 986s Starting job 986s =============================================================================== 986s Validating inputs: 986s 986s Couldn't download sf for 6yvd at https://files.rcsb.org/download/6yvd-sf.cif.gz. 986s Cryo-EM map saved to /tmp/autopkgtest.irYrF2/autopkgtest_tmp/python3.13/emd_10944.map.gz 986s 986s =============================================================================== 986s Job complete 986s Total CPU time: 0.47 seconds 986s Starting iotbx.fetch_pdb 986s on Sat Mar 22 13:57:13 2025 by ubuntu 986s =============================================================================== 986s 986s Processing files: 986s ------------------------------------------------------------------------------- 986s 986s No files found 986s 986s Processing PHIL parameters: 986s ------------------------------------------------------------------------------- 986s 986s Adding command-line PHIL: 986s ------------------------- 986s action=half_maps 986s 986s Final processed PHIL parameters: 986s ------------------------------------------------------------------------------- 986s fetch { 986s pdb_ids = "6yvd" 986s action = model data sequence *half_maps all 986s } 986s 986s 986s Starting job 986s =============================================================================== 986s Validating inputs: 986s 986s Cryo-EM half map 1 saved to /tmp/autopkgtest.irYrF2/autopkgtest_tmp/python3.13/emd_10944_half_map_1.map.gz 986s Cryo-EM half map 2 saved to /tmp/autopkgtest.irYrF2/autopkgtest_tmp/python3.13/emd_10944_half_map_2.map.gz 986s 986s =============================================================================== 986s Job complete 986s Total CPU time: 0.52 seconds 986s Starting iotbx.fetch_pdb 986s on Sat Mar 22 13:57:17 2025 by ubuntu 986s =============================================================================== 986s 986s Processing files: 986s ------------------------------------------------------------------------------- 986s 986s No files found 986s 986s Processing PHIL parameters: 986s ------------------------------------------------------------------------------- 986s 986s Adding command-line PHIL: 986s ------------------------- 986s action=sequence 986s 986s Final processed PHIL parameters: 986s ------------------------------------------------------------------------------- 986s fetch { 986s pdb_ids = "6yvd" 986s action = model data *sequence half_maps all 986s } 986s 986s 986s Starting job 986s =============================================================================== 986s Validating inputs: 986s 986s Sequence saved to /tmp/autopkgtest.irYrF2/autopkgtest_tmp/python3.13/6yvd.fa 986s 986s =============================================================================== 986s Job complete 986s Total CPU time: 0.45 seconds 986s Starting iotbx.fetch_pdb 986s on Sat Mar 22 13:57:18 2025 by ubuntu 986s =============================================================================== 986s 986s Processing files: 986s ------------------------------------------------------------------------------- 986s 986s No files found 986s 986s Processing PHIL parameters: 986s ------------------------------------------------------------------------------- 986s 986s Adding command-line PHIL: 986s ------------------------- 986s action=all 986s 986s Final processed PHIL parameters: 986s ------------------------------------------------------------------------------- 986s fetch { 986s pdb_ids = "6yvd" 986s action = model data sequence half_maps *all 986s } 986s 986s 986s Starting job 986s =============================================================================== 986s Validating inputs: 986s 986s Model in PDB format saved to /tmp/autopkgtest.irYrF2/autopkgtest_tmp/python3.13/6yvd.pdb 986s Model in mmCIF format saved to /tmp/autopkgtest.irYrF2/autopkgtest_tmp/python3.13/6yvd.cif 986s Couldn't download sf for 6yvd at https://files.rcsb.org/download/6yvd-sf.cif.gz. 986s Cryo-EM map saved to /tmp/autopkgtest.irYrF2/autopkgtest_tmp/python3.13/emd_10944.map.gz 986s Cryo-EM half map 1 saved to /tmp/autopkgtest.irYrF2/autopkgtest_tmp/python3.13/emd_10944_half_map_1.map.gz 986s Cryo-EM half map 2 saved to /tmp/autopkgtest.irYrF2/autopkgtest_tmp/python3.13/emd_10944_half_map_2.map.gz 986s Sequence saved to /tmp/autopkgtest.irYrF2/autopkgtest_tmp/python3.13/6yvd.fa 986s 986s =============================================================================== 986s Job complete 986s Total CPU time: 0.57 seconds 986s OK 986s u+s,u,s: 0.39 0.33 0.06 987s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp_state.py" [OK] 0.9s 987s Time: 0.86 987s Return code: 0 987s OKs: 3 987s Standard out: 987s Running threading test with 1 processes, 1 threads, 3 tasks 987s (0xe604837baba0-11257) object in state -init- 987s (0xe604837baba0-11257) changing state from -init- to HJDI9Z 987s (0xe604837baba0-11257) changing state from HJDI9Z to XPTOU6 987s (0xe604837baba0-11257) changing state from XPTOU6 to 3FBATG 987s (0xe604837baba0-11257) object in state 3FBATG 987s OK 987s Running threading test with 2 processes, 1 threads, 3 tasks 987s (0xe60483682210-11257) object in state -init- 987s (0xe60483682210-11257) changing state from -init- to 6JSVQT 987s (0xe60483682210-11257) changing state from 6JSVQT to XRYK5T 987s (0xe60483682210-11257) changing state from XRYK5T to GJW47R 987s (0xe60483682210-11257) object in state GJW47R 987s OK 987s Running multiprocessing test with 1 processes, 1 threads, 3 tasks 987s (0xe60483682210-11257) object in state -init- 987s (0xe60483682210-11257) changing state from -init- to 96YGMJ 987s (0xe60483682210-11257) changing state from 96YGMJ to HZHMKX 987s (0xe60483682210-11257) changing state from HZHMKX to Z69ELK 987s (0xe60483682210-11257) object in state Z69ELK 987s OK 987s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_pickle.py" [OK] 0.1s 987s Time: 0.08 987s Return code: 0 987s OKs: 1 987s Standard out: 987s test.dat 987s dump: 0.00 s 987s load buffered: 0.00 s 987s load direct: 0.00 s 987s test.dat.gz 987s dump: 0.00 s 987s load buffered: 0.00 s 987s load direct: 0.00 s 987s dumps/loads 987s dump: 0.00 s 987s load buffered: 0.00 s 987s OK 987s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_fully_buffered_timeout.py" [OK] 0.1s 987s Time: 0.11 987s Return code: 0 987s OKs: 0 987s Standard out: 987s Skipping test: probe not configured 990s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp.py" [OK] 4.8s 990s Time: 4.82 990s Return code: 0 990s OKs: 1 990s Standard out: 990s multiprocessing pool size: 2 990s wall clock time: 0.01 seconds 990s OK 992s libtbx.python "/usr/lib/python3/dist-packages/libtbx/easy_run.py" [OK] 2.4s 992s Time: 2.40 992s Return code: 0 992s OKs: 1 992s Standard out: 992s OK 993s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_containers.py" [OK] 0.0s 993s Time: 0.03 993s Return code: 0 993s OKs: 1 993s Standard out: 993s OK 993s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_path.py" [OK] 0.1s 993s Time: 0.08 993s Return code: 0 993s OKs: 1 993s Standard out: 993s OK 993s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_math_utils.py" [OK] 0.3s 993s Time: 0.33 993s Return code: 0 993s OKs: 1 993s Standard out: 993s OK 993s libtbx.python "/usr/lib/python3/dist-packages/libtbx/assert_utils.py" [OK] 0.2s 993s Time: 0.17 993s Return code: 0 993s OKs: 1 993s Standard out: 993s OK 993s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_str_utils.py" [OK] 0.3s 993s Time: 0.34 993s Return code: 0 993s OKs: 1 993s Standard out: 993s OK 993s libtbx.python "/usr/lib/python3/dist-packages/libtbx/table_utils.py" [OK] 0.0s 993s Time: 0.05 993s Return code: 0 993s OKs: 1 993s Standard out: 993s OK 995s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_scheduling.py" [OK] 8.3s 995s Time: 8.34 995s Return code: 0 995s OKs: 0 995s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_tokenizer.py" [OK] 0.1s 995s Time: 0.07 995s Return code: 0 995s OKs: 1 995s Standard out: 995s OK 995s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_dlite.py" [OK] 2.1s 995s Time: 2.08 995s Return code: 0 995s OKs: 1 995s Standard out: 995s OK 995s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_experimental.py" [OK] 0.1s 995s Time: 0.07 995s Return code: 0 995s OKs: 1 995s Standard out: 995s OK 995s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst.py" [OK] 0.2s 995s Time: 0.23 995s Return code: 0 995s OKs: 1 995s Standard out: 995s OK 996s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_interface.py" [OK] 0.1s 996s Time: 0.13 996s Return code: 0 996s OKs: 1 996s Standard out: 996s phenix module not available: skipping advanced tests 996s phaser module not available: skipping advanced tests 996s OK 996s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_object_oriented_patterns.py" [OK] 0.1s 996s Time: 0.10 996s Return code: 0 996s OKs: 0 996s libtbx.python "/usr/lib/python3/dist-packages/libtbx/find_reference_cycles.py" [OK] 0.0s 996s Time: 0.05 996s Return code: 0 996s OKs: 1 996s Standard out: 996s OK 996s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_binary_search.py" [OK] 0.0s 996s Time: 0.04 996s Return code: 0 996s OKs: 1 996s Standard out: 996s OK 996s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_topological_sort.py" [OK] 0.0s 996s Time: 0.04 996s Return code: 0 996s OKs: 1 996s Standard out: 996s OK 996s libtbx.python "/usr/lib/python3/dist-packages/libtbx/clusterTests.py" [OK] 0.2s 996s Time: 0.17 996s Return code: 0 996s OKs: 1 996s Standard out: 996s ---------------------------------------------------------------------- 996s Ran 13 tests in 0.081s 996s 996s OK 996s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_python_code_parsing.py" [OK] 0.0s 996s Time: 0.05 996s Return code: 0 996s OKs: 1 996s Standard out: 996s OK 996s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_citations.py" [OK] 0.2s 996s Time: 0.19 996s Return code: 0 996s OKs: 1 996s Standard out: 996s OK 996s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_representation.py" [OK] 0.0s 996s Time: 0.04 996s Return code: 0 996s OKs: 0 996s Standard out: 996s 99999999999999950039963891867 996s 99999999999999963917751699682 996s 99999999999999977795539507496 996s 99999999999999991673327315311 996s 100000000000000005551115123125 996s 100000000000000019428902930940 996s 100000000000000033306690738754 996s 100000000000000047184478546569 996s 100000000000000061062266354383 996s 100000000000000074940054162198 996s 100000000000000088817841970012 996s 100000000000000102695629777826 996s 100000000000000116573417585641 996s 100000000000000130451205393455 996s 100000000000000144328993201270 996s 100000000000000158206781009084 996s 100000000000000172084568816899 996s 100000000000000185962356624713 996s 100000000000000199840144432528 996s 100000000000000213717932240342 996s 100000000000000227595720048157 996s 100000000000000241473507855971 996s 100000000000000255351295663786 996s 100000000000000269229083471600 996s 100000000000000283106871279414 996s 100000000000000296984659087229 996s 100000000000000310862446895043 996s 100000000000000324740234702858 996s 100000000000000338618022510672 996s 100000000000000352495810318487 996s BEst 450359962737049.6 996s 900719925474099.2 996s 55.32192809488736 996s 56.32192809488736 996s True 996s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_find_unused_imports.py" [OK] 0.0s 996s Time: 0.04 996s Return code: 0 996s OKs: 1 996s Standard out: 996s OK 996s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_version.py" [OK] 0.1s 996s Time: 0.09 996s Return code: 0 996s OKs: 0 996s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_program_template.py" [OK] 0.3s 996s Time: 0.33 996s Return code: 0 996s OKs: 0 996s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp_multicore.py" [OK] 0.4s 996s Time: 0.39 996s Return code: 0 996s OKs: 0 996s Standard out: 996s [1] 1 996s [2] 2 996s [3] 6 996s [4] 24 996s [5] 120 996s [6] 720 996s [7] 5040 1000s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1000s 1 1000s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1000s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_xmlrpc_utils.py" [EXPECTED FAIL] 3.2s 1000s Standard error: 1000s Traceback (most recent call last): 1000s File "/usr/lib/python3/dist-packages/libtbx/tst_xmlrpc_utils.py", line 42, in 1000s exercise() 1000s ~~~~~~~~^^ 1000s File "/usr/lib/python3/dist-packages/libtbx/tst_xmlrpc_utils.py", line 15, in exercise 1000s server = xmlrpc_utils.external_program_server(command=full_cmd, 1000s program_id="TEST", 1000s timeout=None, 1000s cache_requests=True, 1000s log=log) 1000s TypeError: external_program_server.__init__() got an unexpected keyword argument 'command' 1000s Time: 3.21 1000s Return code: 1 1000s OKs: 0 1002s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_runtime_utils.py" [OK] 6.0s 1002s Time: 6.02 1002s Return code: 0 1002s OKs: 1 1002s Standard out: 1002s OK 1003s Standard error: 1003s Segmentation fault (core dumped) 1003s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1003s 139 1003s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1003s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_smoothing.py" [FAIL] 3.8s 1003s Time: 3.78 1003s Return code: 139 1003s OKs: 0 1007s Standard error: 1007s Segmentation fault (core dumped) 1007s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1007s 139 1007s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1007s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_genetic_algorithm_with_mp.py" [FAIL] 4.5s 1007s Time: 4.54 1007s Return code: 139 1007s OKs: 0 1007s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_1" [OK] 0.0s 1007s Time: 0.01 1007s Return code: 0 1007s OKs: 1 1007s Standard out: 1007s Total OK: 511 1007s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_2" [OK] 0.0s 1007s Time: 0.01 1007s Return code: 0 1007s OKs: 1 1007s Standard out: 1007s Total OK: 268 1007s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_3" [OK] 0.0s 1007s Time: 0.01 1007s Return code: 0 1007s OKs: 1 1007s Standard out: 1007s Total OK: 164 1007s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_4" [OK] 0.0s 1007s Time: 0.01 1007s Return code: 0 1007s OKs: 1 1007s Standard out: 1007s Total OK: 1420 1007s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_5" [OK] 0.0s 1007s Time: 0.01 1007s Return code: 0 1007s OKs: 1 1007s Standard out: 1007s Total OK: 23 1007s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_vec3" [OK] 0.0s 1007s Time: 0.01 1007s Return code: 0 1007s OKs: 1 1007s Standard out: 1007s Total OK: 83 1007s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_unsigned_float_arithmetic" [OK] 0.0s 1007s Time: 0.01 1007s Return code: 0 1007s OKs: 1 1007s Standard out: 1007s OK 1007s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_mat3" [OK] 0.0s 1007s Time: 0.01 1007s Return code: 0 1007s OKs: 1 1007s Standard out: 1007s Total OK: 129 1007s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_sym_mat3" [OK] 0.0s 1007s Time: 0.01 1007s Return code: 0 1007s OKs: 1 1007s Standard out: 1007s Total OK: 91 1007s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_ref_matrix_facet" [OK] 0.0s 1007s Time: 0.01 1007s Return code: 0 1007s OKs: 1 1007s Standard out: 1007s OK 1007s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_accessors" [OK] 0.0s 1007s Time: 0.01 1007s Return code: 0 1007s OKs: 1 1007s Standard out: 1007s Total OK: 1730 1007s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_optional_copy" [OK] 0.0s 1007s Time: 0.01 1007s Return code: 0 1007s OKs: 1 1007s Standard out: 1007s OK 1007s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_rectangular_full_packed" [OK] 0.0s 1007s Time: 0.01 1007s Return code: 0 1007s OKs: 0 1007s Standard out: 1007s Test of accessor for rectangular full packed format skipped 1007s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex_argument_passing.py" [OK] 0.2s 1007s Time: 0.17 1007s Return code: 0 1007s OKs: 1 1007s Standard out: 1007s OK 1007s "/usr/lib/cctbx/python3.13/scitbx/serialization/tst_base_256" [OK] 0.3s 1007s Time: 0.28 1007s Return code: 0 1007s OKs: 1 1007s Standard out: 1007s OK 1010s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1010s 139 1010s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1010s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_basic.py" [FAIL] 6.9s 1010s Time: 6.93 1010s Return code: 139 1010s OKs: 1 1010s Standard out: 1010s b'\n\xc3\x85 LATIN CAPITAL LETTER A WITH RING ABOVE\n\xc2\xb0 DEGREE SIGN\n\xce\x91 GREEK CAPITAL LETTER ALPHA\n\xce\x92 GREEK CAPITAL LETTER BETA\n\xce\x93 GREEK CAPITAL LETTER GAMMA = gamma function\n\xce\x94 GREEK CAPITAL LETTER DELTA\n\xce\x95 GREEK CAPITAL LETTER EPSILON\n\xce\x96 GREEK CAPITAL LETTER ZETA\n\xce\x97 GREEK CAPITAL LETTER ETA\n\xce\x98 GREEK CAPITAL LETTER THETA\n\xce\x99 GREEK CAPITAL LETTER IOTA = iota adscript\n\xce\x9a GREEK CAPITAL LETTER KAPPA\n\xce\x9b GREEK CAPITAL LETTER LAMDA\n\xce\x9c GREEK CAPITAL LETTER MU\n\xce\x9d GREEK CAPITAL LETTER NU\n\xce\x9e GREEK CAPITAL LETTER XI\n\xce\x9f GREEK CAPITAL LETTER OMICRON\n\xce\xa0 GREEK CAPITAL LETTER PI\n\xce\xa1 GREEK CAPITAL LETTER RHO\n\xce\xa3 GREEK CAPITAL LETTER SIGMA\n\xce\xa4 GREEK CAPITAL LETTER TAU\n\xce\xa5 GREEK CAPITAL LETTER UPSILON\n\xce\xa6 GREEK CAPITAL LETTER PHI\n\xce\xa7 GREEK CAPITAL LETTER CHI\n\xce\xa8 GREEK CAPITAL LETTER PSI\n\xce\xa9 GREEK CAPITAL LETTER OMEGA\n\xcf\x86 GREEK SMALL LETTER PHI\n\xcf\x87 GREEK SMALL LETTER CHI\n\xcf\x88 GREEK SMALL LETTER PSI\n\xcf\x89 GREEK SMALL LETTER OMEGA\n\xce\xb2 greek small letter beta\n\xce\xb8 greek small letter theta\n\xce\xa5 greek capital letter upsilon\n\xcf\x86 greek small letter phi\n\xcf\x80 greek small letter pi\n\xce\xb2 GREEK SMALL LETTER BETA\n\xc3\x9f latin small letter sharp s\n\xce\xb3 GREEK SMALL LETTER GAMMA\n\xce\xb4 GREEK SMALL LETTER DELTA\n\xce\xb5 GREEK SMALL LETTER EPSILON\n\xce\xb6 GREEK SMALL LETTER ZETA\n\xce\xb7 GREEK SMALL LETTER ETA\n\xce\xb8 GREEK SMALL LETTER THETA\n\xce\xb9 GREEK SMALL LETTER IOTA\n\xce\xba GREEK SMALL LETTER KAPPA\n\xce\xbb GREEK SMALL LETTER LAMDA = lambda\n\xce\xbc GREEK SMALL LETTER MU\n\xc2\xb5 micro sign\n\xce\xbd GREEK SMALL LETTER NU\n\xce\xbe GREEK SMALL LETTER XI\n\xce\xbf GREEK SMALL LETTER OMICRON\n\xcf\x80 GREEK SMALL LETTER PI math constant 3.141592...\n\xcf\x81 GREEK SMALL LETTER RHO\n\xcf\x82 GREEK SMALL LETTER FINAL SIGMA\n\xcf\x83 GREEK SMALL LETTER SIGMA\n\xcf\x84 GREEK SMALL LETTER TAU\n\xcf\x85 GREEK SMALL LETTER UPSILON\n' 1010s Size of an empty container. 1010s Some of those containers store a pointer to a raw storage: 1010s the 'cumulative' entry refers to the total memory footprint 1010s whereas the other entry does not include the raw storage. 1010s 1010s int : 4 1010s af::ref : 32 1010s scitbx::auto_array : 8 1010s boost::shared_array : 16 1010s boost::ptr_vector : 24 1010s std::vector : 24 1010s af::shared : 16 1010s af::shared [cumulative] : 64 1010s std::valarray : 16 1010s af::versa : 24 1010s af::versa > : 280 1010s af::versa > [cumulative] : 328 1010s 1010s double : 8 1010s af::ref : 32 1010s scitbx::auto_array : 8 1010s boost::shared_array : 16 1010s boost::ptr_vector : 24 1010s std::vector : 24 1010s af::shared : 16 1010s af::shared [cumulative] : 64 1010s std::valarray : 16 1010s af::versa : 24 1010s af::versa > : 280 1010s af::versa > [cumulative] : 328 1010s 1010s OK 1010s Standard error: 1010s Segmentation fault (core dumped) 1014s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1014s 139 1014s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1014s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_minimum_covering_ellipsoid.py" [FAIL] 6.4s 1014s Time: 6.35 1014s Return code: 139 1014s OKs: 0 1014s Standard error: 1014s Segmentation fault (core dumped) 1017s Standard error: 1017s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1017s 139 1017s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1017s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian_fit_1d_analytical.py" [FAIL] 6.6s 1017s Time: 6.59 1017s Return code: 139 1017s OKs: 0 1017s Segmentation fault (core dumped) 1017s "/usr/lib/cctbx/python3.13/scitbx/math/tests/tst" [OK] 0.0s 1017s Time: 0.01 1017s Return code: 0 1017s OKs: 2 1017s Standard out: 1017s copysign(3.f, +0.f) = 3 instead of 0.f as per C99 1017s copysign(3.f, -0.f) = -3 instead of -0.f as per C99 1017s linear interpolation test OK 1017s OK 1017s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_givens" [OK] 0.0s 1017s Time: 0.01 1017s Return code: 0 1017s OKs: 1 1017s Standard out: 1017s OK 1017s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_householder" [OK] 0.0s 1017s Time: 0.01 1017s Return code: 0 1017s OKs: 1 1017s Standard out: 1017s OK 1017s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_svd" [OK] 0.0s 1017s Time: 0.01 1017s Return code: 0 1017s OKs: 1 1017s Standard out: 1017s OK 1017s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_cholesky" [OK] 0.1s 1017s Time: 0.11 1017s Return code: 0 1017s OKs: 1 1017s Standard out: 1017s Exercising sizes up to 100 1017s Hilbert 1017s Condition 1 1017s Condition 2 1017s Condition 3 1017s Condition 4 1017s OK 1017s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/tests/tst_row_echelon.py" [OK] 0.1s 1017s Time: 0.09 1017s Return code: 0 1017s OKs: 1 1017s Standard out: 1017s OK 1017s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/tests/tst_householder.py" [OK] 0.2s 1017s Time: 0.21 1017s Return code: 0 1017s OKs: 1 1017s Standard out: 1017s OK 1018s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_matrix.py" [OK] 0.2s 1018s Time: 0.21 1018s Return code: 0 1018s OKs: 1 1018s Standard out: 1018s OK 1020s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1020s 139 1020s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1020s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_cubic_equation.py" [FAIL] 6.6s 1020s Time: 6.60 1020s Return code: 139 1020s OKs: 0 1020s Standard error: 1020s Segmentation fault (core dumped) 1024s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1024s 139 1024s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1024s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_cholesky.py" [FAIL] 6.1s 1024s Time: 6.15 1024s Return code: 139 1024s OKs: 0 1024s Standard error: 1024s Segmentation fault (core dumped) 1027s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1027s 139 1027s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1027s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_svd.py" [FAIL] 6.8s 1027s Time: 6.81 1027s Return code: 139 1027s OKs: 0 1027s Standard error: 1027s Segmentation fault (core dumped) 1030s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1030s 139 1030s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1030s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_eigensystem.py" [FAIL] 6.7s 1030s Time: 6.68 1030s Return code: 139 1030s OKs: 0 1030s Standard error: 1030s Segmentation fault (core dumped) 1034s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1034s 139 1034s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1034s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_svd.py" [FAIL] 6.6s 1034s Time: 6.64 1034s Return code: 139 1034s OKs: 0 1034s Standard error: 1034s Segmentation fault (core dumped) 1034s libtbx.python "/usr/lib/python3/dist-packages/scitbx/error/tst_error.py" [OK] 0.1s 1034s Time: 0.10 1034s Return code: 0 1034s OKs: 1 1034s Standard out: 1034s OK 1034s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_map.py" [OK] 0.1s 1034s Time: 0.07 1034s Return code: 0 1034s OKs: 1 1034s Standard out: 1034s OK 1034s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_set.py" [OK] 0.1s 1034s Time: 0.07 1034s Return code: 0 1034s OKs: 1 1034s Standard out: 1034s OK 1034s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_vector.py" [OK] 0.1s 1034s Time: 0.07 1034s Return code: 0 1034s OKs: 1 1034s Standard out: 1034s OK 1037s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1037s 139 1037s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1037s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_dsyev.py" [FAIL] 6.8s 1037s Time: 6.76 1037s Return code: 139 1037s OKs: 0 1037s Standard error: 1037s Segmentation fault (core dumped) 1040s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1040s 139 1040s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1040s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/regression_test.py" [FAIL] 6.4s 1040s Time: 6.43 1040s Return code: 139 1040s OKs: 0 1040s Standard error: 1040s Segmentation fault (core dumped) 1044s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1044s 139 1044s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1044s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex.py" [FAIL] 7.0s 1044s Time: 7.01 1044s Return code: 139 1044s OKs: 0 1044s Standard error: 1044s Segmentation fault (core dumped) 1047s Standard error: 1047s Segmentation fault (core dumped) 1047s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1047s 139 1047s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1047s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_numpy_bridge.py" [FAIL] 6.8s 1047s Time: 6.84 1047s Return code: 139 1047s OKs: 0 1051s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1051s 139 1051s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1051s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_smart_selection.py" [FAIL] 6.4s 1051s Time: 6.44 1051s Return code: 139 1051s OKs: 0 1051s Standard error: 1051s Segmentation fault (core dumped) 1054s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1054s 139 1054s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1054s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_shared.py" [FAIL] 6.6s 1054s Time: 6.57 1054s Return code: 139 1054s OKs: 0 1054s Standard error: 1054s Segmentation fault (core dumped) 1057s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_cost_of_m_handle_in_af_shared.py" [OK] 3.0s 1057s Time: 3.03 1057s Return code: 0 1057s OKs: 1 1057s Standard out: 1057s Loop over af::shared: 1057s data_size=1000, n_repeats=30000 1057s size+begin inside loop: 0.26 s 1057s begin outside loop: 0.20 s 1057s size+begin outside loop: 0.11 s 1057s 1057s data_size=10000, n_repeats=3000 1057s size+begin inside loop: 0.23 s 1057s begin outside loop: 0.17 s 1057s size+begin outside loop: 0.11 s 1057s 1057s data_size=100000, n_repeats=300 1057s size+begin inside loop: 0.25 s 1057s begin outside loop: 0.17 s 1057s size+begin outside loop: 0.11 s 1057s 1057s data_size=1000000, n_repeats=30 1057s size+begin inside loop: 0.25 s 1057s begin outside loop: 0.18 s 1057s size+begin outside loop: 0.11 s 1057s 1057s data_size=10000000, n_repeats=3 1057s size+begin inside loop: 0.27 s 1057s begin outside loop: 0.18 s 1057s size+begin outside loop: 0.11 s 1057s 1057s OK 1057s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_cubicle_neighbors.py" [OK] 0.2s 1057s Time: 0.18 1057s Return code: 0 1057s OKs: 1 1057s Standard out: 1057s OK 1057s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_r3_utils.py" [OK] 0.2s 1057s Time: 0.20 1057s Return code: 0 1057s OKs: 1 1057s Standard out: 1057s OK 1058s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_regular_grid_on_unit_sphere.py" [OK] 0.6s 1058s Time: 0.62 1058s Return code: 0 1058s OKs: 0 1062s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1062s 139 1062s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1062s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/__init__.py" [FAIL] 3.9s 1062s Time: 3.85 1062s Return code: 139 1062s OKs: 0 1062s Standard error: 1062s Segmentation fault (core dumped) 1066s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1066s 139 1066s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1066s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_random_transform.py" [FAIL] 3.9s 1066s Standard error: 1066s Segmentation fault (core dumped) 1066s Time: 3.91 1066s Return code: 139 1066s OKs: 0 1066s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_graph.py" [OK] 0.1s 1066s Time: 0.06 1066s Return code: 0 1066s OKs: 1 1066s Standard out: 1066s OK 1066s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_robust.py" [OK] 0.2s 1066s Time: 0.17 1066s Return code: 0 1066s OKs: 1 1066s Standard out: 1066s OK 1069s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1069s 139 1069s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1069s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/superpose.py" [FAIL] 3.4s 1069s Time: 3.44 1069s Return code: 139 1069s OKs: 0 1069s Standard error: 1069s Segmentation fault (core dumped) 1073s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1073s 139 1073s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1073s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/spe.py" [FAIL] 3.4s 1073s Time: 3.39 1073s Return code: 139 1073s OKs: 0 1073s Standard error: 1073s Segmentation fault (core dumped) 1077s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1077s 139 1077s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1077s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/incremental_SO3_sampling.py" [FAIL] 4.7s 1077s Time: 4.74 1077s Return code: 139 1077s OKs: 0 1077s Standard error: 1077s Segmentation fault (core dumped) 1079s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_integer_offsets_vs_pointers.py" [OK] 28.1s 1079s Time: 28.08 1079s Return code: 0 1079s OKs: 1 1079s Standard out: 1079s data_size = 1000 n_repeats = 30000 1079s use_pointers = False 1079s use_iterators = 0 time = 0.32 s overhead = 0.00 s (d[p[i]] -8.52653e-09) 1079s use_iterators = 1 time = 0.13 s overhead = 0.00 s (d[*p++] -8.52653e-09) 1079s use_pointers = True 1079s use_iterators = 0 time = 0.28 s overhead = 0.00 s (*dp[i] -8.52653e-09) 1079s use_iterators = 1 time = 0.48 s overhead = 0.00 s (**dpi++ -8.52653e-09) 1079s use_iterators = 2 time = 0.04 s overhead = 0.00 s (**dpp++ -8.52653e-09) 1079s data_size = 10000 n_repeats = 3000 1079s use_pointers = False 1079s use_iterators = 0 time = 0.32 s overhead = 0.00 s (d[p[i]] 4.91124e-08) 1079s use_iterators = 1 time = 0.13 s overhead = 0.00 s (d[*p++] 4.91124e-08) 1079s use_pointers = True 1079s use_iterators = 0 time = 0.24 s overhead = 0.00 s (*dp[i] 4.91124e-08) 1079s use_iterators = 1 time = 0.48 s overhead = 0.00 s (**dpi++ 4.91124e-08) 1079s use_iterators = 2 time = 0.04 s overhead = 0.00 s (**dpp++ 4.91124e-08) 1079s data_size = 100000 n_repeats = 300 1079s use_pointers = False 1079s use_iterators = 0 time = 0.53 s overhead = 0.00 s (d[p[i]] 4.35978e-09) 1079s use_iterators = 1 time = 0.31 s overhead = 0.00 s (d[*p++] 4.35978e-09) 1079s use_pointers = True 1079s use_iterators = 0 time = 0.38 s overhead = 0.00 s (*dp[i] 4.35978e-09) 1079s use_iterators = 1 time = 0.80 s overhead = 0.00 s (**dpi++ 4.35978e-09) 1079s use_iterators = 2 time = 0.11 s overhead = 0.00 s (**dpp++ 4.35978e-09) 1079s data_size = 1000000 n_repeats = 30 1079s use_pointers = False 1079s use_iterators = 0 time = 2.22 s overhead = 0.02 s (d[p[i]] -5.93784e-07) 1079s use_iterators = 1 time = 1.31 s overhead = 0.02 s (d[*p++] -5.93784e-07) 1079s use_pointers = True 1079s use_iterators = 0 time = 1.49 s overhead = 0.02 s (*dp[i] -5.93784e-07) 1079s use_iterators = 1 time = 3.39 s overhead = 0.02 s (**dpi++ -5.93784e-07) 1079s use_iterators = 2 time = 0.46 s overhead = 0.02 s (**dpp++ -5.93784e-07) 1079s data_size = 10000000 n_repeats = 3 1079s use_pointers = False 1079s use_iterators = 0 time = 2.80 s overhead = 0.20 s (d[p[i]] -2.01229e-06) 1079s use_iterators = 1 time = 1.77 s overhead = 0.19 s (d[*p++] -2.01229e-06) 1079s use_pointers = True 1079s use_iterators = 0 time = 1.94 s overhead = 0.19 s (*dp[i] -2.01229e-06) 1079s use_iterators = 1 time = 4.12 s overhead = 0.19 s (**dpi++ -2.01229e-06) 1079s use_iterators = 2 time = 0.73 s overhead = 0.19 s (**dpp++ -2.01229e-06) 1079s OK 1081s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1081s 139 1081s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1081s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_curve_fitting.py" [FAIL] 3.5s 1081s Time: 3.48 1081s Return code: 139 1081s OKs: 0 1081s Standard error: 1081s Segmentation fault (core dumped) 1081s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_similarity_indices.py" [OK] 0.2s 1081s Time: 0.18 1081s Return code: 0 1081s OKs: 1 1081s Standard out: 1081s OK 1084s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1084s 139 1084s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1084s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_weighted_correlation.py" [FAIL] 5.4s 1084s Time: 5.40 1084s Return code: 139 1084s OKs: 0 1084s Standard error: 1084s Segmentation fault (core dumped) 1084s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_fit_quadratic_function.py" [OK] 0.2s 1084s Time: 0.23 1084s Return code: 0 1084s OKs: 1 1084s Standard out: 1084s OK 1085s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gcd.py" [OK] 0.6s 1085s Time: 0.58 1085s Return code: 0 1085s OKs: 1 1085s Standard out: 1085s compare_with_boost_rational_gcd(gcd_int_simple) 1085s compare_with_boost_rational_gcd(gcd_long_simple) 1085s compare_with_boost_rational_gcd(gcd_long_binary) 1085s gcd_int_boost 999 w=0.04 u+s=0.03 1085s gcd_int_simple 999 w=0.02 u+s=0.02 1085s gcd_long_boost 999 w=0.04 u+s=0.03 1085s gcd_long_simple 999 w=0.02 u+s=0.03 1085s gcd_unsigned_long_binary 999 w=0.08 u+s=0.08 1085s gcd_long_binary 999 w=0.08 u+s=0.08 1085s OK 1088s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1088s 139 1088s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1088s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_exp_functions.py" [FAIL] 6.4s 1088s Time: 6.42 1088s Return code: 139 1088s OKs: 0 1088s Standard error: 1088s Segmentation fault (core dumped) 1090s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_r3_rotation.py" [OK] 2.8s 1090s Time: 2.76 1090s Return code: 0 1090s OKs: 0 1090s Standard out: 1090s times unit quaternion <-> matrix 1090s py: 0.03 0.02 s 1090s c++: 0.05 0.06 s 1090s ratio: 0.63 0.38 1090s u+s,u,s: 2.70 2.67 0.03 1091s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1091s 139 1091s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1091s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_math.py" [FAIL] 6.2s 1091s Time: 6.19 1091s Return code: 139 1091s OKs: 0 1091s Standard error: 1091s Segmentation fault (core dumped) 1091s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_line_search.py" [OK] 0.2s 1091s Time: 0.22 1091s Return code: 0 1091s OKs: 1 1091s Standard out: 1091s OK 1094s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1094s 139 1094s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1094s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_resample.py" [FAIL] 3.8s 1094s Time: 3.82 1094s Return code: 139 1094s OKs: 0 1094s Standard error: 1094s Segmentation fault (core dumped) 1097s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1097s 139 1097s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1097s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian.py" [FAIL] 6.1s 1097s Time: 6.09 1097s Return code: 139 1097s OKs: 0 1097s Standard error: 1097s Segmentation fault (core dumped) 1098s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_bessel.py" [OK] 0.2s 1098s Time: 0.21 1098s Return code: 0 1098s OKs: 0 1101s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1101s 139 1101s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1101s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_quadrature.py" [FAIL] 6.4s 1101s Time: 6.41 1101s Return code: 139 1101s OKs: 0 1101s Standard error: 1101s Segmentation fault (core dumped) 1101s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_euler_angles.py" [OK] 0.8s 1101s Time: 0.79 1101s Return code: 0 1101s OKs: 0 1101s Standard out: 1101s u+s,u,s: 0.73 0.72 0.01 1102s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_superpose.py" [OK] 0.3s 1102s Time: 0.29 1102s Return code: 0 1102s OKs: 1 1102s Standard out: 1102s OK 1102s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_uniform_rotation_matrix.py" [OK] 0.2s 1102s Time: 0.21 1102s Return code: 0 1102s OKs: 1 1102s Standard out: 1102s OK 1104s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1104s 139 1104s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1104s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_halton.py" [FAIL] 6.1s 1104s Time: 6.12 1104s Return code: 139 1104s OKs: 0 1104s Standard error: 1104s Segmentation fault (core dumped) 1104s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike_mom.py" [OK] 0.2s 1104s Time: 0.21 1104s Return code: 0 1104s OKs: 1 1104s Standard out: 1104s OK 1104s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/sieve_of_eratosthenes.py" [OK] 0.0s 1104s Time: 0.03 1104s Return code: 0 1104s OKs: 1 1104s Standard out: 1104s OK 1104s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/besselk.py" [OK] 0.0s 1104s Time: 0.03 1104s Return code: 0 1104s OKs: 1 1104s Standard out: 1104s OK 1107s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1107s 139 1107s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1107s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/scale_curves.py" [FAIL] 3.4s 1107s Time: 3.40 1107s Return code: 139 1107s OKs: 0 1107s Standard error: 1107s Segmentation fault (core dumped) 1111s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1111s 139 1111s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1111s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_fit_peak.py" [FAIL] 3.4s 1111s Time: 3.40 1111s Return code: 139 1111s OKs: 0 1111s Standard error: 1111s Segmentation fault (core dumped) 1114s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1114s 139 1114s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1114s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_clustering.py" [FAIL] 3.3s 1114s Time: 3.30 1114s Return code: 139 1114s OKs: 0 1114s Standard error: 1114s Segmentation fault (core dumped) 1114s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_orthonormal_basis.py" [OK] 0.2s 1114s Time: 0.22 1114s Return code: 0 1114s OKs: 1 1114s Standard out: 1114s OK 1115s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_g_function.py" [OK] 0.2s 1115s Time: 0.22 1115s Return code: 0 1115s OKs: 0 1115s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_angle_derivative.py" [OK] 0.2s 1115s Time: 0.21 1115s Return code: 0 1115s OKs: 1 1115s Standard out: 1115s OK 1118s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1118s 139 1118s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1118s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike.py" [FAIL] 16.3s 1118s Time: 16.32 1118s Return code: 139 1118s OKs: 0 1118s Standard error: 1118s Segmentation fault (core dumped) 1121s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1121s 139 1121s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1121s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_periodogram.py" [FAIL] 6.5s 1121s Time: 6.47 1121s Return code: 139 1121s OKs: 0 1121s Standard error: 1121s Segmentation fault (core dumped) 1121s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_tetrahedron.py" [OK] 0.2s 1121s Time: 0.23 1121s Return code: 0 1121s OKs: 1 1121s Standard out: 1121s OK 1122s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_undirected_graph.py" [OK] 0.2s 1122s Time: 0.20 1122s Return code: 0 1122s OKs: 0 1122s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_so3_lie_algebra.py" [OK] 0.2s 1122s Time: 0.19 1122s Return code: 0 1122s OKs: 0 1122s libtbx.python "/usr/lib/python3/dist-packages/scitbx/minpack/tst.py" [OK] 0.2s 1122s Time: 0.20 1122s Return code: 0 1122s OKs: 1 1122s Standard out: 1122s OK 1122s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_ext.py" [OK] 0.2s 1122s Time: 0.18 1122s Return code: 0 1122s OKs: 1 1122s Standard out: 1122s OK 1124s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1124s 139 1124s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1124s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_error_propagation_matrix_inverse.py" [FAIL] 6.1s 1124s Time: 6.13 1124s Return code: 139 1124s OKs: 0 1124s Standard error: 1124s Segmentation fault (core dumped) 1128s Standard error: 1128s Segmentation fault (core dumped) 1128s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1128s 139 1128s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1128s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_curvatures.py" [FAIL] 5.3s 1128s Time: 5.31 1128s Return code: 139 1128s OKs: 0 1128s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_func_free_line_search.py" [OK] 0.2s 1128s Time: 0.21 1128s Return code: 0 1128s OKs: 1 1128s Standard out: 1128s The answer is: [2, -5, 500] 1128s The start value is: [-100, 203, 999] 1128s scitbx.lbfgs: use gradient_only line search: True 1128s scitbx.lbfgs: use gradient_only line search: False 1128s OK 1128s "/usr/lib/cctbx/python3.13/scitbx/lbfgs/tst_lbfgs" [OK] 0.0s 1128s Time: 0.01 1128s Return code: 0 1128s OKs: 0 1128s Standard out: 1128s n: 100 1128s m: 5 1128s xtol: 1e-16 1128s f: 254.065 gnorm: 325.365 1128s 1 2 0.000607303 1128s f: 207.819 gnorm: 54.5204 1128s 2 3 1 1128s f: 206.329 gnorm: 12.6873 1128s 3 4 1 1128s f: 206.158 gnorm: 12.9705 1128s 4 5 1 1128s f: 204.568 gnorm: 36.0649 1128s 5 6 1 1128s f: 201.009 gnorm: 69.9702 1128s 6 7 1 1128s f: 132.076 gnorm: 99.1014 1128s 7 11 2.30835 1128s f: 131.557 gnorm: 80.1033 1128s 8 13 0.152436 1128s f: 120.196 gnorm: 66.244 1128s 9 15 5 1128s f: 105.948 gnorm: 116.627 1128s 10 16 1 1128s f: 87.4002 gnorm: 17.1325 1128s 11 17 1 1128s f: 72.7773 gnorm: 32.6968 1128s 12 18 1 1128s f: 67.7306 gnorm: 49.5851 1128s 13 20 0.213662 1128s f: 60.0913 gnorm: 52.8678 1128s 14 21 1 1128s f: 45.9493 gnorm: 28.0796 1128s 15 22 1 1128s f: 37.3669 gnorm: 39.3487 1128s 16 23 1 1128s f: 23.0492 gnorm: 14.5867 1128s 17 24 1 1128s f: 19.8468 gnorm: 17.9762 1128s 18 26 0.156708 1128s f: 17.6677 gnorm: 48.6045 1128s 19 27 1 1128s f: 13.9465 gnorm: 22.2498 1128s 20 28 1 1128s f: 9.11604 gnorm: 28.0105 1128s 21 29 1 1128s f: 5.82159 gnorm: 10.2151 1128s 22 30 1 1128s f: 4.75971 gnorm: 28.511 1128s 23 32 0.436181 1128s f: 2.35807 gnorm: 22.65 1128s 24 33 1 1128s f: 1.55734 gnorm: 15.4752 1128s 25 34 1 1128s f: 0.810498 gnorm: 2.3865 1128s 26 36 0.404632 1128s f: 0.508703 gnorm: 9.94499 1128s 27 38 0.247512 1128s f: 0.363447 gnorm: 15.2129 1128s 28 39 1 1128s f: 0.167247 gnorm: 9.7728 1128s 29 40 1 1128s f: 0.0372373 gnorm: 1.32586 1128s 30 41 1 1128s f: 0.0098316 gnorm: 4.14194 1128s 31 42 1 1128s f: 0.000471098 gnorm: 0.567595 1128s 32 43 1 1128s f: 3.2788e-06 gnorm: 0.027547 1128s 33 44 1 1128s f: 2.34044e-08 gnorm: 0.00607363 1128s 34 45 1 1128s f: 2.09469e-13 gnorm: 1.31535e-05 1128s 35 46 1 1131s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1131s 139 1131s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1131s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgsb/boost_python/tst_lbfgsb.py" [FAIL] 3.5s 1131s Time: 3.54 1131s Return code: 139 1131s OKs: 0 1131s Standard error: 1131s Segmentation fault (core dumped) 1135s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1135s 139 1135s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1135s libtbx.python "/usr/lib/python3/dist-packages/scitbx/fftpack/boost_python/tst_fftpack.py" [FAIL] 3.5s 1135s Time: 3.54 1135s Return code: 139 1135s OKs: 0 1135s Standard error: 1135s Segmentation fault (core dumped) 1137s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" [OK] 12.6s 1137s Time: 12.63 1137s Return code: 0 1137s OKs: 1 1137s Standard out: 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 5 -1 0 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 5 -1 0 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 5 -1 0 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 4 -1 1 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 4 -1 1 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 4 -1 1 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 5 -1 2 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 5 -1 2 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 5 -1 2 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 5 -1 3 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 5 -1 3 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 5 -1 3 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 6 0 0 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 6 0 0 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 6 0 0 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 6 0 1 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 6 0 1 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 6 0 1 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 4 0 2 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 4 0 2 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 4 0 2 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 2 0 3 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 2 0 3 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 2 0 3 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 6 1 0 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 6 1 0 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 6 1 0 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 4 1 1 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 4 1 1 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 4 1 1 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 7 1 2 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 7 1 2 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 7 1 2 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 7 1 3 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 7 1 3 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 7 1 3 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 5 2 0 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 5 2 0 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 5 2 0 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 4 2 1 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 4 2 1 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 4 2 1 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 4 2 2 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 4 2 2 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 4 2 2 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 6 2 3 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 6 2 3 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 6 2 3 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 5 3 0 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 5 3 0 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 5 3 0 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 2 3 1 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 2 3 1 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 2 3 1 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 2 3 2 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 2 3 2 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 2 3 2 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 7 3 3 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 7 3 3 1137s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 7 3 3 1137s usr+sys time: 0.38 seconds 1137s wall clock time: 12.42 seconds 1137s OK 1137s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_array_loops.py" [OK] 0.2s 1137s Time: 0.16 1137s Return code: 0 1137s OKs: 1 1137s Standard out: 1137s 10.0 1137s 11.0 1137s 12.0 1137s 1137s 10.0 1137s 11.0 1137s 12.0 1137s 1137s 0 10.0 1137s 1 11.0 1137s 2 12.0 1137s 1137s 100.0 1137s 110.0 1137s 120.0 1137s 1137s 200.0 1137s 210.0 1137s 220.0 1137s 1137s OK 1137s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/principal_axes_of_inertia.py" [OK] 0.2s 1137s Time: 0.18 1137s Return code: 0 1137s OKs: 0 1137s Standard out: 1137s (7.796692307692308, 1.365076923076923, 8.357692307692307) 1137s (38.140037692307715, 97.02526753846156, 79.0222196923077, -19.808558307692305, 35.14258523076924, 7.6620366923076935) 1137s [104.22746487361265, 97.26642591377534, 12.693634135689015] 1137s [-0.43905397167468396, 0.8222124337102901, -0.36221309171382476, 0.3037216796237081, 0.5152398514117881, 0.8014243799908461, 0.8455677094610694, 0.24185658843488295, -0.4759418445014057] 1137s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_recipe.py" [OK] 0.2s 1137s Time: 0.16 1137s Return code: 0 1137s OKs: 1 1137s Standard out: 1137s refinery 1137s compute_functional_and_gradients 1137s callback_after_step 1137s OK 1138s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1138s 139 1138s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1138s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_grid.py" [FAIL] 3.3s 1138s Time: 3.30 1138s Return code: 139 1138s OKs: 0 1138s Standard error: 1138s Segmentation fault (core dumped) 1141s Standard error: 1141s Segmentation fault (core dumped) 1141s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1141s 139 1141s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1141s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_linear_least_squares_fit.py" [FAIL] 3.7s 1141s Time: 3.71 1141s Return code: 139 1141s OKs: 0 1144s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1144s 139 1144s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1144s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/chebyshev_lsq_example.py" [FAIL] 6.0s 1144s Time: 6.05 1144s Return code: 139 1144s OKs: 0 1144s Standard error: 1144s Segmentation fault (core dumped) 1144s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/rigid_body_refinement_core.py" [OK] 0.2s 1144s Time: 0.17 1144s Return code: 0 1144s OKs: 1 1144s Standard out: 1144s an ea: [0.0, 0.0, 0.0] 1144s fd ea: [2.9856131013692537e-15, 8.482502921596884e-16, 3.956636706594845e-15] 1144s an lt: [-0.0, -0.0, -0.0] 1144s fd lt: [0.0, 0.0, 0.0] 1144s 1144s an ea: [1.4293798315070272, -4.7699199336056015, -3.2848275925325994] 1144s fd ea: [1.4293798322739804, -4.769919932368083, -3.284827593041939] 1144s an lt: [-2.6395370381698946, 3.8546779254822816, -3.7648774634679576] 1144s fd lt: [-2.6395370364973303, 3.8546779261849906, -3.764877463563465] 1144s 1144s an ea: [-4.386454471339835, 2.1848899436111178, 5.0802158076235635] 1144s fd ea: [-4.386454468985335, 2.184889945411328, 5.080215810693289] 1144s an lt: [-4.688132824683539, -10.874759921610867, -1.9393316543209416] 1144s fd lt: [-4.688132825947378, -10.874759922785415, -1.939331655265164] 1144s 1144s an ea: [-5.097458993694191, 2.0225151159319297, 4.479103261227751] 1144s fd ea: [-5.097458993574833, 2.0225151207142744, 4.479103258958617] 1144s an lt: [-2.8154365578392593, -5.157085781215166, -17.014046644874668] 1144s fd lt: [-2.8154365576682494, -5.157085780638226, -17.014046648000658] 1144s 1144s OK 1148s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1148s 139 1148s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1148s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/immoptibox_ports.py" [FAIL] 6.5s 1148s Time: 6.47 1148s Return code: 139 1148s OKs: 0 1148s Standard error: 1148s Segmentation fault (core dumped) 1151s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1151s 139 1151s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1151s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/integrating_a_weighted_sinc_function.py" [FAIL] 6.3s 1151s Time: 6.30 1151s Return code: 139 1151s OKs: 0 1151s Standard error: 1151s Segmentation fault (core dumped) 1151s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_utils.py" [OK] 0.0s 1151s Time: 0.04 1151s Return code: 0 1151s OKs: 1 1151s Standard out: 1151s OK 1151s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/rigidity.py" [OK] 0.0s 1151s Time: 0.04 1151s Return code: 0 1151s OKs: 0 1151s Standard out: 1151s double banana 3D dof (method=integer): 7 1151s double banana 3D dof (method=float): 7 1151s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_rigidity.py" [OK] 0.2s 1151s Time: 0.21 1151s Return code: 0 1151s OKs: 0 1151s Standard out: 1151s repeat_log = {0: 85} 1151s u+s,u,s: 0.19 0.19 0.00 1151s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/rigidity_matrix_symbolic.py" [OK] 0.2s 1151s Time: 0.20 1151s Return code: 0 1151s OKs: 0 1151s Standard out: 1151s u+s,u,s: 0.17 0.17 0.00 1153s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree_find_paths.py" [OK] 1.9s 1153s Time: 1.90 1153s Return code: 0 1153s OKs: 1 1153s Standard out: 1153s OK 1154s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1154s 139 1154s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1154s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/minimizer_comparisons.py" [FAIL] 6.1s 1154s Time: 6.08 1154s Return code: 139 1154s OKs: 0 1154s Standard error: 1154s Segmentation fault (core dumped) 1154s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/test_cases_tardy_pdb.py" [OK] 0.1s 1154s Time: 0.07 1154s Return code: 0 1154s OKs: 0 1157s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1157s 139 1157s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1157s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree.py" [FAIL] 3.9s 1157s Time: 3.87 1157s Return code: 139 1157s OKs: 0 1157s Standard error: 1157s Segmentation fault (core dumped) 1160s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1160s 139 1160s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1160s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_basic.py" [FAIL] 6.2s 1160s Time: 6.20 1160s Return code: 139 1160s OKs: 0 1160s Standard error: 1160s Segmentation fault (core dumped) 1163s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1163s 139 1163s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1163s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_tardy.py" [FAIL] 6.1s 1163s Time: 6.12 1163s Return code: 139 1163s OKs: 0 1163s Standard error: 1163s Segmentation fault (core dumped) 1166s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1166s 139 1166s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1166s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_energy_plots.py" [FAIL] 6.0s 1166s Time: 5.99 1166s Return code: 139 1166s OKs: 0 1166s Standard error: 1166s Segmentation fault (core dumped) 1166s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/free_motion_reference_impl.py" [OK] 0.0s 1166s Time: 0.04 1166s Return code: 0 1166s OKs: 1 1166s Standard out: 1166s e_kin tot ang lin: 0.04066059413038476 0.012310594130384761 0.02835 1166s e_pot: 0.6403087877704161 1166s e_tot: 0.6809693819008009 1166s ang acc 3D: (0.4499405243671747, -0.22736369685250066, -0.6859763000328927) 1166s lin acc 3D: (0.2108121283092794, 0.3044814367238479, -0.7824311428947446) 1166s 1166s e_kin tot ang lin: 0.043334386720177365 0.012335145793951681 0.030999240926225684 1166s e_pot: 0.6375204431681878 1166s e_tot: 0.6808548298883652 1166s ang acc 3D: (0.4491523283824315, -0.2233952828755118, -0.688364609039924) 1166s lin acc 3D: (0.2063305410676703, 0.3022012812609254, -0.7827791077048256) 1166s 1166s e_kin tot ang lin: 0.04624491637806352 0.012390841212545118 0.0338540751655184 1166s e_pot: 0.6344966498401754 1166s e_tot: 0.6807415662182389 1166s ang acc 3D: (0.4482905223840879, -0.2193464063160701, -0.6906197519803725) 1166s lin acc 3D: (0.20168867739512958, 0.299808900299363, -0.7830079270607541) 1166s 1166s e_kin tot ang lin: 0.049389854602061224 0.01247763222642335 0.036912222375637876 1166s e_pot: 0.6312398275384674 1166s e_tot: 0.6806296821405287 1166s ang acc 3D: (0.44735466644443667, -0.21521902126722914, -0.692740958483326) 1166s lin acc 3D: (0.19688964121862268, 0.29730414639378616, -0.7831155604559972) 1166s 1166s e_kin tot ang lin: 0.05276668787891577 0.012595448079626585 0.04017123979928919 1166s e_pot: 0.6277525800757479 1166s e_tot: 0.6805192679546637 1166s ang acc 3D: (0.4463443200247767, -0.2110151239756078, -0.694727476553102) 1166s lin acc 3D: (0.1919366941490876, 0.29468687861617315, -0.783099948460292) 1166s 1166s e_kin tot ang lin: 0.05637271969939971 0.012744195480724368 0.043628524218675344 1166s e_pot: 0.6240376932449352 1166s e_tot: 0.6804104129443349 1166s ang acc 3D: (0.4452590426839754, -0.2067367517215091, -0.6965785731789051) 1166s lin acc 3D: (0.18683325327725137, 0.29195696483157874, -0.7829590159403469) 1166s 1166s e_kin tot ang lin: 0.060205072713709167 0.012923758676161239 0.04728131403754793 1166s e_pot: 0.6200981325993219 1166s e_tot: 0.680303205313031 1166s ang acc 3D: (0.44409839480429714, -0.20238598167333133, -0.6982935349568492) 1166s lin acc 3D: (0.18158288880693388, 0.2891142841060344, -0.7826906753299725) 1166s 1166s e_kin tot ang lin: 0.06426069102522652 0.013133999536143382 0.051126691489083144 1166s e_pot: 0.6159370410950341 1166s e_tot: 0.6801977321202606 1166s ang acc 3D: (0.4428619383337592, -0.1979649297164907, -0.6998716687235316) 1166s lin acc 3D: (0.17618932152521946, 0.2861587292410898, -0.7822928299444691) 1166s 1166s e_kin tot ang lin: 0.06853634262082685 0.013374757653013635 0.05516158496781321 1166s e_pot: 0.6115577365976127 1166s e_tot: 0.6800940792184396 1166s ang acc 3D: (0.4415492375442347, -0.1934757492571058, -0.7013123022002559) 1166s lin acc 3D: (0.17065642010895676, 0.2830902094290727, -0.7817633773339945) 1166s 1166s e_kin tot ang lin: 0.07302862193581516 0.013645850452066947 0.059382771483748216 1166s e_pot: 0.6069637092547071 1166s e_tot: 0.6799923311905223 1166s ang acc 3D: (0.44015985980451133, -0.18892063000069204, -0.702614784647033) 1166s lin acc 3D: (0.16498819826718966, 0.2799086530227533, -0.7811002126706817) 1166s 1166s OK 1169s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1169s 139 1169s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1169s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/tst.py" [FAIL] 6.0s 1169s Standard error: 1169s Segmentation fault (core dumped) 1169s Time: 6.00 1169s Return code: 139 1169s OKs: 0 1172s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1172s 139 1172s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1172s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_featherstone.py" [FAIL] 5.9s 1172s Time: 5.94 1172s Return code: 139 1172s OKs: 0 1172s Standard error: 1172s Segmentation fault (core dumped) 1175s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1175s 139 1175s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1175s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion.py" [FAIL] 6.0s 1175s Time: 6.05 1175s Return code: 139 1175s OKs: 0 1175s Standard error: 1175s Segmentation fault (core dumped) 1178s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1178s 139 1178s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1178s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion_hard.py" [FAIL] 6.1s 1178s Time: 6.07 1178s Return code: 139 1178s OKs: 0 1178s Standard error: 1178s Segmentation fault (core dumped) 1181s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1181s 139 1181s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1181s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_joint_lib.py" [FAIL] 6.0s 1181s Time: 6.04 1181s Return code: 139 1181s OKs: 0 1181s Standard error: 1181s Segmentation fault (core dumped) 1181s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_spherical_refinement.py" [OK] 0.3s 1181s Time: 0.32 1181s Return code: 0 1181s OKs: 1 1181s Standard out: 1181s OK 1181s usr+sys time: 0.26 seconds 1181s wall clock time: 0.26 seconds 1184s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1184s 139 1184s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1184s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_singular.py" [FAIL] 6.1s 1184s Standard error: 1184s Segmentation fault (core dumped) 1184s Time: 6.13 1184s Return code: 139 1184s OKs: 0 1187s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1187s 139 1187s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1187s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_molecules.py" [FAIL] 5.7s 1187s Time: 5.74 1187s Return code: 139 1187s OKs: 0 1187s Standard error: 1187s Segmentation fault (core dumped) 1190s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1190s 139 1190s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1190s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_sparse.py" [FAIL] 6.1s 1190s Time: 6.05 1190s Return code: 139 1190s OKs: 0 1190s Standard error: 1190s Segmentation fault (core dumped) 1193s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1193s 139 1193s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1193s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_lu_factorization.py" [FAIL] 6.0s 1193s Time: 5.95 1193s Return code: 139 1193s OKs: 0 1193s Standard error: 1193s Segmentation fault (core dumped) 1196s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1196s 139 1196s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1196s libtbx.python "/usr/lib/python3/dist-packages/scitbx/iso_surface/tst_iso_surface.py" [FAIL] 6.0s 1196s Time: 5.97 1196s Return code: 139 1196s OKs: 0 1196s Standard error: 1196s Segmentation fault (core dumped) 1199s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1199s 139 1199s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1199s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/simplex.py" [FAIL] 6.0s 1199s Time: 5.98 1199s Return code: 139 1199s OKs: 0 1199s Standard error: 1199s Segmentation fault (core dumped) 1199s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/golden_section_search.py" [OK] 0.0s 1199s Time: 0.03 1199s Return code: 0 1199s OKs: 0 1202s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1202s 139 1202s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1202s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/differential_evolution.py" [FAIL] 5.9s 1202s Time: 5.86 1202s Return code: 139 1202s OKs: 0 1202s Standard error: 1202s Segmentation fault (core dumped) 1205s Standard error: 1205s Segmentation fault (core dumped) 1205s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1205s 139 1205s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1205s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/direct_search_simulated_annealing.py" [FAIL] 5.7s 1205s Time: 5.72 1205s Return code: 139 1205s OKs: 0 1208s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1208s 139 1208s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1208s libtbx.python "/usr/lib/python3/dist-packages/scitbx/random/tests/tst_random.py" [FAIL] 6.2s 1208s Time: 6.18 1208s Return code: 139 1208s OKs: 0 1208s Standard error: 1208s Segmentation fault (core dumped) 1208s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/test_problems.py" [OK] 0.2s 1208s Time: 0.19 1208s Return code: 0 1208s OKs: 0 1211s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1211s 139 1211s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1211s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/tst_normal_equations.py" [FAIL] 6.3s 1211s Time: 6.34 1211s Return code: 139 1211s OKs: 0 1211s Standard error: 1211s Segmentation fault (core dumped) 1214s Standard error: 1214s Segmentation fault (core dumped) 1214s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1214s 139 1214s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1214s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_basic.py" [FAIL] 3.2s 1214s Time: 3.19 1214s Return code: 139 1214s OKs: 0 1216s libtbx.python "/usr/lib/python3/dist-packages/scitbx/glmtbx/tests/tst.py" [OK] 7.3s 1216s Time: 7.27 1216s Return code: 0 1216s OKs: 2 1216s Standard out: 1216s OK 1216s OK 1218s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1218s 139 1218s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1218s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_booth.py" [FAIL] 3.2s 1218s Time: 3.16 1218s Return code: 139 1218s OKs: 0 1218s Standard error: 1218s Segmentation fault (core dumped) 1218s libtbx.python "/usr/lib/python3/dist-packages/scitbx/suffixtree/test/tst_single.py" [OK] 0.1s 1218s Time: 0.09 1218s Return code: 0 1218s OKs: 0 1221s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1221s 139 1221s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1221s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_twisted.py" [FAIL] 4.8s 1221s Time: 4.83 1221s Return code: 139 1221s OKs: 0 1221s Standard error: 1221s Segmentation fault (core dumped) 1224s Standard error: 1224s Segmentation fault (core dumped) 1224s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1224s 139 1224s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1224s libtbx.python "/usr/lib/python3/dist-packages/smtbx/absolute_structure/tests/tst_absolute_structure.py" --fix_random_seeds [FAIL] 6.3s 1224s Time: 6.33 1224s Return code: 139 1224s OKs: 0 1227s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1227s 139 1227s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1227s libtbx.python "/usr/lib/python3/dist-packages/smtbx/ab_initio/tests/tst_ab_initio_ext.py" [FAIL] 6.5s 1227s Time: 6.54 1227s Return code: 139 1227s OKs: 0 1227s Standard error: 1227s Segmentation fault (core dumped) 1230s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1230s 139 1230s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1230s libtbx.python "/usr/lib/python3/dist-packages/smtbx/ab_initio/tests/tst_charge_flipping.py" --fix_seed --on=E "hall: P 1" "hall: P 3" "hall: -P 2ybc" [FAIL] 6.3s 1230s Standard error: 1230s Segmentation fault (core dumped) 1230s Time: 6.33 1230s Return code: 139 1230s OKs: 0 1234s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1234s 139 1234s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1234s libtbx.python "/usr/lib/python3/dist-packages/smtbx/masks/tests/tst_masks.py" [FAIL] 6.6s 1234s Time: 6.59 1234s Return code: 139 1234s OKs: 0 1234s Standard error: 1234s Segmentation fault (core dumped) 1237s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1237s 139 1237s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1237s libtbx.python "/usr/lib/python3/dist-packages/smtbx/structure_factors/direct/tests/tst_standard_xray.py" [FAIL] 6.6s 1237s Time: 6.59 1237s Return code: 139 1237s OKs: 0 1237s Standard error: 1237s Segmentation fault (core dumped) 1240s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1240s 139 1240s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1240s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_weighting_schemes.py" --fix_random_seeds [FAIL] 6.7s 1240s Time: 6.72 1240s Return code: 139 1240s OKs: 0 1240s Standard error: 1240s Segmentation fault (core dumped) 1240s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_reparametrisation" [OK] 0.0s 1240s Time: 0.01 1240s Return code: 0 1240s OKs: 1 1240s Standard out: 1240s sizeof(parameter) = 32 1240s OK 1244s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1244s 139 1244s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1244s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_lbfgs.py" [FAIL] 6.7s 1244s Time: 6.68 1244s Return code: 139 1244s OKs: 0 1244s Standard error: 1244s Segmentation fault (core dumped) 1244s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens" [OK] 0.0s 1244s Time: 0.01 1244s Return code: 0 1244s OKs: 1 1244s Standard out: 1244s OK 1247s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1247s 139 1247s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1247s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_occupancies.py" [FAIL] 6.6s 1247s Time: 6.63 1247s Return code: 139 1247s OKs: 0 1247s Standard error: 1247s Segmentation fault (core dumped) 1247s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_special_position" [OK] 0.0s 1247s Time: 0.01 1247s Return code: 0 1247s OKs: 1 1247s Standard out: 1247s OK 1250s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1250s 139 1250s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1250s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_same_group.py" [FAIL] 6.8s 1250s Time: 6.84 1250s Return code: 139 1250s OKs: 0 1250s Standard error: 1250s Segmentation fault (core dumped) 1254s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1254s 139 1254s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1254s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_reparametrisation.py" [FAIL] 6.6s 1254s Time: 6.63 1254s Return code: 139 1254s OKs: 0 1254s Standard error: 1254s Segmentation fault (core dumped) 1257s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1257s 139 1257s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1257s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=naive [FAIL] 6.5s 1257s Time: 6.50 1257s Return code: 139 1257s OKs: 0 1257s Standard error: 1257s Segmentation fault (core dumped) 1261s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1261s 139 1261s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1261s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_disorder.py" [FAIL] 6.9s 1261s Time: 6.94 1261s Return code: 139 1261s OKs: 0 1261s Standard error: 1261s Segmentation fault (core dumped) 1261s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1261s 139 1261s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1261s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=levenberg-marquardt [FAIL] 3.7s 1261s Time: 3.70 1261s Return code: 139 1261s OKs: 0 1261s Standard error: 1261s Segmentation fault (core dumped) 1264s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1264s 139 1264s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1264s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_direction.py" [FAIL] 3.5s 1264s Time: 3.52 1264s Return code: 139 1264s OKs: 0 1264s Standard error: 1264s Segmentation fault (core dumped) 1268s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1268s 139 1268s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1268s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_rigid.py" [FAIL] 7.1s 1268s Time: 7.10 1268s Return code: 139 1268s OKs: 0 1268s Standard error: 1268s Segmentation fault (core dumped) 1271s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1271s 139 1271s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1271s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_adp_restraints.py" [FAIL] 7.0s 1271s Time: 6.97 1271s Return code: 139 1271s OKs: 0 1271s Standard error: 1271s Segmentation fault (core dumped) 1275s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1275s 139 1275s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1275s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_manager.py" [FAIL] 7.0s 1275s Time: 6.95 1275s Return code: 139 1275s OKs: 0 1275s Standard error: 1275s Segmentation fault (core dumped) 1278s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1278s 139 1278s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1278s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_restraints.py" --verbose --scatterers=5 --resolution=0.2 [FAIL] 7.1s 1278s Time: 7.08 1278s Return code: 139 1278s OKs: 0 1278s Standard error: 1278s Segmentation fault (core dumped) 1282s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1282s 139 1282s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1282s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_refine.py" [FAIL] 7.4s 1282s Time: 7.38 1282s Return code: 139 1282s OKs: 0 1282s Standard error: 1282s Segmentation fault (core dumped) 1288s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1288s 1 1288s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1288s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py" [FAIL] 10.2s 1288s Time: 10.24 1288s Return code: 1 1288s OKs: 0 1288s Standard out: 1288s smtbx.anom_refine /usr/lib/python3/dist-packages/smtbx/regression/test_data/thpp.cif /usr/lib/python3/dist-packages/smtbx/regression/test_data/thpp.hkl F -e13000 -t -O -d0 -s0 -c25 1288s Standard error: 1288s Traceback (most recent call last): 1288s File "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py", line 37, in 1288s run() 1288s ~~~^^ 1288s File "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py", line 27, in run 1288s run_buf.raise_if_errors() 1288s ~~~~~~~~~~~~~~~~~~~~~~~^^ 1288s File "/usr/lib/python3/dist-packages/libtbx/easy_run.py", line 46, in raise_if_errors 1288s raise Error(msg) 1288s RuntimeError: child process stderr output: 1288s command: 'smtbx.anom_refine /usr/lib/python3/dist-packages/smtbx/regression/test_data/thpp.cif /usr/lib/python3/dist-packages/smtbx/regression/test_data/thpp.hkl F -e13000 -t -O -d0 -s0 -c25' 1288s Segmentation fault (core dumped) 1289s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1289s 139 1289s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1289s libtbx.python "/usr/lib/python3/dist-packages/smtbx/tests/tst_utils.py" [FAIL] 6.9s 1289s Time: 6.87 1289s Return code: 139 1289s OKs: 0 1289s Standard error: 1289s Segmentation fault (core dumped) 1292s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1292s 139 1292s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1292s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_least_squares.py" [EXPECTED UNSTABLE] 3.9s 1292s Time: 3.89 1292s Return code: 139 1292s OKs: 0 1292s Standard error: 1292s Segmentation fault (core dumped) 1293s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_predict.py" [OK] 0.3s 1293s Time: 0.26 1293s Return code: 0 1293s OKs: 1 1293s Standard out: 1293s OK 1293s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_ewald_sphere.py" [OK] 0.2s 1293s Time: 0.23 1293s Return code: 0 1293s OKs: 1 1293s Standard out: 1293s OK 1293s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_partial_derivatives.py" [OK] 0.2s 1293s Time: 0.22 1293s Return code: 0 1293s OKs: 1 1293s Standard out: 1293s OK 1295s Standard error: 1295s Segmentation fault (core dumped) 1295s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1295s 139 1295s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1295s libtbx.python "/usr/lib/python3/dist-packages/rstbx/dps_core/tst_iotbx_converter.py" [FAIL] 6.5s 1295s Time: 6.46 1295s Return code: 139 1295s OKs: 0 1299s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1299s 139 1299s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1299s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/fastbragg/tst_bragg_minimal.py" [FAIL] 5.6s 1299s Time: 5.62 1299s Return code: 139 1299s OKs: 0 1299s Standard error: 1299s Segmentation fault (core dumped) 1302s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1302s 139 1302s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1302s libtbx.python "/usr/lib/python3/dist-packages/rstbx/sublattice_support/tst_sublattice.py" [FAIL] 6.5s 1302s Time: 6.49 1302s Return code: 139 1302s OKs: 0 1302s Standard error: 1302s Segmentation fault (core dumped) 1302s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/core_toolbox/boost_python/tst_small_image.py" [OK] 0.4s 1302s Time: 0.43 1302s Return code: 0 1302s OKs: 1 1302s Standard out: 1302s OK 1302s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/diffraction/geometry.py" [OK] 0.2s 1302s Time: 0.20 1302s Return code: 0 1302s OKs: 1 1302s Standard out: 1302s OK 1303s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/math_support/sphere_formulae.py" [OK] 0.0s 1303s Time: 0.03 1303s Return code: 0 1303s OKs: 1 1303s Standard out: 1303s OK 1303s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1303s 139 1303s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1303s libtbx.python -c "from rstbx.run_tests import run; run()" [FAIL] 4.8s 1303s Time: 4.79 1303s Return code: 139 1303s OKs: 0 1303s Standard error: 1303s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s ================================================================================ 1304s 1304s Tests finished. Elapsed time: 1060.71s 1304s 1304s Distribution of test runtimes: 1304s 0.0s - 4.2s: 275 1304s 4.2s - 8.3s: 252 1304s 8.3s - 12.5s: 13 1304s 12.5s - 16.7s: 3 1304s 16.7s - 20.8s: 0 1304s 20.8s - 25.0s: 1 1304s 25.0s - 29.1s: 1 1304s 29.1s - 33.3s: 0 1304s 33.3s - 37.5s: 0 1304s 37.5s - 41.6s: 1 1304s 1304s 1304s Warning: the following are 5 longest jobs: 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_fetch.py": 41.6s 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_integer_offsets_vs_pointers.py": 28.1s 1304s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_thread_utils.py": 22.3s 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike.py": 16.3s 1304s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_separate_files.py": 14.8s 1304s Please try to reduce overall runtime - consider splitting up these tests. 1304s 1304s 1304s Error: the following jobs returned non-zero exit codes or suspicious stderr output: 1304s 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sf_low_res_accuracy.py" [FAIL] 4.8s 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Time: 4.80 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_double_step_filtration.py" [FAIL] 4.3s 1304s Time: 4.31 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_is_periodic.py" [FAIL] 6.9s 1304s Time: 6.89 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_reindexing.py" [FAIL] 7.0s 1304s Time: 6.97 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_data_manipulation.py" [FAIL] 6.2s 1304s Time: 6.25 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_bfgs.py" [FAIL] 6.6s 1304s Time: 6.56 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_dev.py" P31 [FAIL] 6.6s 1304s Time: 6.55 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry/tests/tst_geometry.py" [FAIL] 6.4s 1304s Time: 6.37 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/covariance/tests/tst_covariance.py" [FAIL] 6.7s 1304s Time: 6.68 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_goodness_of_symmetry.py" [FAIL] 7.1s 1304s Time: 7.15 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_from_map.py" P312 [FAIL] 6.9s 1304s Time: 6.86 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_xray.py" [FAIL] 6.0s 1304s Time: 5.99 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray.py" I41/acd [FAIL] 7.2s 1304s Time: 7.20 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_r1.py" [FAIL] 6.8s 1304s Time: 6.83 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_shelxl_wght_ls.py" [FAIL] 6.6s 1304s Time: 6.56 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_f_model.py" [FAIL] 6.7s 1304s Time: 6.69 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/array_family/boost_python/tst_flex.py" [FAIL] 6.7s 1304s Time: 6.66 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_uctbx.py" [FAIL] 6.7s 1304s Time: 6.73 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_crystal_orientation.py" [FAIL] 6.6s 1304s Time: 6.61 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_sgtbx.py" [FAIL] 6.9s 1304s Time: 6.87 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_ext.py" [FAIL] 7.7s 1304s Time: 7.72 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_distance_based_connectivity.py" [FAIL] 7.5s 1304s Time: 7.51 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_super_cell.py" [FAIL] 7.7s 1304s Time: 7.65 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adptbx/boost_python/tst_adptbx.py" [FAIL] 7.9s 1304s Time: 7.88 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/boost_python/tst_miller.py" [FAIL] 6.8s 1304s Time: 6.83 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_xray_scattering.py" [FAIL] 6.4s 1304s Time: 6.43 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_formula.py" [FAIL] 5.6s 1304s Time: 5.64 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_attenuation_coefficient.py" [FAIL] 6.5s 1304s Time: 6.47 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/boost_python/tst_maptbx.py" [FAIL] 6.5s 1304s Time: 6.55 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_bcr.py" [FAIL] 7.3s 1304s Time: 7.35 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_loft.py" [FAIL] 7.3s 1304s Time: 7.32 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/dmtbx/boost_python/tst_dmtbx.py" [FAIL] 6.5s 1304s Time: 6.46 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/translation_search/boost_python/tst_translation_search.py" [FAIL] 6.5s 1304s Time: 6.45 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_ext.py" [FAIL] 6.8s 1304s Time: 6.75 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_angle_derivs.py" [FAIL] 4.8s 1304s Time: 4.83 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adp_restraints/tst_ext.py" [FAIL] 6.3s 1304s Time: 6.27 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_krivy_gruber.py" --Quick [FAIL] 6.8s 1304s Time: 6.84 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx.py" [FAIL] 6.6s 1304s Time: 6.60 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_space_group_type_tidy_cb_op_t.py" [FAIL] 6.3s 1304s Time: 6.29 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_denominators.py" P31 [FAIL] 6.7s 1304s Time: 6.72 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_subgroups.py" [FAIL] 6.4s 1304s Time: 6.45 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_lattice_symmetry.py" [FAIL] 6.2s 1304s Time: 6.15 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints.py" P3 [FAIL] 6.2s 1304s Time: 6.25 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints_cartesian.py" [FAIL] 6.5s 1304s Time: 6.47 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reflection_statistics.py" [FAIL] 6.0s 1304s Time: 6.01 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_harker.py" [FAIL] 6.2s 1304s Time: 6.25 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_special_op_simplifier.py" [FAIL] 6.2s 1304s Time: 6.21 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_twin_target.py" [FAIL] 6.5s 1304s Time: 6.49 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/symbol_confidence.py" [FAIL] 6.4s 1304s Time: 6.37 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/bravais_types.py" [FAIL] 6.3s 1304s Time: 6.27 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_lookup_utils.py" [FAIL] 6.6s 1304s Time: 6.64 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal.py" I41/acd [FAIL] 6.9s 1304s Time: 6.88 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_direct_space_asu.py" I41/acd [FAIL] 6.8s 1304s Time: 6.78 1304s Return code: 139 1304s OKs: 0 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pair_asu_table.py" [FAIL] 6.7s 1304s Time: 6.65 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_asu_clusters.py" [FAIL] 6.6s 1304s Time: 6.65 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_close_packing.py" R-3mr [FAIL] 6.5s 1304s Time: 6.45 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fourier_transform_real_part_at_x.py" P31 [FAIL] 6.5s 1304s Time: 6.53 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller.py" P31 [FAIL] 6.5s 1304s Time: 6.48 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem.py" [FAIL] 6.8s 1304s Time: 6.79 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reciprocal_space_asu.py" P312 [FAIL] 6.2s 1304s Time: 6.16 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_triplet_generator.py" P41 [FAIL] 6.4s 1304s Time: 6.37 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_emma.py" P31 [FAIL] 6.8s 1304s Time: 6.77 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_expand_to_p1.py" P31 [FAIL] 7.0s 1304s Time: 6.97 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_change_basis.py" P31 [FAIL] 6.6s 1304s Time: 6.62 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wilson_plot.py" P31 [FAIL] 6.4s 1304s Time: 6.43 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_derivatives.py" P31 [FAIL] 6.6s 1304s Time: 6.65 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_fast_gradients.py" P31 [FAIL] 6.8s 1304s Time: 6.81 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F P31 [FAIL] 7.1s 1304s Time: 7.12 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F_sq P31 [FAIL] 3.8s 1304s Time: 3.77 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_weights_for_symmetry_summation.py" Pmmm [FAIL] 3.6s 1304s Time: 3.63 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_structure_factors.py" P31 [FAIL] 7.1s 1304s Time: 7.06 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_real_space_refinement_simple.py" [FAIL] 6.6s 1304s Time: 6.64 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation.py" [FAIL] 6.4s 1304s Time: 6.37 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation_2.py" [FAIL] 7.2s 1304s Time: 7.21 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_loc_res.py" [FAIL] 10.2s 1304s Time: 10.19 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_target_and_gradients.py" [FAIL] 9.4s 1304s Time: 9.43 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_merge_equivalents.py" P31 [FAIL] 6.6s 1304s Time: 6.63 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grouped_data.py" P31 [FAIL] 6.8s 1304s Time: 6.79 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_fft_map.py" P31 [FAIL] 6.9s 1304s Time: 6.91 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sampled_model_density.py" P31 [FAIL] 6.9s 1304s Time: 6.86 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fast_nv1995.py" F222 [FAIL] 6.7s 1304s Time: 6.69 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_lbfgs.py" [FAIL] 5.8s 1304s Time: 5.78 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_2.py" [FAIL] 6.7s 1304s Time: 6.69 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_french_wilson.py" [FAIL] 6.3s 1304s Time: 6.26 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/make_cns_input.py" P31 [FAIL] 6.3s 1304s Time: 6.32 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pointgroup_tools.py" [FAIL] 5.8s 1304s Time: 5.79 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/sub_lattice_tools.py" [FAIL] 7.4s 1304s Time: 7.41 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/rational_matrices_point_groups.py" [FAIL] 7.3s 1304s Time: 7.27 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/cosets.py" [FAIL] 6.8s 1304s Time: 6.81 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_pg_tools.py" [FAIL] 7.0s 1304s Time: 7.02 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_twin_laws.py" [FAIL] 6.9s 1304s Time: 6.91 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_find_best_cell.py" [FAIL] 6.6s 1304s Time: 6.57 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_amplitude_normalisation.py" [FAIL] 6.6s 1304s Time: 6.62 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_statistics_graphs.py" [FAIL] 7.3s 1304s Time: 7.27 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_web_change_basis.py" [FAIL] 7.3s 1304s Time: 7.27 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/direct_space_asu/proto/tst_asu.py" [FAIL] 7.0s 1304s Time: 6.96 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_tidy_pickling.py" [FAIL] 7.1s 1304s Time: 7.13 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/masks/tests/tst_flood_fill.py" [FAIL] 6.9s 1304s Time: 6.86 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_r_free_utils.py" [FAIL] 7.2s 1304s Time: 7.17 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_ccp.py" [FAIL] 7.0s 1304s Time: 7.03 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_mask.py" [FAIL] 7.0s 1304s Time: 7.04 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_map_peak_3d_as_2d.py" [FAIL] 7.3s 1304s Time: 7.33 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_asymmetric_map.py" [FAIL] 7.1s 1304s Time: 7.13 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_peak_volume_estimate.py" [FAIL] 6.8s 1304s Time: 6.78 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_resolution_from_map_and_model.py" [FAIL] 6.8s 1304s Time: 6.81 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_curves.py" [FAIL] 6.6s 1304s Time: 6.60 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_radius_as_central_peak_width.py" [FAIL] 6.7s 1304s Time: 6.69 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_get_percentile_cutoffs.py" [FAIL] 7.0s 1304s Time: 6.97 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sphericity.py" [FAIL] 5.5s 1304s Time: 5.51 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_statistics.py" [FAIL] 6.9s 1304s Time: 6.91 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/r Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Traceback (most recent call last): 1304s File "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py", line 140, in 1304s exercise() 1304s ~~~~~~~~^^ 1304s File "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py", line 126, in exercise 1304s assert not easy_run.call(cmd) 1304s ^^^^^^^^^^^^^^^^^^^^^^ 1304s AssertionError 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Traceback (most recent call last): 1304s File "/usr/lib/python3.13/urllib/request.py", line 1541, in ftp_open 1304s fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout) 1304s File "/usr/lib/python3.13/urllib/request.py", line 1561, in connect_ftp 1304s return ftpwrapper(user, passwd, host, port, dirs, timeout, 1304s persistent=False) 1304s File "/usr/lib/python3.13/urllib/request.py", line 2409, in __init__ 1304s self.init() 1304s ~~~~~~~~~^^ 1304s File "/usr/lib/python3.13/urllib/request.py", line 2418, in init 1304s self.ftp.connect(self.host, self.port, self.timeout) 1304s ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1304s File "/usr/lib/python3.13/ftplib.py", line 158, in connect 1304s self.sock = socket.create_connection((self.host, self.port), self.timeout, 1304s ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1304s source_address=self.source_address) 1304s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1304s File "/usr/lib/python3.13/socket.py", line 864, in create_connection 1304s raise exceptions[0] 1304s File "/usr/lib/python3.13/socket.py", line 849, in create_connection 1304s sock.connect(sa) 1304s ~~~~~~~~~~~~^^^^ 1304s ConnectionRefusedError: [Errno 111] Connection refused 1304s 1304s The above exception was the direct cause of the following exception: 1304s 1304s Traceback (most recent call last): 1304s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 327, in 1304s exercise(sys.argv[1:]) 1304s ~~~~~~~~^^^^^^^^^^^^^^ 1304s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 26, in exercise 1304s exercise_validation() 1304s ~~~~~~~~~~~~~~~~~~~^^ 1304s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 29, in exercise_validation 1304s cd = validation.smart_load_dictionary(name="cif_core.dic") 1304s File "/usr/lib/python3/dist-packages/iotbx/cif/validation.py", line 111, in smart_load_dictionary 1304s url = locate_dictionary(name, registry_location=registry_location) 1304s File "/usr/lib/python3/dist-packages/iotbx/cif/validation.py", line 129, in locate_dictionary 1304s cm = cif.reader(file_object=urlopen(registry_location)).model() 1304s ~~~~~~~^^^^^^^^^^^^^^^^^^^ 1304s File "/usr/lib/python3.13/urllib/request.py", line 189, in urlopen 1304s return opener.open(url, data, timeout) 1304s ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1304s File "/usr/lib/python3.13/urllib/request.py", line 489, in open 1304s response = self._open(req, data) 1304s File "/usr/lib/python3.13/urllib/request.py", line 506, in _open 1304s result = self._call_chain(self.handle_open, protocol, protocol + 1304s '_open', req) 1304s File "/usr/lib/python3.13/urllib/request.py", line 466, in _call_chain 1304s result = func(*args) 1304s File "/usr/lib/python3.13/urllib/request.py", line 1558, in ftp_open 1304s raise URLError(exp) from exp 1304s urllib.error.URLError: 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s *** buffer overflow detected ***: terminated 1304s Aborted (core dumped)egression/tst_connectivity.py" [FAIL] 6.3s 1304s Time: 6.29 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity_allsym.py" [FAIL] 6.7s 1304s Time: 6.66 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py" [FAIL] 9.4s 1304s Time: 9.40 1304s Return code: 1 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_prepare_map_for_docking.py" [FAIL] 7.4s 1304s Time: 7.42 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/cma_es/tst_cma_es.py" [FAIL] 6.6s 1304s Time: 6.56 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mrc_io.py" [FAIL] 4.1s 1304s Time: 4.07 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/gui_tools/tst.py" [FAIL] 4.2s 1304s Time: 4.15 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phil.py" [FAIL] 5.9s 1304s Time: 5.92 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_manager.py" [FAIL] 7.5s 1304s Time: 7.47 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager_wrapping.py" [FAIL] 7.9s 1304s Time: 7.92 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager.py" [FAIL] 7.2s 1304s Time: 7.24 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry.py" [FAIL] 4.9s 1304s Time: 4.90 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry_cif.py" [FAIL] 8.8s 1304s Time: 8.82 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_tools.py" [FAIL] 7.1s 1304s Time: 7.11 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_atom_selections_10k.py" [FAIL] 6.3s 1304s Time: 6.31 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_crystal_symmetry_from_any.py" [FAIL] 7.0s 1304s Time: 7.00 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/kriber/tst_strudat.py" [FAIL] 7.1s 1304s Time: 7.07 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_geometry.py" [FAIL] 7.3s 1304s Time: 7.28 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_lex_parse_build.py" [FAIL] 7.9s 1304s Time: 7.87 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model.py" [FAIL] 7.5s 1304s Time: 7.52 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py" [FAIL] 3.4s 1304s Time: 3.41 1304s Return code: 1 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_restraints.py" [FAIL] 7.7s 1304s Time: 7.72 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_hklf.py" [FAIL] 3.7s 1304s Time: 3.69 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_lex_parse_build.py" [FAIL] 7.2s 1304s Time: 7.24 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_writer.py" [FAIL] 7.4s 1304s Time: 7.36 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_fvar_encoding.py" [FAIL] 7.5s 1304s Time: 7.47 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_pdb.py" [FAIL] 7.1s 1304s Time: 7.10 1304s Return code: 134 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy.py" [FAIL] 7.2s 1304s Time: 7.22 1304s Return code: 134 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy.py" [FAIL] 4.4s 1304s Time: 4.37 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_ext.py" [FAIL] 6.8s 1304s Time: 6.81 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection.py" [FAIL] 7.1s 1304s Time: 7.08 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation.py" [FAIL] 6.1s 1304s Time: 6.09 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection_string.py" [FAIL] 6.5s 1304s Time: 6.51 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_utils.py" [FAIL] 6.1s 1304s Time: 6.13 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_truncate_to_ala/tst.py" [FAIL] 4.4s 1304s Time: 4.43 1304s Return code: 134 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_examples.py" [FAIL] 7.5s 1304s Time: 7.52 1304s Return code: 139 1304s OKs: 0 1304s 1304s Standard error: 1304s *** buffer overflow detected ***: terminated 1304s Aborted (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s *** buffer overflow detected ***: terminated 1304s Aborted (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s /usr/lib/python3/dist-packages/ccp4io_adaptbx/__init__.py:25: UserWarning: ccp4io_adaptbx: cannot locate syminfo.lib 1304s warnings.warn("ccp4io_adaptbx: cannot locate syminfo.lib") 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/space_group_symbols.py" [FAIL] 7.4s 1304s Time: 7.37 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/tst_cns.py" [FAIL] 6.8s 1304s Time: 6.80 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_merge.py" P31 [FAIL] 7.0s 1304s Time: 6.97 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/no_merge_original_index.py" [FAIL] 6.8s 1304s Time: 6.80 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/ccp4_map/tst.py" [FAIL] 6.8s 1304s Time: 6.82 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_ext.py" [FAIL] 7.1s 1304s Time: 7.05 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_extract_from_symmetry_lib.py" [FAIL] 7.1s 1304s Time: 7.06 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_dano.py" [FAIL] 6.7s 1304s Time: 6.70 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst.py" P31 [FAIL] 6.1s 1304s Time: 6.13 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_utils.py" [FAIL] 7.2s 1304s Time: 7.18 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xplor/tst_xplormap.py" [FAIL] 7.6s 1304s Time: 7.58 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phases.py" P31 [FAIL] 7.3s 1304s Time: 7.34 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py" [FAIL] 10.4s 1304s Time: 10.35 1304s Return code: 1 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_statistics.py" Fdd2 P31m [FAIL] 7.7s 1304s Time: 7.68 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_file_reader.py" [FAIL] 4.0s 1304s Time: 4.01 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py" [FAIL] 10.8s 1304s Time: 10.78 1304s Return code: 1 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_segids.py" [FAIL] 8.3s 1304s Time: 8.28 1304s Return code: 134 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_forward_compatible_pdb.py" [FAIL] 4.3s 1304s Time: 4.26 1304s Return code: 134 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_symmetry.py" [FAIL] 5.7s 1304s Time: 5.75 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_editor.py" [FAIL] 6.2s 1304s Time: 6.23 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py" [FAIL] 9.3s 1304s Time: 9.30 1304s Return code: 1 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_map_coefficients.py" [FAIL] 5.9s 1304s Time: 5.94 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py" [FAIL] 7.8s 1304s Time: 7.77 1304s Return code: 1 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_integrate_hkl.py" [FAIL] 7.9s 1304s Time: 7.92 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_no_merge_original_index.py" [FAIL] 3.8s 1304s Time: 3.80 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_export_scalepack_unmerged.py" [FAIL] 6.7s 1304s Time: 6.73 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/dsn6/tst.py" P31 [FAIL] 6.8s 1304s Time: 6.77 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_ligs.py" [FAIL] 5.7s 1304s Time: 5.73 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_broken_chain.py" [FAIL] 7.1s 1304s Time: 7.15 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_shortcut_1.py" [FAIL] 7.2s 1304s Time: 7.24 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_groups_preprocessing.py" [FAIL] 7.9s 1304s Time: 7.89 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_input.py" [FAIL] 7.6s 1304s Time: 7.62 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_user_selections.py" [FAIL] 6.9s 1304s Time: 6.91 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs.py" [FAIL] 7.9s 1304s Time: 7.89 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_without_validation.py" [FAIL] 8.2s 1304s Time: 8.17 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_read_mtrix_records_from_cif.py" [FAIL] 7.9s 1304s Time: 7.92 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_show_systematic_absences.py" [FAIL] 7.8s 1304s Time: 7.76 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_miller_sort_asu.py" [FAIL] 7.1s 1304s Time: 7.09 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_xray_scale.py" [FAIL] 7.5s 1304s Time: 7.51 1304s Return code: 134 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_as_pdb_1atom.py" [FAIL] 7.3s 1304s Time: 7.34 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_1.py" [FAIL] 8.4s 1304s Time: 8.40 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py" [FAIL] 11.8s 1304s Time: 11.83 1304s Return code: 1 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_all_chain_ids.py" [FAIL] 9.1s 1304s Time: 9.10 1304s Return code: 134 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_extract_xtal_data.py" [FAIL] 4.9s 1304s Time: 4.94 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cli_parser.py" [FAIL] 7.9s 1304s Time: 7.92 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_occupancies_rounding.py" [FAIL] 7.2s 1304s Time: 7.16 1304s Return code: 134 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_debug_write.py" [FAIL] 3.6s 1304s Time: 3.57 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_smoothing.py" [FAIL] 3.8s 1304s Time: 3.78 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_genetic_algorithm_with_mp.py" [FAIL] 4.5s 1304s Time: 4.54 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_basic.py" [FAIL] 6.9s 1304s Time: 6.93 1304s Return code: 139 1304s OKs: 1 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_minimum_covering_ellipsoid.py" [FAIL] 6.4s 1304s Time: 6.35 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian_fit_1d_analytical.py" [FAIL] 6.6s 1304s Time: 6.59 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_cubic_equation.py" [FAIL] 6.6s 1304s Time: 6.60 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_cholesky.py" [FAIL] 6.1s 1304s Time: 6.15 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_svd.py" [FAIL] 6.8s 1304s Time: 6.81 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_eigensystem.py" [FAIL] 6.7s 1304s Time: 6.68 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_svd.py" [FAIL] 6.6s 1304s Time: 6.64 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_dsyev.py" [FAIL] 6.8s 1304s Time: 6.76 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/regression_test.py" [FAIL] 6.4s 1304s Time: 6.43 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex.py" [FAIL] 7.0s 1304s Time: 7.01 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_numpy_bridge.py" [FAIL] 6.8s 1304s Time: 6.84 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_smart_selection.py" [FAIL] 6.4s 1304s Time: 6.44 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_shared.py" [FAIL] 6.6s 1304s Time: 6.57 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/__init__.py" [FAIL] 3.9s 1304s Time: 3.85 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_random_transform.py" [FAIL] 3.9s 1304s Time: 3.91 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/superpose.py" [FAIL] 3.4s 1304s Time: 3.44 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/spe.py" [FAIL] 3.4s 1304s Time: 3.39 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/incremental_SO3_sampling.py" [FAIL] 4.7s 1304s Time: 4.74 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_curve_fitting.py" [FAIL] 3.5s 1304s Time: 3.48 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_weighted_correlation.py" [FAIL] 5.4s 1304s Time: 5.40 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_exp_functions.py" [FAIL] 6.4s 1304s Time: 6.42 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_math.py" [FAIL] 6.2s 1304s Time: 6.19 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_resample.py" [FAIL] 3.8s 1304s Time: 3.82 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian.py" [FAIL] 6.1s 1304s Time: 6.09 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_quadrature.py" [FAIL] 6.4s 1304s Time: 6.41 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_halton.py" [FAIL] 6.1s 1304s Time: 6.12 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/scale_curves.py" [FAIL] 3.4s 1304s Time: 3.40 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_fit_peak.py" [FAIL] 3.4s 1304s Time: 3.40 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_clustering.py" [FAIL] 3.3s 1304s Time: 3.30 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike.py" [FAIL] 16.3s 1304s Time: 16.32 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_periodogram.py" [FAIL] 6.5s 1304s Time: 6.47 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_error_propagation_matrix_inverse.py" [FAIL] 6.1s 1304s Time: 6.13 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_curvatures.py" [FAIL] 5.3s 1304s Time: 5.31 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgsb/boost_python/tst_lbfgsb.py" [FAIL] 3.5s 1304s Time: 3.54 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/fftpack/boost_python/tst_fftpack.py" [FAIL] 3.5s 1304s Time: 3.54 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_grid.py" [FAIL] 3.3s 1304s Time: 3.30 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_linear_least_squares_fit.py" [FAIL] 3.7s 1304s Time: 3.71 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/chebyshev_lsq_example.py" [FAIL] 6.0s 1304s Time: 6.05 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/immoptibox_ports.py" [FAIL] 6.5s 1304s Time: 6.47 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/integrating_a_weighted_sinc_function.py" [FAIL] 6.3s 1304s Time: 6.30 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/minimizer_comparisons.py" [FAIL] 6.1s 1304s Time: 6.08 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree.py" [FAIL] 3.9s 1304s Time: 3.87 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_basic.py" [FAIL] 6.2s 1304s Time: 6.20 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_tardy.py" [FAIL] 6.1s 1304s Time: 6.12 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_energy_plots.py" [FAIL] 6.0s 1304s Time: 5.99 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/tst.py" [FAIL] 6.0s 1304s Time: 6.00 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_featherstone.py" [FAIL] 5.9s 1304s Time: 5.94 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion.py" [FAIL] 6.0s 1304s Time: 6.05 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion_hard.py" [FAIL] 6.1s 1304s Time: 6.07 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_joint_lib.py" [FAIL] 6.0s 1304s Time: 6.04 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_singular.py" [FAIL] 6.1s 1304s Time: 6.13 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_molecules.py" [FAIL] 5.7s 1304s Time: 5.74 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_sparse.py" [FAIL] 6.1s 1304s Time: 6.05 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_lu_factorization.py" [FAIL] 6.0s 1304s Time: 5.95 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/iso_surface/tst_iso_surface.py" [FAIL] 6.0s 1304s Time: 5.97 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/simplex.py" [FAIL] 6.0s 1304s Time: 5.98 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/differential_evolution.py" [FAIL] 5.9s 1304s Time: 5.86 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/direct_search_simulated_annealing.py" [FAIL] 5.7s 1304s Time: 5.72 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/random/tests/tst_random.py" [FAIL] 6.2s 1304s Time: 6.18 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/tst_normal_equations.py" [FAIL] 6.3s 1304s Time: 6.34 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_basic.py" [FAIL] 3.2s 1304s Time: 3.19 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_booth.py" [FAIL] 3.2s 1304s Time: 3.16 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_twisted.py" [FAIL] 4.8s 1304s Time: 4.83 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/absolute_structure/tests/tst_absolute_structure.py" --fix_random_seeds [FAIL] 6.3s 1304s Time: 6.33 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/ab_initio/tests/tst_ab_initio_ext.py" [FAIL] 6.5s 1304s Time: 6.54 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/ab_initio/tests/tst_charge_flipping.py" --fix_seed --on=E "hall: P 1" "hall: P 3" "hall: -P 2ybc" [FAIL] 6.3s 1304s Time: 6.33 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/masks/tests/tst_masks.py" [FAIL] 6.6s 1304s Time: 6.59 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/structure_factors/direct/tests/tst_standard_xray.py" [FAIL] 6.6s 1304s Time: 6.59 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_weighting_schemes.py" --fix_random_seeds [FAIL] 6.7s 1304s Time: 6.72 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_lbfgs.py" [FAIL] 6.7s 1304s Time: 6.68 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_occupancies.py" [FAIL] 6.6s 1304s Time: 6.63 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_same_group.py" [FAIL] 6.8s 1304s Time: 6.84 1304s Return code: 139 1304s OKs: 0 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Traceback (most recent call last): 1304s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 477, in 1304s exercise(sys.argv[1:]) 1304s ~~~~~~~~^^^^^^^^^^^^^^ 1304s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 22, in exercise 1304s run_and_compare( 1304s ~~~~~~~~~~~~~~~^ 1304s ['iotbx.lattice_symmetry' 1304s ^^^^^^^^^^^^^^^^^^^^^^^^^ 1304s ...<31 lines>... 1304s 1304s 1304s """) 1304s ^^^^ 1304s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 17, in run_and_compare 1304s command=command).raise_if_errors().stdout_lines 1304s ~~~~~~~~~~~~~~~^^ 1304s File "/usr/lib/python3/dist-packages/libtbx/easy_run.py", line 46, in raise_if_errors 1304s raise Error(msg) 1304s RuntimeError: child process stderr output: 1304s command: 'iotbx.lattice_symmetry --unit_cell="12.7923,12.8923,29.4356,102.846,103.846,22.7475"' 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s *** buffer overflow detected ***: terminated 1304s Aborted (core dumped) 1304s Traceback (most recent call last): 1304s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py", line 138, in 1304s exercise() 1304s ~~~~~~~~^^ 1304s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py", line 48, in exercise 1304s assert not easy_run.call("iotbx.pdb.box_around_molecule %s.pdb" % ( 1304s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1304s prefix)) 1304s ^^^^^^^^ 1304s AssertionError 1304s Standard error: 1304s *** buffer overflow detected ***: terminated 1304s Aborted (core dumped) 1304s Standard error: 1304s *** buffer overflow detected ***: terminated 1304s Aborted (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Traceback (most recent call last): 1304s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py", line 60, in 1304s exercise() 1304s ~~~~~~~~^^ 1304s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py", line 48, in exercise 1304s assert (len(out.stdout_lines) == 2) and (len(out.stderr_lines) == 0) 1304s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1304s AssertionError 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Traceback (most recent call last): 1304s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py", line 815, in 1304s exercise_1() 1304s ~~~~~~~~~~^^ 1304s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py", line 806, in exercise_1 1304s assert not easy_run.call(cmd) 1304s ^^^^^^^^^^^^^^^^^^^^^^ 1304s AssertionError 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_reparametrisation.py" [FAIL] 6.6s 1304s Time: 6.63 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=naive [FAIL] 6.5s 1304s Time: 6.50 1304s Return code: 139 1304s OKs: 0 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s *** buffer overflow detected ***: terminated 1304s Aborted (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Traceback (most recent call last): 1304s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py", line 395, in 1304s tst_1() 1304s ~~~~~^^ 1304s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py", line 370, in tst_1 1304s assert os.path.isfile('%s.cif_%s_000.mtz' % (prefix, bn)) 1304s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1304s AssertionError 1304s Standard error: 1304s *** buffer overflow detected ***: terminated 1304s Aborted (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s *** buffer overflow detected ***: terminated 1304s Aborted (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_disorder.py" [FAIL] 6.9s 1304s Time: 6.94 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=levenberg-marquardt [FAIL] 3.7s 1304s Time: 3.70 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_direction.py" [FAIL] 3.5s 1304s Time: 3.52 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_rigid.py" [FAIL] 7.1s 1304s Time: 7.10 1304s Return code: 139 1304s OKs: 0 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_adp_restraints.py" [FAIL] 7.0s 1304s Time: 6.97 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_manager.py" [FAIL] 7.0s 1304s Time: 6.95 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_restraints.py" --verbose --scatterers=5 --resolution=0.2 [FAIL] 7.1s 1304s Time: 7.08 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_refine.py" [FAIL] 7.4s 1304s Time: 7.38 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py" [FAIL] 10.2s 1304s Time: 10.24 1304s Return code: 1 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/tests/tst_utils.py" [FAIL] 6.9s 1304s Time: 6.87 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/rstbx/dps_core/tst_iotbx_converter.py" [FAIL] 6.5s 1304s Time: 6.46 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/fastbragg/tst_bragg_minimal.py" [FAIL] 5.6s 1304s Time: 5.62 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python "/usr/lib/python3/dist-packages/rstbx/sublattice_support/tst_sublattice.py" [FAIL] 6.5s 1304s Time: 6.49 1304s Return code: 139 1304s OKs: 0 1304s libtbx.python -c "from rstbx.run_tests import run; run()" [FAIL] 4.8s 1304s Time: 4.79 1304s Return code: 139 1304s OKs: 0 1304s 1304s Please verify these tests manually. 1304s 1304s Summary: 1304s Tests run : 546 1304s Failures : 284 1304s Warnings (possible failures) : 0 1304s Known Failures ( 4) : 4 1304s Known Unstable ( 3) : 2 1304s Stderr output (discouraged) : 291 1304s 1304s See run_tests_parallel_zlog for full output. 1304s 1304s 1304s ******************************************************************************** 1304s ERROR: 284 TEST FAILURES. PLEASE FIX BEFORE COMMITTING CODE. 1304s ******************************************************************************** 1304s 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Traceback (most recent call last): 1304s File "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py", line 37, in 1304s run() 1304s ~~~^^ 1304s File "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py", line 27, in run 1304s run_buf.raise_if_errors() 1304s ~~~~~~~~~~~~~~~~~~~~~~~^^ 1304s File "/usr/lib/python3/dist-packages/libtbx/easy_run.py", line 46, in raise_if_errors 1304s raise Error(msg) 1304s RuntimeError: child process stderr output: 1304s command: 'smtbx.anom_refine /usr/lib/python3/dist-packages/smtbx/regression/test_data/thpp.cif /usr/lib/python3/dist-packages/smtbx/regression/test_data/thpp.hkl F -e13000 -t -O -d0 -s0 -c25' 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s Standard error: 1304s Segmentation fault (core dumped) 1304s autopkgtest [14:02:48]: test cctbx: -----------------------] 1305s autopkgtest [14:02:49]: test cctbx: - - - - - - - - - - results - - - - - - - - - - 1305s cctbx FAIL non-zero exit status 1 1305s autopkgtest [14:02:49]: test dxtbx: preparing testbed 1406s autopkgtest [14:04:30]: testbed dpkg architecture: arm64 1406s autopkgtest [14:04:30]: testbed apt version: 2.9.34 1407s autopkgtest [14:04:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup 1407s autopkgtest [14:04:31]: testbed release detected to be: plucky 1408s autopkgtest [14:04:32]: updating testbed package index (apt update) 1408s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 1408s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 1408s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 1408s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 1408s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [292 kB] 1409s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [1232 B] 1409s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [30.7 kB] 1409s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [12.2 kB] 1409s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [39.1 kB] 1409s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1292 B] 1409s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 1409s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [198 kB] 1409s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [11.1 kB] 1409s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [3684 B] 1409s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [216 B] 1410s Fetched 716 kB in 1s (944 kB/s) 1411s Reading package lists... 1411s autopkgtest [14:04:35]: upgrading testbed (apt dist-upgrade and autopurge) 1412s Reading package lists... 1412s Building dependency tree... 1412s Reading state information... 1412s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 1412s Starting 2 pkgProblemResolver with broken count: 0 1412s Done 1413s Entering ResolveByKeep 1413s 1413s Calculating upgrade... 1414s The following packages will be upgraded: 1414s gcc-15-base libatomic1 libgcc-s1 libstdc++6 1414s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1414s Need to get 879 kB of archives. 1414s After this operation, 0 B of additional disk space will be used. 1414s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libatomic1 arm64 15-20250319-1ubuntu1 [11.2 kB] 1414s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-15-base arm64 15-20250319-1ubuntu1 [53.6 kB] 1414s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-s1 arm64 15-20250319-1ubuntu1 [61.1 kB] 1414s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++6 arm64 15-20250319-1ubuntu1 [753 kB] 1415s Fetched 879 kB in 1s (1590 kB/s) 1415s (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 ... 117732 files and directories currently installed.) 1415s Preparing to unpack .../libatomic1_15-20250319-1ubuntu1_arm64.deb ... 1415s Unpacking libatomic1:arm64 (15-20250319-1ubuntu1) over (15-20250315-1ubuntu1) ... 1415s Preparing to unpack .../gcc-15-base_15-20250319-1ubuntu1_arm64.deb ... 1415s Unpacking gcc-15-base:arm64 (15-20250319-1ubuntu1) over (15-20250315-1ubuntu1) ... 1415s Setting up gcc-15-base:arm64 (15-20250319-1ubuntu1) ... 1415s (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 ... 117732 files and directories currently installed.) 1415s Preparing to unpack .../libgcc-s1_15-20250319-1ubuntu1_arm64.deb ... 1415s Unpacking libgcc-s1:arm64 (15-20250319-1ubuntu1) over (15-20250315-1ubuntu1) ... 1415s Setting up libgcc-s1:arm64 (15-20250319-1ubuntu1) ... 1415s (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 ... 117732 files and directories currently installed.) 1415s Preparing to unpack .../libstdc++6_15-20250319-1ubuntu1_arm64.deb ... 1415s Unpacking libstdc++6:arm64 (15-20250319-1ubuntu1) over (15-20250315-1ubuntu1) ... 1415s Setting up libstdc++6:arm64 (15-20250319-1ubuntu1) ... 1415s Setting up libatomic1:arm64 (15-20250319-1ubuntu1) ... 1415s Processing triggers for libc-bin (2.41-1ubuntu2) ... 1416s Reading package lists... 1416s Building dependency tree... 1416s Reading state information... 1416s Starting pkgProblemResolver with broken count: 0 1416s Starting 2 pkgProblemResolver with broken count: 0 1416s Done 1417s Solving dependencies... 1417s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1420s Reading package lists... 1420s Building dependency tree... 1420s Reading state information... 1420s Starting pkgProblemResolver with broken count: 0 1421s Starting 2 pkgProblemResolver with broken count: 0 1421s Done 1421s The following NEW packages will be installed: 1421s adwaita-icon-theme at-spi2-common bitshuffle blt dconf-gsettings-backend 1421s dconf-service fontconfig fontconfig-config fonts-dejavu-core 1421s fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lyx 1421s gtk-update-icon-cache hicolor-icon-theme libaec0 libamd-comgr2 libamdhip64-5 1421s libann-cctbx-dev libann-cctbx0 libantlr3c-3.4-0 libasan8 1421s libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 libavahi-client3 1421s libavahi-common-data libavahi-common3 libblas3 libboost-numpy1.83.0 1421s libboost-python-dev libboost-python1.83-dev libboost-python1.83.0 1421s libboost-thread1.83.0 libboost-timer1.83.0 libboost1.83-dev 1421s libcairo-gobject2 libcairo2 libcbf1t64 libccp4-data libccp4-dev libccp4c0t64 1421s libccp4f0t64 libcctbx-dev libcctbx0 libcolord2 libcups2t64 libdatrie1 1421s libdconf1 libdeflate0 libdouble-conversion3 libegl-mesa0 libegl1 libepoxy0 1421s libevent-pthreads-2.1-7t64 libexpat1-dev libfabric1 libfontconfig1 libgbm1 1421s libgcc-14-dev libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 1421s libgl1 libgl1-mesa-dri libglew2.2 libglu1-mesa libglut3.12 libglvnd0 1421s libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libgtk-3-0t64 libgtk-3-common 1421s libharfbuzz0b libhdf5-310 libhdf5-hl-310 libhdf5-openmpi-310 1421s libhsa-runtime64-1 libhsakmt1 libhwasan0 libhwloc-plugins libhwloc15 1421s libibmad5 libibumad3 libice6 libimagequant0 libinput-bin libinput10 libitm1 1421s libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 1421s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 liblerc4 1421s libllvm17t64 liblsan0 liblzf1 libmd4c0 libmmdb2-0 libmtdev1t64 libmunge2 1421s libnetcdf22 libnotify4 libopengl0 libopenjp2-7 libopenmpi40 libpango-1.0-0 1421s libpangocairo-1.0-0 libpangoft2-1.0-0 libpciaccess0 libpcre2-16-0 1421s libpcre2-32-0 libpixman-1-0 libpmix2t64 libpython3-dev libpython3.13-dev 1421s libqhull-r8.0 libqt5core5t64 libqt5dbus5t64 libqt5designer5 libqt5gui5t64 1421s libqt5help5 libqt5network5t64 libqt5opengl5t64 libqt5printsupport5t64 1421s libqt5sql5t64 libqt5test5t64 libqt5widgets5t64 libqt5xml5t64 libraqm0 1421s librdmacm1t64 libsharpyuv0 libsm6 libssm2 libstdc++-14-dev libsz2 libtcl8.6 1421s libthai-data libthai0 libtiff6 libtk8.6 libtsan2 libubsan1 libucx0 1421s libvulkan1 libwacom-common libwacom9 libwayland-client0 libwayland-cursor0 1421s libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 libwebpmux3 1421s libwxbase3.2-1t64 libwxgtk-gl3.2-1t64 libwxgtk3.2-1t64 libx11-xcb1 1421s libxcb-dri3-0 libxcb-glx0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 1421s libxcb-present0 libxcb-randr0 libxcb-render-util0 libxcb-render0 1421s libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-util1 libxcb-xfixes0 1421s libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxcomposite1 libxcursor1 1421s libxdamage1 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon-x11-0 1421s libxnvctrl0 libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1 libxtst6 1421s libxxf86vm1 mesa-libgallium ocl-icd-libopencl1 pymol-data 1421s python-matplotlib-data python3-all python3-brotli python3-cctbx 1421s python3-contourpy python3-cycler python3-dateutil python3-decorator 1421s python3-dev python3-dials-data python3-flexcache python3-flexparser 1421s python3-fonttools python3-fs python3-h5py python3-h5py-serial 1421s python3-hdf5plugin python3-importlib-resources python3-iniconfig 1421s python3-kiwisolver python3-legacy-cgi python3-lxml python3-lz4 1421s python3-matplotlib python3-mpmath python3-mrcfile python3-natsort 1421s python3-numpy python3-numpy-dev python3-nxmx python3-opengl 1421s python3-ordered-set python3-packaging python3-pil python3-pil.imagetk 1421s python3-pint python3-platformdirs python3-pluggy python3-procrunner 1421s python3-pycbf python3-pymol python3-pyqt5 python3-pyqt5.qtopengl 1421s python3-pyqt5.sip python3-pytest python3-pytest-datadir python3-pytest-mock 1421s python3-pytest-regressions python3-scipy python3-six python3-sympy 1421s python3-tk python3-tqdm python3-ufolib2 python3-wxgtk4.0 python3.13-dev 1421s python3.13-tk sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data x11-common 1421s zlib1g-dev 1422s 0 upgraded, 264 newly installed, 0 to remove and 0 not upgraded. 1422s Need to get 255 MB of archives. 1422s After this operation, 1273 MB of additional disk space will be used. 1422s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-lato all 2.015-1 [2781 kB] 1422s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 1422s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 1422s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250319-1ubuntu1 [443 kB] 1422s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 1422s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 1422s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [8004 B] 1422s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 1422s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 1422s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 1422s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 1422s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 1422s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 1422s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 1422s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 1423s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-2 [147 kB] 1423s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 gtk-update-icon-cache arm64 4.18.2+ds-1 [52.8 kB] 1423s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 hicolor-icon-theme all 0.18-2 [13.3 kB] 1423s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 adwaita-icon-theme all 48.0-1 [578 kB] 1423s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 at-spi2-common all 2.56.0-2 [9108 B] 1423s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 1423s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 1423s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-310 arm64 1.14.5+repack-3 [1331 kB] 1423s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [59.8 kB] 1423s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 1423s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.13.0-1 [1126 kB] 1423s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.13.0-1 [7978 B] 1423s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250319-1ubuntu1 [147 kB] 1423s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10 [7922 B] 1423s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 librdmacm1t64 arm64 56.0-3ubuntu1 [71.5 kB] 1423s Get:31 http://ftpmaster.internal/ubuntu plucky/universe arm64 libfabric1 arm64 1.17.0-3.1 [542 kB] 1423s Get:32 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhwloc15 arm64 2.12.0-1 [162 kB] 1423s Get:33 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmunge2 arm64 0.5.16-1 [15.2 kB] 1423s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libpciaccess0 arm64 0.17-3build1 [18.9 kB] 1423s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu4 [12.4 kB] 1423s Get:36 http://ftpmaster.internal/ubuntu plucky/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1build1 [37.6 kB] 1423s Get:37 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhwloc-plugins arm64 2.12.0-1 [15.9 kB] 1423s Get:38 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpmix2t64 arm64 5.0.6-5 [666 kB] 1423s Get:39 http://ftpmaster.internal/ubuntu plucky/universe arm64 libllvm17t64 arm64 1:17.0.6-21 [24.9 MB] 1424s Get:40 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3build2 [14.1 MB] 1425s Get:41 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhsakmt1 arm64 5.7.0-1build1 [63.6 kB] 1425s Get:42 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhsa-runtime64-1 arm64 5.7.1-2build1 [286 kB] 1425s Get:43 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamdhip64-5 arm64 5.7.1-5build1 [9707 kB] 1425s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libibumad3 arm64 56.0-3ubuntu1 [31.1 kB] 1425s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libibmad5 arm64 56.0-3ubuntu1 [44.0 kB] 1425s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 libucx0 arm64 1.18.1+ds-2 [1161 kB] 1425s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenmpi40 arm64 5.0.7-1 [2419 kB] 1425s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-openmpi-310 arm64 1.14.5+repack-3 [1388 kB] 1426s Get:49 http://ftpmaster.internal/ubuntu plucky/universe arm64 bitshuffle arm64 0.5.2-1build2 [157 kB] 1426s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 1426s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 1426s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 1426s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2.1ubuntu1 [37.7 kB] 1426s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2.1ubuntu1 [144 kB] 1426s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 1426s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 1426s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 1426s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 1426s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 1426s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-8 [624 kB] 1426s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-8 [4824 B] 1426s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 libdconf1 arm64 0.40.0-5 [40.0 kB] 1426s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 dconf-service arm64 0.40.0-5 [27.1 kB] 1426s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 dconf-gsettings-backend arm64 0.40.0-5 [22.3 kB] 1426s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2.1ubuntu1 [191 kB] 1426s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 1426s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.3-1 [171 kB] 1426s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 libann-cctbx0 arm64 1.1.2+doc-9build1 [32.8 kB] 1426s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 libann-cctbx-dev arm64 1.1.2+doc-9build1 [45.1 kB] 1426s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 libantlr3c-3.4-0 arm64 3.4+dfsg-4build2 [45.7 kB] 1426s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250319-1ubuntu1 [2922 kB] 1426s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libatk1.0-0t64 arm64 2.56.0-2 [55.4 kB] 1426s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libxi6 arm64 2:1.8.2-1 [32.4 kB] 1426s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libatspi2.0-0t64 arm64 2.56.0-2 [84.5 kB] 1426s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libatk-bridge2.0-0t64 arm64 2.56.0-2 [66.7 kB] 1426s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-common-data arm64 0.8-16ubuntu2 [31.0 kB] 1426s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-common3 arm64 0.8-16ubuntu2 [22.9 kB] 1426s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-client3 arm64 0.8-16ubuntu2 [26.9 kB] 1426s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-python1.83.0 arm64 1.83.0-4.1ubuntu2 [309 kB] 1426s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 libboost-numpy1.83.0 arm64 1.83.0-4.1ubuntu2 [242 kB] 1426s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250319-1ubuntu1 [28.0 kB] 1426s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250319-1ubuntu1 [1318 kB] 1426s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250319-1ubuntu1 [2693 kB] 1426s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250319-1ubuntu1 [1178 kB] 1426s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250319-1ubuntu1 [1641 kB] 1426s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-19ubuntu1 [2593 kB] 1427s Get:87 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-19ubuntu1 [2501 kB] 1427s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost1.83-dev arm64 1.83.0-4.1ubuntu2 [10.7 MB] 1427s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 libexpat1-dev arm64 2.6.4-1 [129 kB] 1427s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 1427s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-dev arm64 3.13.2-2 [5399 kB] 1427s Get:92 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-dev arm64 3.13.2-2 [10.7 kB] 1427s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-dev arm64 3.13.2-2 [509 kB] 1428s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 1428s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 1428s Get:96 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 1428s Get:97 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dev arm64 3.13.2-2 [26.7 kB] 1428s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 libboost-python1.83-dev arm64 1.83.0-4.1ubuntu2 [336 kB] 1428s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 libboost-python-dev arm64 1.83.0.2ubuntu1 [4516 B] 1428s Get:100 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-thread1.83.0 arm64 1.83.0-4.1ubuntu2 [276 kB] 1428s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 libboost-timer1.83.0 arm64 1.83.0-4.1ubuntu2 [242 kB] 1428s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 1428s Get:103 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 1428s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 1428s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.4-1 [560 kB] 1428s Get:106 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo-gobject2 arm64 1.18.4-1 [127 kB] 1428s Get:107 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcbf1t64 arm64 0.9.7+dfsg1-5build1 [356 kB] 1428s Get:108 http://ftpmaster.internal/ubuntu plucky/universe arm64 libccp4-data all 8.0.0-4 [65.2 kB] 1428s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 libccp4c0t64 arm64 8.0.0-4 [93.5 kB] 1428s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmmdb2-0 arm64 2.0.22-1 [347 kB] 1428s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 libccp4f0t64 arm64 8.0.0-4 [202 kB] 1428s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 libccp4-dev arm64 8.0.0-4 [42.3 kB] 1428s Get:113 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 libcctbx0 arm64 2024.10+ds2+~3.22.1+ds1-4build2 [2016 kB] 1428s Get:114 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 libcctbx-dev arm64 2024.10+ds2+~3.22.1+ds1-4build2 [1192 kB] 1428s Get:115 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 1428s Get:116 http://ftpmaster.internal/ubuntu plucky/main arm64 libcolord2 arm64 1.4.7-3 [151 kB] 1428s Get:117 http://ftpmaster.internal/ubuntu plucky/main arm64 libcups2t64 arm64 2.4.11-0ubuntu2 [274 kB] 1428s Get:118 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 1428s Get:119 http://ftpmaster.internal/ubuntu plucky/universe arm64 libdouble-conversion3 arm64 3.3.1-1 [38.8 kB] 1428s Get:120 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-server0 arm64 1.23.1-3 [36.1 kB] 1428s Get:121 http://ftpmaster.internal/ubuntu plucky/main arm64 libx11-xcb1 arm64 2:1.8.10-2 [8020 B] 1428s Get:122 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-dri3-0 arm64 1.17.0-2 [7606 B] 1428s Get:123 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-present0 arm64 1.17.0-2 [6224 B] 1428s Get:124 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-randr0 arm64 1.17.0-2 [18.5 kB] 1428s Get:125 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-sync1 arm64 1.17.0-2 [9688 B] 1428s Get:126 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-xfixes0 arm64 1.17.0-2 [10.6 kB] 1428s Get:127 http://ftpmaster.internal/ubuntu plucky/main arm64 libxshmfence1 arm64 1.3-1build5 [4938 B] 1428s Get:128 http://ftpmaster.internal/ubuntu plucky/main arm64 mesa-libgallium arm64 25.0.1-2ubuntu2 [9452 kB] 1429s Get:129 http://ftpmaster.internal/ubuntu plucky/main arm64 libgbm1 arm64 25.0.1-2ubuntu2 [33.7 kB] 1429s Get:130 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-client0 arm64 1.23.1-3 [27.0 kB] 1429s Get:131 http://ftpmaster.internal/ubuntu plucky/main arm64 libegl-mesa0 arm64 25.0.1-2ubuntu2 [122 kB] 1429s Get:132 http://ftpmaster.internal/ubuntu plucky/main arm64 libepoxy0 arm64 1.5.10-2 [236 kB] 1429s Get:133 http://ftpmaster.internal/ubuntu plucky/main arm64 libvulkan1 arm64 1.4.304.0-1 [158 kB] 1429s Get:134 http://ftpmaster.internal/ubuntu plucky/main arm64 libgl1-mesa-dri arm64 25.0.1-2ubuntu2 [35.4 kB] 1429s Get:135 http://ftpmaster.internal/ubuntu plucky/main arm64 libglvnd0 arm64 1.7.0-1build1 [60.6 kB] 1429s Get:136 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-glx0 arm64 1.17.0-2 [25.5 kB] 1429s Get:137 http://ftpmaster.internal/ubuntu plucky/main arm64 libxxf86vm1 arm64 1:1.1.4-1build4 [9130 B] 1429s Get:138 http://ftpmaster.internal/ubuntu plucky/main arm64 libglx-mesa0 arm64 25.0.1-2ubuntu2 [151 kB] 1429s Get:139 http://ftpmaster.internal/ubuntu plucky/main arm64 libglx0 arm64 1.7.0-1build1 [33.2 kB] 1429s Get:140 http://ftpmaster.internal/ubuntu plucky/main arm64 libgl1 arm64 1.7.0-1build1 [106 kB] 1429s Get:141 http://ftpmaster.internal/ubuntu plucky/universe arm64 libglew2.2 arm64 2.2.0-4build1 [191 kB] 1429s Get:142 http://ftpmaster.internal/ubuntu plucky/universe arm64 libglut3.12 arm64 3.4.0-4 [97.1 kB] 1429s Get:143 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 1429s Get:144 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 1429s Get:145 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 1429s Get:146 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 1429s Get:147 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.3-1 [238 kB] 1429s Get:148 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.3-1 [49.8 kB] 1429s Get:149 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.3-1 [27.6 kB] 1429s Get:150 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-cursor0 arm64 1.23.1-3 [10.8 kB] 1429s Get:151 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-egl1 arm64 1.23.1-3 [6180 B] 1429s Get:152 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcomposite1 arm64 1:0.4.6-1 [6626 B] 1429s Get:153 http://ftpmaster.internal/ubuntu plucky/main arm64 libxfixes3 arm64 1:6.0.0-2build1 [11.2 kB] 1429s Get:154 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcursor1 arm64 1:1.2.3-1 [22.2 kB] 1429s Get:155 http://ftpmaster.internal/ubuntu plucky/main arm64 libxdamage1 arm64 1:1.1.6-1build1 [6236 B] 1429s Get:156 http://ftpmaster.internal/ubuntu plucky/main arm64 libxinerama1 arm64 2:1.1.4-3build1 [6394 B] 1429s Get:157 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrandr2 arm64 2:1.5.4-1 [19.6 kB] 1429s Get:158 http://ftpmaster.internal/ubuntu plucky/main arm64 libgtk-3-common all 3.24.49-2ubuntu1 [1424 kB] 1429s Get:159 http://ftpmaster.internal/ubuntu plucky/main arm64 libgtk-3-0t64 arm64 3.24.49-2ubuntu1 [2918 kB] 1429s Get:160 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 1429s Get:161 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 1429s Get:162 http://ftpmaster.internal/ubuntu plucky/main arm64 libwacom-common all 2.14.0-1 [103 kB] 1429s Get:163 http://ftpmaster.internal/ubuntu plucky/main arm64 libwacom9 arm64 2.14.0-1 [26.7 kB] 1429s Get:164 http://ftpmaster.internal/ubuntu plucky/main arm64 libinput-bin arm64 1.27.1-1 [23.5 kB] 1429s Get:165 http://ftpmaster.internal/ubuntu plucky/main arm64 libmtdev1t64 arm64 1.1.7-1 [14.6 kB] 1429s Get:166 http://ftpmaster.internal/ubuntu plucky/main arm64 libinput10 arm64 1.27.1-1 [136 kB] 1429s Get:167 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 1429s Get:168 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 1429s Get:169 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmd4c0 arm64 0.5.2-2 [42.4 kB] 1429s Get:170 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnetcdf22 arm64 1:4.9.3-1 [504 kB] 1429s Get:171 http://ftpmaster.internal/ubuntu plucky/main arm64 libnotify4 arm64 0.8.4-1 [26.5 kB] 1429s Get:172 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-16-0 arm64 10.45-1 [222 kB] 1429s Get:173 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-32-0 arm64 10.45-1 [210 kB] 1429s Get:174 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 1429s Get:175 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5core5t64 arm64 5.15.15+dfsg-4ubuntu1 [1999 kB] 1429s Get:176 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5dbus5t64 arm64 5.15.15+dfsg-4ubuntu1 [222 kB] 1429s Get:177 http://ftpmaster.internal/ubuntu plucky/main arm64 libegl1 arm64 1.7.0-1build1 [29.5 kB] 1429s Get:178 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5network5t64 arm64 5.15.15+dfsg-4ubuntu1 [735 kB] 1429s Get:179 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 1429s Get:180 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-icccm4 arm64 0.4.2-1 [10.9 kB] 1429s Get:181 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-util1 arm64 0.4.1-1 [10.9 kB] 1429s Get:182 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-image0 arm64 0.4.0-2build1 [10.8 kB] 1429s Get:183 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-keysyms1 arm64 0.4.1-1 [8802 B] 1429s Get:184 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render-util0 arm64 0.3.10-1 [10.5 kB] 1429s Get:185 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shape0 arm64 1.17.0-2 [6246 B] 1429s Get:186 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-xinerama0 arm64 1.17.0-2 [5590 B] 1429s Get:187 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-xinput0 arm64 1.17.0-2 [34.2 kB] 1429s Get:188 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-xkb1 arm64 1.17.0-2 [32.5 kB] 1429s Get:189 http://ftpmaster.internal/ubuntu plucky/main arm64 libxkbcommon-x11-0 arm64 1.7.0-2 [13.8 kB] 1429s Get:190 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5gui5t64 arm64 5.15.15+dfsg-4ubuntu1 [3680 kB] 1429s Get:191 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5widgets5t64 arm64 5.15.15+dfsg-4ubuntu1 [2568 kB] 1430s Get:192 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5xml5t64 arm64 5.15.15+dfsg-4ubuntu1 [124 kB] 1430s Get:193 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5designer5 arm64 5.15.15-6build1 [2840 kB] 1430s Get:194 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5sql5t64 arm64 5.15.15+dfsg-4ubuntu1 [123 kB] 1430s Get:195 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5help5 arm64 5.15.15-6build1 [165 kB] 1430s Get:196 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5opengl5t64 arm64 5.15.15+dfsg-4ubuntu1 [149 kB] 1430s Get:197 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5printsupport5t64 arm64 5.15.15+dfsg-4ubuntu1 [209 kB] 1430s Get:198 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5test5t64 arm64 5.15.15+dfsg-4ubuntu1 [144 kB] 1430s Get:199 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 1430s Get:200 http://ftpmaster.internal/ubuntu plucky/universe arm64 libssm2 arm64 1.4.0-2build1 [83.8 kB] 1430s Get:201 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 1430s Get:202 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 1430s Get:203 http://ftpmaster.internal/ubuntu plucky/universe arm64 libwxbase3.2-1t64 arm64 3.2.6+dfsg-2ubuntu1 [870 kB] 1430s Get:204 http://ftpmaster.internal/ubuntu plucky/main arm64 libxtst6 arm64 2:1.2.5-1 [13.2 kB] 1430s Get:205 http://ftpmaster.internal/ubuntu plucky/universe arm64 libwxgtk3.2-1t64 arm64 3.2.6+dfsg-2ubuntu1 [4426 kB] 1431s Get:206 http://ftpmaster.internal/ubuntu plucky/universe arm64 libwxgtk-gl3.2-1t64 arm64 3.2.6+dfsg-2ubuntu1 [52.8 kB] 1431s Get:207 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu4 [168 kB] 1431s Get:208 http://ftpmaster.internal/ubuntu plucky/universe arm64 pymol-data all 3.1.0+dfsg-1 [1394 kB] 1431s Get:209 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-7build1 [2934 kB] 1431s Get:210 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.13.2-2 [886 B] 1431s Get:211 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build4 [342 kB] 1431s Get:212 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-legacy-cgi all 2.6.2-1 [16.6 kB] 1431s Get:213 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pycbf arm64 0.9.7+dfsg1-5build1 [152 kB] 1431s Get:214 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-hdf5plugin all 5.0.0-1 [23.1 kB] 1431s Get:215 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-4 [80.3 kB] 1431s Get:216 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.3-2 [183 kB] 1431s Get:217 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 11.1.0-5build1 [463 kB] 1431s Get:218 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.2-2 [106 kB] 1431s Get:219 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.13.2-1 [9818 B] 1431s Get:220 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 11.1.0-5build1 [9892 B] 1431s Get:221 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.1-1build1 [182 kB] 1431s Get:222 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 1431s Get:223 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 1431s Get:224 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-7 [90.8 kB] 1431s Get:225 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.1-1build1 [1258 kB] 1431s Get:226 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.4.0+dfsg-1build1 [27.1 kB] 1431s Get:227 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 1431s Get:228 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu2 [16.7 MB] 1432s Get:229 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 1432s Get:230 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-5 [4229 kB] 1433s Get:231 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 1433s Get:232 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 1433s Get:233 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.55.3-2build1 [1466 kB] 1433s Get:234 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-importlib-resources all 6.5.2-1 [24.5 kB] 1433s Get:235 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-3build1 [50.7 kB] 1433s Get:236 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 1433s Get:237 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-7build1 [17.3 MB] 1434s Get:238 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 1434s Get:239 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mrcfile all 1.5.4-2 [116 kB] 1434s Get:240 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-natsort all 8.0.2-2 [33.8 kB] 1434s Get:241 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-flexcache all 0.3-2 [13.4 kB] 1434s Get:242 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-flexparser all 0.4-1 [43.8 kB] 1435s Get:243 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pint all 0.24.4-1 [203 kB] 1435s Get:244 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-nxmx all 0.0.4-1 [16.4 kB] 1435s Get:245 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ordered-set all 4.1.0-1 [9778 B] 1435s Get:246 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-procrunner all 2.3.3-2 [12.0 kB] 1435s Get:247 http://ftpmaster.internal/ubuntu plucky/main arm64 libopengl0 arm64 1.7.0-1build1 [35.1 kB] 1435s Get:248 http://ftpmaster.internal/ubuntu plucky/main arm64 libglu1-mesa arm64 9.0.2-1.1build1 [139 kB] 1435s Get:249 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-opengl all 3.1.9+dfsg-1syncable1 [631 kB] 1435s Get:250 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyqt5.sip arm64 12.17.0-1build1 [67.6 kB] 1435s Get:251 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyqt5 arm64 5.15.11+dfsg-2 [2580 kB] 1435s Get:252 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyqt5.qtopengl arm64 5.15.11+dfsg-2 [119 kB] 1435s Get:253 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pymol arm64 3.1.0+dfsg-1 [3999 kB] 1435s Get:254 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.17.0-1 [13.2 kB] 1435s Get:255 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tqdm all 4.67.1-2 [92.5 kB] 1435s Get:256 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-wxgtk4.0 arm64 4.2.2+dfsg-3build1 [7689 kB] 1436s Get:257 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-cctbx arm64 2024.10+ds2+~3.22.1+ds1-4build2 [28.3 MB] 1438s Get:258 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 1438s Get:259 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 1438s Get:260 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.5-1 [252 kB] 1438s Get:261 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-dials-data all 2.4.0-2 [110 kB] 1438s Get:262 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-datadir all 1.4.1+ds-1 [5386 B] 1438s Get:263 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-mock all 3.14.0-2 [11.7 kB] 1438s Get:264 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-regressions all 2.5.0+ds-2 [39.2 kB] 1438s Fetched 255 MB in 16s (15.8 MB/s) 1438s Selecting previously unselected package fonts-lato. 1438s (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 ... 117732 files and directories currently installed.) 1438s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ... 1438s Unpacking fonts-lato (2.015-1) ... 1438s Selecting previously unselected package python3-numpy-dev:arm64. 1438s Preparing to unpack .../001-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 1438s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 1439s Selecting previously unselected package libblas3:arm64. 1439s Preparing to unpack .../002-libblas3_3.12.1-2_arm64.deb ... 1439s Unpacking libblas3:arm64 (3.12.1-2) ... 1439s Selecting previously unselected package libgfortran5:arm64. 1439s Preparing to unpack .../003-libgfortran5_15-20250319-1ubuntu1_arm64.deb ... 1439s Unpacking libgfortran5:arm64 (15-20250319-1ubuntu1) ... 1439s Selecting previously unselected package liblapack3:arm64. 1439s Preparing to unpack .../004-liblapack3_3.12.1-2_arm64.deb ... 1439s Unpacking liblapack3:arm64 (3.12.1-2) ... 1439s Selecting previously unselected package python3-numpy. 1439s Preparing to unpack .../005-python3-numpy_1%3a2.2.3+ds-5_arm64.deb ... 1439s Unpacking python3-numpy (1:2.2.3+ds-5) ... 1439s Selecting previously unselected package libgdk-pixbuf2.0-common. 1439s Preparing to unpack .../006-libgdk-pixbuf2.0-common_2.42.12+dfsg-2_all.deb ... 1439s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... 1439s Selecting previously unselected package libjpeg-turbo8:arm64. 1439s Preparing to unpack .../007-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 1439s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 1439s Selecting previously unselected package libjpeg8:arm64. 1439s Preparing to unpack .../008-libjpeg8_8c-2ubuntu11_arm64.deb ... 1439s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 1439s Selecting previously unselected package libdeflate0:arm64. 1439s Preparing to unpack .../009-libdeflate0_1.23-1_arm64.deb ... 1439s Unpacking libdeflate0:arm64 (1.23-1) ... 1439s Selecting previously unselected package libjbig0:arm64. 1439s Preparing to unpack .../010-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 1439s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 1439s Selecting previously unselected package liblerc4:arm64. 1439s Preparing to unpack .../011-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 1439s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 1439s Selecting previously unselected package libsharpyuv0:arm64. 1439s Preparing to unpack .../012-libsharpyuv0_1.5.0-0.1_arm64.deb ... 1439s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 1439s Selecting previously unselected package libwebp7:arm64. 1439s Preparing to unpack .../013-libwebp7_1.5.0-0.1_arm64.deb ... 1439s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 1439s Selecting previously unselected package libtiff6:arm64. 1439s Preparing to unpack .../014-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 1439s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 1439s Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64. 1439s Preparing to unpack .../015-libgdk-pixbuf-2.0-0_2.42.12+dfsg-2_arm64.deb ... 1439s Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-2) ... 1439s Selecting previously unselected package gtk-update-icon-cache. 1439s Preparing to unpack .../016-gtk-update-icon-cache_4.18.2+ds-1_arm64.deb ... 1439s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 1439s 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. 1439s Unpacking gtk-update-icon-cache (4.18.2+ds-1) ... 1439s Selecting previously unselected package hicolor-icon-theme. 1439s Preparing to unpack .../017-hicolor-icon-theme_0.18-2_all.deb ... 1439s Unpacking hicolor-icon-theme (0.18-2) ... 1439s Selecting previously unselected package adwaita-icon-theme. 1439s Preparing to unpack .../018-adwaita-icon-theme_48.0-1_all.deb ... 1439s Unpacking adwaita-icon-theme (48.0-1) ... 1439s Selecting previously unselected package at-spi2-common. 1439s Preparing to unpack .../019-at-spi2-common_2.56.0-2_all.deb ... 1439s Unpacking at-spi2-common (2.56.0-2) ... 1440s Selecting previously unselected package libaec0:arm64. 1440s Preparing to unpack .../020-libaec0_1.1.3-1_arm64.deb ... 1440s Unpacking libaec0:arm64 (1.1.3-1) ... 1440s Selecting previously unselected package libsz2:arm64. 1440s Preparing to unpack .../021-libsz2_1.1.3-1_arm64.deb ... 1440s Unpacking libsz2:arm64 (1.1.3-1) ... 1440s Selecting previously unselected package libhdf5-310:arm64. 1440s Preparing to unpack .../022-libhdf5-310_1.14.5+repack-3_arm64.deb ... 1440s Unpacking libhdf5-310:arm64 (1.14.5+repack-3) ... 1440s Selecting previously unselected package libhdf5-hl-310:arm64. 1440s Preparing to unpack .../023-libhdf5-hl-310_1.14.5+repack-3_arm64.deb ... 1440s Unpacking libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 1440s Selecting previously unselected package liblzf1:arm64. 1440s Preparing to unpack .../024-liblzf1_3.6-4_arm64.deb ... 1440s Unpacking liblzf1:arm64 (3.6-4) ... 1440s Selecting previously unselected package python3-h5py-serial. 1440s Preparing to unpack .../025-python3-h5py-serial_3.13.0-1_arm64.deb ... 1440s Unpacking python3-h5py-serial (3.13.0-1) ... 1440s Selecting previously unselected package python3-h5py. 1440s Preparing to unpack .../026-python3-h5py_3.13.0-1_all.deb ... 1440s Unpacking python3-h5py (3.13.0-1) ... 1440s Selecting previously unselected package libgomp1:arm64. 1440s Preparing to unpack .../027-libgomp1_15-20250319-1ubuntu1_arm64.deb ... 1440s Unpacking libgomp1:arm64 (15-20250319-1ubuntu1) ... 1440s Selecting previously unselected package libevent-pthreads-2.1-7t64:arm64. 1440s Preparing to unpack .../028-libevent-pthreads-2.1-7t64_2.1.12-stable-10_arm64.deb ... 1440s Unpacking libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ... 1440s Selecting previously unselected package librdmacm1t64:arm64. 1440s Preparing to unpack .../029-librdmacm1t64_56.0-3ubuntu1_arm64.deb ... 1440s Unpacking librdmacm1t64:arm64 (56.0-3ubuntu1) ... 1440s Selecting previously unselected package libfabric1:arm64. 1440s Preparing to unpack .../030-libfabric1_1.17.0-3.1_arm64.deb ... 1440s Unpacking libfabric1:arm64 (1.17.0-3.1) ... 1440s Selecting previously unselected package libhwloc15:arm64. 1440s Preparing to unpack .../031-libhwloc15_2.12.0-1_arm64.deb ... 1440s Unpacking libhwloc15:arm64 (2.12.0-1) ... 1440s Selecting previously unselected package libmunge2:arm64. 1440s Preparing to unpack .../032-libmunge2_0.5.16-1_arm64.deb ... 1440s Unpacking libmunge2:arm64 (0.5.16-1) ... 1440s Selecting previously unselected package libpciaccess0:arm64. 1440s Preparing to unpack .../033-libpciaccess0_0.17-3build1_arm64.deb ... 1440s Unpacking libpciaccess0:arm64 (0.17-3build1) ... 1440s Selecting previously unselected package libxnvctrl0:arm64. 1440s Preparing to unpack .../034-libxnvctrl0_510.47.03-0ubuntu4_arm64.deb ... 1440s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 1440s Selecting previously unselected package ocl-icd-libopencl1:arm64. 1440s Preparing to unpack .../035-ocl-icd-libopencl1_2.3.2-1build1_arm64.deb ... 1440s Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1build1) ... 1440s Selecting previously unselected package libhwloc-plugins:arm64. 1440s Preparing to unpack .../036-libhwloc-plugins_2.12.0-1_arm64.deb ... 1440s Unpacking libhwloc-plugins:arm64 (2.12.0-1) ... 1440s Selecting previously unselected package libpmix2t64:arm64. 1440s Preparing to unpack .../037-libpmix2t64_5.0.6-5_arm64.deb ... 1440s Unpacking libpmix2t64:arm64 (5.0.6-5) ... 1440s Selecting previously unselected package libllvm17t64:arm64. 1440s Preparing to unpack .../038-libllvm17t64_1%3a17.0.6-21_arm64.deb ... 1440s Unpacking libllvm17t64:arm64 (1:17.0.6-21) ... 1441s Selecting previously unselected package libamd-comgr2:arm64. 1441s Preparing to unpack .../039-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_arm64.deb ... 1441s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ... 1441s Selecting previously unselected package libhsakmt1:arm64. 1441s Preparing to unpack .../040-libhsakmt1_5.7.0-1build1_arm64.deb ... 1441s Unpacking libhsakmt1:arm64 (5.7.0-1build1) ... 1441s Selecting previously unselected package libhsa-runtime64-1. 1441s Preparing to unpack .../041-libhsa-runtime64-1_5.7.1-2build1_arm64.deb ... 1441s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 1441s Selecting previously unselected package libamdhip64-5. 1441s Preparing to unpack .../042-libamdhip64-5_5.7.1-5build1_arm64.deb ... 1441s Unpacking libamdhip64-5 (5.7.1-5build1) ... 1441s Selecting previously unselected package libibumad3:arm64. 1441s Preparing to unpack .../043-libibumad3_56.0-3ubuntu1_arm64.deb ... 1441s Unpacking libibumad3:arm64 (56.0-3ubuntu1) ... 1441s Selecting previously unselected package libibmad5:arm64. 1441s Preparing to unpack .../044-libibmad5_56.0-3ubuntu1_arm64.deb ... 1441s Unpacking libibmad5:arm64 (56.0-3ubuntu1) ... 1441s Selecting previously unselected package libucx0:arm64. 1441s Preparing to unpack .../045-libucx0_1.18.1+ds-2_arm64.deb ... 1441s Unpacking libucx0:arm64 (1.18.1+ds-2) ... 1442s Selecting previously unselected package libopenmpi40:arm64. 1442s Preparing to unpack .../046-libopenmpi40_5.0.7-1_arm64.deb ... 1442s Unpacking libopenmpi40:arm64 (5.0.7-1) ... 1442s Selecting previously unselected package libhdf5-openmpi-310:arm64. 1442s Preparing to unpack .../047-libhdf5-openmpi-310_1.14.5+repack-3_arm64.deb ... 1442s Unpacking libhdf5-openmpi-310:arm64 (1.14.5+repack-3) ... 1442s Selecting previously unselected package bitshuffle. 1442s Preparing to unpack .../048-bitshuffle_0.5.2-1build2_arm64.deb ... 1442s Unpacking bitshuffle (0.5.2-1build2) ... 1442s Selecting previously unselected package libtcl8.6:arm64. 1442s Preparing to unpack .../049-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 1442s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... 1442s Selecting previously unselected package fonts-dejavu-mono. 1442s Preparing to unpack .../050-fonts-dejavu-mono_2.37-8_all.deb ... 1442s Unpacking fonts-dejavu-mono (2.37-8) ... 1442s Selecting previously unselected package fonts-dejavu-core. 1442s Preparing to unpack .../051-fonts-dejavu-core_2.37-8_all.deb ... 1442s Unpacking fonts-dejavu-core (2.37-8) ... 1442s Selecting previously unselected package fontconfig-config. 1442s Preparing to unpack .../052-fontconfig-config_2.15.0-2.1ubuntu1_arm64.deb ... 1442s Unpacking fontconfig-config (2.15.0-2.1ubuntu1) ... 1442s Selecting previously unselected package libfontconfig1:arm64. 1442s Preparing to unpack .../053-libfontconfig1_2.15.0-2.1ubuntu1_arm64.deb ... 1442s Unpacking libfontconfig1:arm64 (2.15.0-2.1ubuntu1) ... 1442s Selecting previously unselected package libxrender1:arm64. 1442s Preparing to unpack .../054-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 1442s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 1442s Selecting previously unselected package libxft2:arm64. 1442s Preparing to unpack .../055-libxft2_2.3.6-1build1_arm64.deb ... 1442s Unpacking libxft2:arm64 (2.3.6-1build1) ... 1442s Selecting previously unselected package x11-common. 1442s Preparing to unpack .../056-x11-common_1%3a7.7+23ubuntu3_all.deb ... 1442s Unpacking x11-common (1:7.7+23ubuntu3) ... 1442s Selecting previously unselected package libxss1:arm64. 1442s Preparing to unpack .../057-libxss1_1%3a1.2.3-1build3_arm64.deb ... 1442s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 1442s Selecting previously unselected package libtk8.6:arm64. 1442s Preparing to unpack .../058-libtk8.6_8.6.16-1_arm64.deb ... 1442s Unpacking libtk8.6:arm64 (8.6.16-1) ... 1442s Selecting previously unselected package tk8.6-blt2.5. 1442s Preparing to unpack .../059-tk8.6-blt2.5_2.5.3+dfsg-8_arm64.deb ... 1442s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 1442s Selecting previously unselected package blt. 1442s Preparing to unpack .../060-blt_2.5.3+dfsg-8_arm64.deb ... 1442s Unpacking blt (2.5.3+dfsg-8) ... 1442s Selecting previously unselected package libdconf1:arm64. 1442s Preparing to unpack .../061-libdconf1_0.40.0-5_arm64.deb ... 1442s Unpacking libdconf1:arm64 (0.40.0-5) ... 1442s Selecting previously unselected package dconf-service. 1442s Preparing to unpack .../062-dconf-service_0.40.0-5_arm64.deb ... 1442s Unpacking dconf-service (0.40.0-5) ... 1443s Selecting previously unselected package dconf-gsettings-backend:arm64. 1443s Preparing to unpack .../063-dconf-gsettings-backend_0.40.0-5_arm64.deb ... 1443s Unpacking dconf-gsettings-backend:arm64 (0.40.0-5) ... 1443s Selecting previously unselected package fontconfig. 1443s Preparing to unpack .../064-fontconfig_2.15.0-2.1ubuntu1_arm64.deb ... 1443s Unpacking fontconfig (2.15.0-2.1ubuntu1) ... 1443s Selecting previously unselected package fonts-font-awesome. 1443s Preparing to unpack .../065-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 1443s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 1443s Selecting previously unselected package fonts-lyx. 1443s Preparing to unpack .../066-fonts-lyx_2.4.3-1_all.deb ... 1443s Unpacking fonts-lyx (2.4.3-1) ... 1443s Selecting previously unselected package libann-cctbx0. 1443s Preparing to unpack .../067-libann-cctbx0_1.1.2+doc-9build1_arm64.deb ... 1443s Unpacking libann-cctbx0 (1.1.2+doc-9build1) ... 1443s Selecting previously unselected package libann-cctbx-dev. 1443s Preparing to unpack .../068-libann-cctbx-dev_1.1.2+doc-9build1_arm64.deb ... 1443s Unpacking libann-cctbx-dev (1.1.2+doc-9build1) ... 1443s Selecting previously unselected package libantlr3c-3.4-0:arm64. 1443s Preparing to unpack .../069-libantlr3c-3.4-0_3.4+dfsg-4build2_arm64.deb ... 1443s Unpacking libantlr3c-3.4-0:arm64 (3.4+dfsg-4build2) ... 1443s Selecting previously unselected package libasan8:arm64. 1443s Preparing to unpack .../070-libasan8_15-20250319-1ubuntu1_arm64.deb ... 1443s Unpacking libasan8:arm64 (15-20250319-1ubuntu1) ... 1443s Selecting previously unselected package libatk1.0-0t64:arm64. 1443s Preparing to unpack .../071-libatk1.0-0t64_2.56.0-2_arm64.deb ... 1443s Unpacking libatk1.0-0t64:arm64 (2.56.0-2) ... 1443s Selecting previously unselected package libxi6:arm64. 1443s Preparing to unpack .../072-libxi6_2%3a1.8.2-1_arm64.deb ... 1443s Unpacking libxi6:arm64 (2:1.8.2-1) ... 1443s Selecting previously unselected package libatspi2.0-0t64:arm64. 1443s Preparing to unpack .../073-libatspi2.0-0t64_2.56.0-2_arm64.deb ... 1443s Unpacking libatspi2.0-0t64:arm64 (2.56.0-2) ... 1443s Selecting previously unselected package libatk-bridge2.0-0t64:arm64. 1443s Preparing to unpack .../074-libatk-bridge2.0-0t64_2.56.0-2_arm64.deb ... 1443s Unpacking libatk-bridge2.0-0t64:arm64 (2.56.0-2) ... 1443s Selecting previously unselected package libavahi-common-data:arm64. 1443s Preparing to unpack .../075-libavahi-common-data_0.8-16ubuntu2_arm64.deb ... 1443s Unpacking libavahi-common-data:arm64 (0.8-16ubuntu2) ... 1443s Selecting previously unselected package libavahi-common3:arm64. 1443s Preparing to unpack .../076-libavahi-common3_0.8-16ubuntu2_arm64.deb ... 1443s Unpacking libavahi-common3:arm64 (0.8-16ubuntu2) ... 1443s Selecting previously unselected package libavahi-client3:arm64. 1443s Preparing to unpack .../077-libavahi-client3_0.8-16ubuntu2_arm64.deb ... 1443s Unpacking libavahi-client3:arm64 (0.8-16ubuntu2) ... 1443s Selecting previously unselected package libboost-python1.83.0. 1443s Preparing to unpack .../078-libboost-python1.83.0_1.83.0-4.1ubuntu2_arm64.deb ... 1443s Unpacking libboost-python1.83.0 (1.83.0-4.1ubuntu2) ... 1443s Selecting previously unselected package libboost-numpy1.83.0. 1443s Preparing to unpack .../079-libboost-numpy1.83.0_1.83.0-4.1ubuntu2_arm64.deb ... 1443s Unpacking libboost-numpy1.83.0 (1.83.0-4.1ubuntu2) ... 1443s Selecting previously unselected package libitm1:arm64. 1443s Preparing to unpack .../080-libitm1_15-20250319-1ubuntu1_arm64.deb ... 1443s Unpacking libitm1:arm64 (15-20250319-1ubuntu1) ... 1443s Selecting previously unselected package liblsan0:arm64. 1443s Preparing to unpack .../081-liblsan0_15-20250319-1ubuntu1_arm64.deb ... 1443s Unpacking liblsan0:arm64 (15-20250319-1ubuntu1) ... 1443s Selecting previously unselected package libtsan2:arm64. 1443s Preparing to unpack .../082-libtsan2_15-20250319-1ubuntu1_arm64.deb ... 1443s Unpacking libtsan2:arm64 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previously unselected package libxcb-render0:arm64. 1446s Preparing to unpack .../102-libxcb-render0_1.17.0-2_arm64.deb ... 1446s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 1446s Selecting previously unselected package libxcb-shm0:arm64. 1446s Preparing to unpack .../103-libxcb-shm0_1.17.0-2_arm64.deb ... 1446s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 1446s Selecting previously unselected package libcairo2:arm64. 1446s Preparing to unpack .../104-libcairo2_1.18.4-1_arm64.deb ... 1446s Unpacking libcairo2:arm64 (1.18.4-1) ... 1446s Selecting previously unselected package libcairo-gobject2:arm64. 1446s Preparing to unpack .../105-libcairo-gobject2_1.18.4-1_arm64.deb ... 1446s Unpacking libcairo-gobject2:arm64 (1.18.4-1) ... 1446s Selecting previously unselected package libcbf1t64:arm64. 1446s Preparing to unpack .../106-libcbf1t64_0.9.7+dfsg1-5build1_arm64.deb ... 1446s Unpacking libcbf1t64:arm64 (0.9.7+dfsg1-5build1) ... 1446s Selecting previously unselected package libccp4-data. 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Selecting previously unselected package libgbm1:arm64. 1448s Preparing to unpack .../128-libgbm1_25.0.1-2ubuntu2_arm64.deb ... 1448s Unpacking libgbm1:arm64 (25.0.1-2ubuntu2) ... 1448s Selecting previously unselected package libwayland-client0:arm64. 1448s Preparing to unpack .../129-libwayland-client0_1.23.1-3_arm64.deb ... 1448s Unpacking libwayland-client0:arm64 (1.23.1-3) ... 1448s Selecting previously unselected package libegl-mesa0:arm64. 1448s Preparing to unpack .../130-libegl-mesa0_25.0.1-2ubuntu2_arm64.deb ... 1448s Unpacking libegl-mesa0:arm64 (25.0.1-2ubuntu2) ... 1448s Selecting previously unselected package libepoxy0:arm64. 1448s Preparing to unpack .../131-libepoxy0_1.5.10-2_arm64.deb ... 1448s Unpacking libepoxy0:arm64 (1.5.10-2) ... 1448s Selecting previously unselected package libvulkan1:arm64. 1448s Preparing to unpack .../132-libvulkan1_1.4.304.0-1_arm64.deb ... 1448s Unpacking libvulkan1:arm64 (1.4.304.0-1) ... 1448s Selecting previously unselected package libgl1-mesa-dri:arm64. 1448s Preparing to unpack .../133-libgl1-mesa-dri_25.0.1-2ubuntu2_arm64.deb ... 1448s Unpacking libgl1-mesa-dri:arm64 (25.0.1-2ubuntu2) ... 1448s Selecting previously unselected package libglvnd0:arm64. 1448s Preparing to unpack .../134-libglvnd0_1.7.0-1build1_arm64.deb ... 1448s Unpacking libglvnd0:arm64 (1.7.0-1build1) ... 1448s Selecting previously unselected package libxcb-glx0:arm64. 1448s Preparing to unpack .../135-libxcb-glx0_1.17.0-2_arm64.deb ... 1448s Unpacking libxcb-glx0:arm64 (1.17.0-2) ... 1448s Selecting previously unselected package libxxf86vm1:arm64. 1448s Preparing to unpack .../136-libxxf86vm1_1%3a1.1.4-1build4_arm64.deb ... 1448s Unpacking libxxf86vm1:arm64 (1:1.1.4-1build4) ... 1448s Selecting previously unselected package libglx-mesa0:arm64. 1448s Preparing to unpack .../137-libglx-mesa0_25.0.1-2ubuntu2_arm64.deb ... 1448s Unpacking libglx-mesa0:arm64 (25.0.1-2ubuntu2) ... 1448s Selecting previously unselected package libglx0:arm64. 1448s 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.../158-libgtk-3-0t64_3.24.49-2ubuntu1_arm64.deb ... 1449s Unpacking libgtk-3-0t64:arm64 (3.24.49-2ubuntu1) ... 1449s Selecting previously unselected package libice6:arm64. 1449s Preparing to unpack .../159-libice6_2%3a1.1.1-1_arm64.deb ... 1449s Unpacking libice6:arm64 (2:1.1.1-1) ... 1449s Selecting previously unselected package libimagequant0:arm64. 1449s Preparing to unpack .../160-libimagequant0_2.18.0-1build1_arm64.deb ... 1449s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 1449s Selecting previously unselected package libwacom-common. 1449s Preparing to unpack .../161-libwacom-common_2.14.0-1_all.deb ... 1449s Unpacking libwacom-common (2.14.0-1) ... 1449s Selecting previously unselected package libwacom9:arm64. 1449s Preparing to unpack .../162-libwacom9_2.14.0-1_arm64.deb ... 1449s Unpacking libwacom9:arm64 (2.14.0-1) ... 1449s Selecting previously unselected package libinput-bin. 1449s Preparing to unpack .../163-libinput-bin_1.27.1-1_arm64.deb ... 1449s Unpacking libinput-bin (1.27.1-1) ... 1449s Selecting previously unselected package libmtdev1t64:arm64. 1449s Preparing to unpack .../164-libmtdev1t64_1.1.7-1_arm64.deb ... 1449s Unpacking libmtdev1t64:arm64 (1.1.7-1) ... 1449s Selecting previously unselected package libinput10:arm64. 1449s Preparing to unpack .../165-libinput10_1.27.1-1_arm64.deb ... 1449s Unpacking libinput10:arm64 (1.27.1-1) ... 1449s Selecting previously unselected package libjs-jquery-ui. 1449s Preparing to unpack .../166-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 1449s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 1450s Selecting previously unselected package liblbfgsb0:arm64. 1450s Preparing to unpack .../167-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 1450s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 1450s Selecting previously unselected package libmd4c0:arm64. 1450s Preparing to unpack .../168-libmd4c0_0.5.2-2_arm64.deb ... 1450s Unpacking libmd4c0:arm64 (0.5.2-2) ... 1450s Selecting previously unselected package libnetcdf22:arm64. 1450s Preparing to unpack .../169-libnetcdf22_1%3a4.9.3-1_arm64.deb ... 1450s Unpacking libnetcdf22:arm64 (1:4.9.3-1) ... 1450s Selecting previously unselected package libnotify4:arm64. 1450s Preparing to unpack .../170-libnotify4_0.8.4-1_arm64.deb ... 1450s Unpacking libnotify4:arm64 (0.8.4-1) ... 1450s Selecting previously unselected package libpcre2-16-0:arm64. 1450s Preparing to unpack .../171-libpcre2-16-0_10.45-1_arm64.deb ... 1450s Unpacking libpcre2-16-0:arm64 (10.45-1) ... 1450s Selecting previously unselected package libpcre2-32-0:arm64. 1450s Preparing to unpack .../172-libpcre2-32-0_10.45-1_arm64.deb ... 1450s Unpacking libpcre2-32-0:arm64 (10.45-1) ... 1450s Selecting previously unselected package libqhull-r8.0:arm64. 1450s Preparing to unpack .../173-libqhull-r8.0_2020.2-6build1_arm64.deb ... 1450s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 1450s Selecting previously unselected package libqt5core5t64:arm64. 1450s Preparing to unpack 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Preparing to unpack .../179-libxcb-icccm4_0.4.2-1_arm64.deb ... 1450s Unpacking libxcb-icccm4:arm64 (0.4.2-1) ... 1450s Selecting previously unselected package libxcb-util1:arm64. 1450s Preparing to unpack .../180-libxcb-util1_0.4.1-1_arm64.deb ... 1450s Unpacking libxcb-util1:arm64 (0.4.1-1) ... 1450s Selecting previously unselected package libxcb-image0:arm64. 1450s Preparing to unpack .../181-libxcb-image0_0.4.0-2build1_arm64.deb ... 1450s Unpacking libxcb-image0:arm64 (0.4.0-2build1) ... 1450s Selecting previously unselected package libxcb-keysyms1:arm64. 1450s Preparing to unpack .../182-libxcb-keysyms1_0.4.1-1_arm64.deb ... 1450s Unpacking libxcb-keysyms1:arm64 (0.4.1-1) ... 1450s Selecting previously unselected package libxcb-render-util0:arm64. 1450s Preparing to unpack .../183-libxcb-render-util0_0.3.10-1_arm64.deb ... 1450s Unpacking libxcb-render-util0:arm64 (0.3.10-1) ... 1450s Selecting previously unselected package libxcb-shape0:arm64. 1450s Preparing to unpack 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Selecting previously unselected package libqt5help5:arm64. 1451s Preparing to unpack .../194-libqt5help5_5.15.15-6build1_arm64.deb ... 1451s Unpacking libqt5help5:arm64 (5.15.15-6build1) ... 1451s Selecting previously unselected package libqt5opengl5t64:arm64. 1451s Preparing to unpack .../195-libqt5opengl5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ... 1451s Unpacking libqt5opengl5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 1451s Selecting previously unselected package libqt5printsupport5t64:arm64. 1451s Preparing to unpack .../196-libqt5printsupport5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ... 1451s Unpacking libqt5printsupport5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 1451s Selecting previously unselected package libqt5test5t64:arm64. 1451s Preparing to unpack .../197-libqt5test5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ... 1451s Unpacking libqt5test5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 1451s Selecting previously unselected package libraqm0:arm64. 1451s Preparing to unpack .../198-libraqm0_0.10.2-1_arm64.deb 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Unpacking python-matplotlib-data (3.8.3-7build1) ... 1452s Selecting previously unselected package python3-all. 1452s Preparing to unpack .../209-python3-all_3.13.2-2_arm64.deb ... 1452s Unpacking python3-all (3.13.2-2) ... 1452s Selecting previously unselected package python3-brotli. 1452s Preparing to unpack .../210-python3-brotli_1.1.0-2build4_arm64.deb ... 1452s Unpacking python3-brotli (1.1.0-2build4) ... 1452s Selecting previously unselected package python3-legacy-cgi. 1452s Preparing to unpack .../211-python3-legacy-cgi_2.6.2-1_all.deb ... 1452s Unpacking python3-legacy-cgi (2.6.2-1) ... 1452s Selecting previously unselected package python3-pycbf. 1452s Preparing to unpack .../212-python3-pycbf_0.9.7+dfsg1-5build1_arm64.deb ... 1452s Unpacking python3-pycbf (0.9.7+dfsg1-5build1) ... 1452s Selecting previously unselected package python3-hdf5plugin. 1452s Preparing to unpack .../213-python3-hdf5plugin_5.0.0-1_all.deb ... 1452s Unpacking python3-hdf5plugin (5.0.0-1) ... 1452s Selecting previously unselected package python3-dateutil. 1452s Preparing to unpack .../214-python3-dateutil_2.9.0-4_all.deb ... 1452s Unpacking python3-dateutil (2.9.0-4) ... 1452s Selecting previously unselected package libopenjp2-7:arm64. 1452s Preparing to unpack .../215-libopenjp2-7_2.5.3-2_arm64.deb ... 1452s Unpacking libopenjp2-7:arm64 (2.5.3-2) ... 1452s Selecting previously unselected package python3-pil:arm64. 1452s Preparing to unpack .../216-python3-pil_11.1.0-5build1_arm64.deb ... 1452s Unpacking python3-pil:arm64 (11.1.0-5build1) ... 1452s Selecting previously unselected package python3.13-tk. 1452s Preparing to unpack .../217-python3.13-tk_3.13.2-2_arm64.deb ... 1452s Unpacking python3.13-tk (3.13.2-2) ... 1452s Selecting previously unselected package python3-tk:arm64. 1452s Preparing to unpack .../218-python3-tk_3.13.2-1_arm64.deb ... 1452s Unpacking python3-tk:arm64 (3.13.2-1) ... 1452s Selecting previously unselected package python3-pil.imagetk:arm64. 1452s Preparing to unpack .../219-python3-pil.imagetk_11.1.0-5build1_arm64.deb ... 1452s Unpacking python3-pil.imagetk:arm64 (11.1.0-5build1) ... 1452s Selecting previously unselected package python3-contourpy. 1452s Preparing to unpack .../220-python3-contourpy_1.3.1-1build1_arm64.deb ... 1452s Unpacking python3-contourpy (1.3.1-1build1) ... 1452s Selecting previously unselected package python3-cycler. 1452s Preparing to unpack .../221-python3-cycler_0.12.1-1_all.deb ... 1452s Unpacking python3-cycler (0.12.1-1) ... 1452s Selecting previously unselected package python3-platformdirs. 1452s Preparing to unpack .../222-python3-platformdirs_4.3.6-1_all.deb ... 1452s Unpacking python3-platformdirs (4.3.6-1) ... 1452s Selecting previously unselected package python3-fs. 1452s Preparing to unpack .../223-python3-fs_2.4.16-7_all.deb ... 1452s Unpacking python3-fs (2.4.16-7) ... 1452s Selecting previously unselected package python3-lxml:arm64. 1452s Preparing to unpack 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python3-sympy (1.13.3-5) ... 1453s Selecting previously unselected package python3-ufolib2. 1453s Preparing to unpack .../230-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 1453s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 1453s Selecting previously unselected package unicode-data. 1453s Preparing to unpack .../231-unicode-data_15.1.0-1_all.deb ... 1453s Unpacking unicode-data (15.1.0-1) ... 1454s Selecting previously unselected package python3-fonttools. 1454s Preparing to unpack .../232-python3-fonttools_4.55.3-2build1_arm64.deb ... 1454s Unpacking python3-fonttools (4.55.3-2build1) ... 1454s Selecting previously unselected package python3-importlib-resources. 1454s Preparing to unpack .../233-python3-importlib-resources_6.5.2-1_all.deb ... 1454s Unpacking python3-importlib-resources (6.5.2-1) ... 1454s Selecting previously unselected package python3-kiwisolver. 1454s Preparing to unpack .../234-python3-kiwisolver_1.4.7-3build1_arm64.deb ... 1454s Unpacking python3-kiwisolver 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previously unselected package python3-flexcache. 1454s Preparing to unpack .../240-python3-flexcache_0.3-2_all.deb ... 1454s Unpacking python3-flexcache (0.3-2) ... 1454s Selecting previously unselected package python3-flexparser. 1454s Preparing to unpack .../241-python3-flexparser_0.4-1_all.deb ... 1454s Unpacking python3-flexparser (0.4-1) ... 1454s Selecting previously unselected package python3-pint. 1454s Preparing to unpack .../242-python3-pint_0.24.4-1_all.deb ... 1454s Unpacking python3-pint (0.24.4-1) ... 1454s Selecting previously unselected package python3-nxmx. 1454s Preparing to unpack .../243-python3-nxmx_0.0.4-1_all.deb ... 1454s Unpacking python3-nxmx (0.0.4-1) ... 1454s Selecting previously unselected package python3-ordered-set. 1455s Preparing to unpack .../244-python3-ordered-set_4.1.0-1_all.deb ... 1455s Unpacking python3-ordered-set (4.1.0-1) ... 1455s Selecting previously unselected package python3-procrunner. 1455s Preparing to unpack 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1476s Setting up libucx0:arm64 (1.18.1+ds-2) ... 1476s Setting up blt (2.5.3+dfsg-8) ... 1476s Setting up python3-tk:arm64 (3.13.2-1) ... 1476s Setting up python3-opengl (3.1.9+dfsg-1syncable1) ... 1476s /usr/lib/python3/dist-packages/OpenGL/GL/AMD/vertex_shader_tessellator.py:30: SyntaxWarning: invalid escape sequence '\ ' 1476s |\ |\ 1478s Setting up libboost-python-dev (1.83.0.2ubuntu1) ... 1478s Setting up libqt5gui5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 1478s Setting up python3-pil.imagetk:arm64 (11.1.0-5build1) ... 1478s Setting up libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4build2) ... 1478s Setting up libopenmpi40:arm64 (5.0.7-1) ... 1478s Setting up libqt5widgets5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 1478s Setting up libhdf5-openmpi-310:arm64 (1.14.5+repack-3) ... 1478s Setting up libqt5help5:arm64 (5.15.15-6build1) ... 1478s Setting up libqt5opengl5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 1478s Setting up libqt5printsupport5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 1478s Setting up bitshuffle (0.5.2-1build2) ... 1478s Setting up libqt5designer5:arm64 (5.15.15-6build1) ... 1478s Setting up python3-pyqt5 (5.15.11+dfsg-2) ... 1478s Setting up python3-pyqt5.qtopengl (5.15.11+dfsg-2) ... 1478s Setting up python3-pymol (3.1.0+dfsg-1) ... 1479s Setting up python3-fonttools (4.55.3-2build1) ... 1479s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 1480s Setting up python3-matplotlib (3.8.3-7build1) ... 1481s Processing triggers for libc-bin (2.41-1ubuntu2) ... 1481s Processing triggers for man-db (2.13.0-1) ... 1482s Processing triggers for libglib2.0-0t64:arm64 (2.84.0-1) ... 1482s Setting up libgtk-3-0t64:arm64 (3.24.49-2ubuntu1) ... 1482s Processing triggers for udev (257.4-1ubuntu1) ... 1483s Setting up libwxgtk3.2-1t64:arm64 (3.2.6+dfsg-2ubuntu1) ... 1483s Setting up libwxgtk-gl3.2-1t64:arm64 (3.2.6+dfsg-2ubuntu1) ... 1483s Setting up python3-wxgtk4.0 (4.2.2+dfsg-3build1) ... 1484s Setting up python3-cctbx (2024.10+ds2+~3.22.1+ds1-4build2) ... 1487s /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:18: SyntaxWarning: invalid escape sequence '\{' 1487s []_,.;:"&<>()/\{}'`~!@#$%*|+- 1487s /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:46: SyntaxWarning: invalid escape sequence '\/' 1487s special_characters = """[]_,.;:"&<>()\/\{}'`~!@#$%*|+-""" 1496s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:724: SyntaxWarning: invalid escape sequence '\o' 1496s width=pairwise_differences_db, label='$\omega_{hkl}$' 1496s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:739: SyntaxWarning: invalid escape sequence '\o' 1496s axes[0].set_ylabel('Distribution of $\omega_{hbk}$') 1496s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:740: SyntaxWarning: invalid escape sequence '\o' 1496s axes[0].set_xlabel('Normalized PD ($\omega_{hbk}$)') 1496s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:759: SyntaxWarning: invalid escape sequence '\o' 1496s axes[1].set_xlabel('Sorted Normalized PD ($\omega_{hbk}$)') 1496s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:778: SyntaxWarning: invalid escape sequence '\s' 1496s axes[2].set_ylabel('Standard Deviation of $I_{hbk}/\sigma_{hbk}$') 1496s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:807: SyntaxWarning: invalid escape sequence '\m' 1496s axes_sadd.set_ylabel('$s_{\mathrm{fac}}^2 \\times s_{\mathrm{add}}^2$') 1496s Processing triggers for libc-bin (2.41-1ubuntu2) ... 1514s autopkgtest [14:06:18]: test dxtbx: [----------------------- 1514s Testing dxtbx with python3.13: 1517s Fatal Python error: Segmentation fault 1517s 1517s Current thread 0x0000e7796bea0760 (most recent call first): 1517s File "/usr/lib/python3/dist-packages/cctbx/sgtbx/__init__.py", line 102 in __init__ 1517s File "/usr/lib/python3/dist-packages/cctbx/crystal/__init__.py", line 75 in __init__ 1517s File "/tmp/autopkgtest.irYrF2/autopkgtest_tmp/tests/test_crystal_model_equivalence.py", line 28 in 1517s File "/usr/lib/python3/dist-packages/_pytest/assertion/rewrite.py", line 185 in exec_module 1517s File "", line 935 in _load_unlocked 1517s File "", line 1331 in _find_and_load_unlocked 1517s File "", line 1360 in _find_and_load 1517s File "", line 1387 in _gcd_import 1517s File "/usr/lib/python3.13/importlib/__init__.py", line 88 in import_module 1517s File "/usr/lib/python3/dist-packages/_pytest/pathlib.py", line 587 in import_path 1517s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 493 in importtestmodule 1517s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 546 in _getobj 1517s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 284 in obj 1517s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 562 in _register_setup_module_fixture 1517s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 549 in collect 1517s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389 in collect 1517s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341 in from_call 1517s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 391 in pytest_make_collect_report 1517s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall 1517s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec 1517s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ 1517s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 567 in collect_one_node 1517s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 835 in _collect_one_node 1517s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 970 in genitems 1517s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 975 in genitems 1517s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 975 in genitems 1517s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 809 in perform_collect 1517s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 347 in pytest_collection 1517s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall 1517s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec 1517s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ 1517s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 336 in _main 1517s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 283 in wrap_session 1517s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 330 in pytest_cmdline_main 1517s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall 1517s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec 1517s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ 1517s File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 175 in main 1517s File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 201 in console_main 1517s File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 9 in 1517s File "", line 88 in _run_code 1517s File "", line 198 in _run_module_as_main 1517s 1517s Extension modules: _brotli, yaml._yaml, h5py._debian_h5py_serial._errors, h5py._debian_h5py_serial.defs, h5py._debian_h5py_serial._objects, h5py._debian_h5py_serial.h5, numpy._core._multiarray_umath, numpy.linalg._umath_linalg, h5py._debian_h5py_serial.utils, h5py._debian_h5py_serial.h5t, h5py._debian_h5py_serial.h5s, h5py._debian_h5py_serial.h5ac, h5py._debian_h5py_serial.h5p, h5py._debian_h5py_serial.h5r, h5py._debian_h5py_serial._proxy, h5py._debian_h5py_serial._conv, h5py._debian_h5py_serial.h5z, h5py._debian_h5py_serial.h5a, h5py._debian_h5py_serial.h5d, h5py._debian_h5py_serial.h5ds, h5py._debian_h5py_serial.h5g, h5py._debian_h5py_serial.h5i, h5py._debian_h5py_serial.h5o, h5py._debian_h5py_serial.h5f, h5py._debian_h5py_serial.h5fd, h5py._debian_h5py_serial.h5pl, h5py._debian_h5py_serial.h5l, h5py._debian_h5py_serial._selector, h5py.atexit, h5py._errors, h5py.defs, h5py._objects, h5py.h5, h5py.utils, h5py.h5t, h5py.h5s, h5py.h5ac, h5py.h5p, h5py.h5r, h5py._proxy, h5py._conv, h5py.h5z, h5py.h5a, h5py.h5d, h5py.h5ds, h5py.h5g, h5py.h5i, h5py.h5o, h5py.h5f, h5py.h5fd, h5py.h5pl, h5py.h5l, h5py._selector, scipy._lib._ccallback_c, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, boost_python_meta_ext, boost_optional_ext, std_pair_ext, scitbx_array_family_flex_ext, scitbx_stl_set_ext, scitbx_stl_vector_ext, scitbx_stl_map_ext, scitbx_random_ext, cctbx_array_family_flex_ext, cctbx_crystal_ext, scitbx_array_family_shared_ext, cctbx_uctbx_ext, cctbx_sgtbx_ext, boost_rational_ext, cctbx_covariance_ext, cctbx_geometry_ext, scitbx_cubicle_neighbors_ext, dxtbx_format_image_ext, dxtbx_imageset_ext, dxtbx_ext, _pycbf, dxtbx_model_ext, cctbx_eltbx_attenuation_coefficient_ext, iotbx_detectors_ext, iotbx_detectors_bruker_ext, omptbx_ext, dxtbx_masking_ext, dxtbx_format_nexus_ext, scitbx_math_ext, scitbx_linalg_ext, cctbx_orientation_ext, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.optimize._group_columns, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, iotbx_cif_ext, cctbx_miller_ext, cctbx_asymmetric_map_ext, cctbx_maptbx_ext, cctbx_adptbx_ext, scitbx_fftpack_ext, cctbx_xray_ext, cctbx_eltbx_xray_scattering_ext, cctbx_math_ext, cctbx_eltbx_neutron_ext, scitbx_lbfgs_ext (total: 168) 1521s Segmentation fault (core dumped) 1521s autopkgtest [14:06:25]: test dxtbx: -----------------------] 1521s dxtbx FAIL non-zero exit status 139 1521s autopkgtest [14:06:25]: test dxtbx: - - - - - - - - - - results - - - - - - - - - - 1522s autopkgtest [14:06:26]: @@@@@@@@@@@@@@@@@@@@ summary 1522s cctbx FAIL non-zero exit status 1 1522s dxtbx FAIL non-zero exit status 139 1527s nova [W] Using flock in prodstack6-arm64 1527s flock: timeout while waiting to get lock 1527s Creating nova instance adt-plucky-arm64-cctbx-20250322-130601-juju-7f2275-prod-proposed-migration-environment-20-fb72ca39-dc3f-43f5-8d0a-fd0ddc18fa1c from image adt/ubuntu-plucky-arm64-server-20250322.img (UUID 990d3f09-34a1-43c2-b4bb-c53f06ad3af8)... 1527s nova [W] Timed out waiting for 5cd2facd-8830-4ca9-b4e6-00b011aa4ded to get deleted. 1527s nova [W] Using flock in prodstack6-arm64 1527s Creating nova instance adt-plucky-arm64-cctbx-20250322-130601-juju-7f2275-prod-proposed-migration-environment-20-fb72ca39-dc3f-43f5-8d0a-fd0ddc18fa1c from image adt/ubuntu-plucky-arm64-server-20250322.img (UUID 990d3f09-34a1-43c2-b4bb-c53f06ad3af8)... 1527s nova [W] Timed out waiting for 5339a637-f3d6-4470-932b-17aeb4458af0 to get deleted.