0s autopkgtest [13:06:00]: starting date and time: 2025-03-22 13:06:00+0000 0s autopkgtest [13:06:00]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [13:06:00]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.17jb1lgh/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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-18.secgroup --name adt-plucky-s390x-cctbx-20250322-130600-juju-7f2275-prod-proposed-migration-environment-20-c0208a91-2f27-4bbf-9999-d7601a55e3e1 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-s390x -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/ 603s autopkgtest [13:16:03]: testbed dpkg architecture: s390x 603s autopkgtest [13:16:03]: testbed apt version: 2.9.33 604s autopkgtest [13:16:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup 604s autopkgtest [13:16:04]: testbed release detected to be: None 604s autopkgtest [13:16:04]: updating testbed package index (apt update) 605s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 605s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 605s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 605s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 605s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [1232 B] 605s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [288 kB] 605s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [29.9 kB] 605s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [11.5 kB] 605s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [41.5 kB] 605s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1264 B] 606s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 606s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [182 kB] 606s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [10.7 kB] 606s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [2512 B] 606s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [316 B] 606s Fetched 695 kB in 1s (731 kB/s) 607s Reading package lists... 607s autopkgtest [13:16:07]: upgrading testbed (apt dist-upgrade and autopurge) 608s Reading package lists... 608s Building dependency tree... 608s Reading state information... 608s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 608s Starting 2 pkgProblemResolver with broken count: 0 608s Done 608s Entering ResolveByKeep 608s 608s Calculating upgrade... 608s The following packages will be upgraded: 608s apparmor apt apt-utils dpkg dpkg-dev fwupd gcc-14-base ibverbs-providers 608s libapparmor1 libapt-pkg7.0 libdpkg-perl libfwupd3 libibverbs1 libldap-common 608s libldap2 libxmlb2 ubuntu-pro-client ubuntu-pro-client-l10n 609s 18 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 609s Need to get 12.7 MB of archives. 609s After this operation, 180 kB of additional disk space will be used. 609s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libapt-pkg7.0 s390x 2.9.34 [1114 kB] 609s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x dpkg s390x 1.22.18ubuntu2 [1300 kB] 609s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x apt s390x 2.9.34 [1424 kB] 609s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x apt-utils s390x 2.9.34 [215 kB] 609s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14-base s390x 14.2.0-19ubuntu1 [53.9 kB] 609s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libapparmor1 s390x 4.1.0~beta5-0ubuntu11 [55.0 kB] 609s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x ubuntu-pro-client-l10n s390x 35 [19.7 kB] 609s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x ubuntu-pro-client s390x 35 [257 kB] 609s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x apparmor s390x 4.1.0~beta5-0ubuntu11 [759 kB] 609s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libibverbs1 s390x 56.0-3ubuntu1 [70.0 kB] 609s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x ibverbs-providers s390x 56.0-3ubuntu1 [415 kB] 609s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x dpkg-dev all 1.22.18ubuntu2 [1089 kB] 610s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libdpkg-perl all 1.22.18ubuntu2 [281 kB] 610s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x fwupd s390x 2.0.6-7 [5235 kB] 611s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libfwupd3 s390x 2.0.6-7 [134 kB] 611s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libxmlb2 s390x 0.3.22-1 [69.2 kB] 611s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libldap-common all 2.6.9+dfsg-2ubuntu1 [35.5 kB] 611s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libldap2 s390x 2.6.9+dfsg-2ubuntu1 [206 kB] 611s Preconfiguring packages ... 611s Fetched 12.7 MB in 2s (7560 kB/s) 611s (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 ... 81426 files and directories currently installed.) 611s Preparing to unpack .../libapt-pkg7.0_2.9.34_s390x.deb ... 611s Unpacking libapt-pkg7.0:s390x (2.9.34) over (2.9.33) ... 611s Setting up libapt-pkg7.0:s390x (2.9.34) ... 611s (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 ... 81426 files and directories currently installed.) 611s Preparing to unpack .../dpkg_1.22.18ubuntu2_s390x.deb ... 611s Unpacking dpkg (1.22.18ubuntu2) over (1.22.15ubuntu1) ... 611s Setting up dpkg (1.22.18ubuntu2) ... 611s (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 ... 81425 files and directories currently installed.) 611s Preparing to unpack .../archives/apt_2.9.34_s390x.deb ... 611s Unpacking apt (2.9.34) over (2.9.33) ... 611s Setting up apt (2.9.34) ... 611s (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 ... 81425 files and directories currently installed.) 611s Preparing to unpack .../00-apt-utils_2.9.34_s390x.deb ... 611s Unpacking apt-utils (2.9.34) over (2.9.33) ... 611s Preparing to unpack .../01-gcc-14-base_14.2.0-19ubuntu1_s390x.deb ... 611s Unpacking gcc-14-base:s390x (14.2.0-19ubuntu1) over (14.2.0-17ubuntu3) ... 611s Preparing to unpack .../02-libapparmor1_4.1.0~beta5-0ubuntu11_s390x.deb ... 611s Unpacking libapparmor1:s390x (4.1.0~beta5-0ubuntu11) over (4.1.0~beta5-0ubuntu9) ... 611s Preparing to unpack .../03-ubuntu-pro-client-l10n_35_s390x.deb ... 611s Unpacking ubuntu-pro-client-l10n (35) over (34.1.3) ... 612s Preparing to unpack .../04-ubuntu-pro-client_35_s390x.deb ... 612s Unpacking ubuntu-pro-client (35) over (34.1.3) ... 612s Preparing to unpack .../05-apparmor_4.1.0~beta5-0ubuntu11_s390x.deb ... 612s Unpacking apparmor (4.1.0~beta5-0ubuntu11) over (4.1.0~beta5-0ubuntu9) ... 612s Preparing to unpack .../06-libibverbs1_56.0-3ubuntu1_s390x.deb ... 612s Unpacking libibverbs1:s390x (56.0-3ubuntu1) over (55.0-1ubuntu1) ... 612s Preparing to unpack .../07-ibverbs-providers_56.0-3ubuntu1_s390x.deb ... 612s Unpacking ibverbs-providers:s390x (56.0-3ubuntu1) over (55.0-1ubuntu1) ... 612s Preparing to unpack .../08-dpkg-dev_1.22.18ubuntu2_all.deb ... 612s Unpacking dpkg-dev (1.22.18ubuntu2) over (1.22.15ubuntu1) ... 612s Preparing to unpack .../09-libdpkg-perl_1.22.18ubuntu2_all.deb ... 612s Unpacking libdpkg-perl (1.22.18ubuntu2) over (1.22.15ubuntu1) ... 612s Preparing to unpack .../10-fwupd_2.0.6-7_s390x.deb ... 612s Unpacking fwupd (2.0.6-7) over (2.0.6-5) ... 612s Preparing to unpack .../11-libfwupd3_2.0.6-7_s390x.deb ... 612s Unpacking libfwupd3:s390x (2.0.6-7) over (2.0.6-5) ... 612s Preparing to unpack .../12-libxmlb2_0.3.22-1_s390x.deb ... 612s Unpacking libxmlb2:s390x (0.3.22-1) over (0.3.21-1) ... 612s Preparing to unpack .../13-libldap-common_2.6.9+dfsg-2ubuntu1_all.deb ... 612s Unpacking libldap-common (2.6.9+dfsg-2ubuntu1) over (2.6.9+dfsg-1~exp2ubuntu1) ... 613s Preparing to unpack .../14-libldap2_2.6.9+dfsg-2ubuntu1_s390x.deb ... 613s Unpacking libldap2:s390x (2.6.9+dfsg-2ubuntu1) over (2.6.9+dfsg-1~exp2ubuntu1) ... 613s Setting up libibverbs1:s390x (56.0-3ubuntu1) ... 613s Setting up libapparmor1:s390x (4.1.0~beta5-0ubuntu11) ... 613s Setting up apt-utils (2.9.34) ... 613s Setting up ibverbs-providers:s390x (56.0-3ubuntu1) ... 613s Setting up gcc-14-base:s390x (14.2.0-19ubuntu1) ... 613s Setting up libxmlb2:s390x (0.3.22-1) ... 613s Setting up libfwupd3:s390x (2.0.6-7) ... 613s Setting up libldap-common (2.6.9+dfsg-2ubuntu1) ... 613s Setting up apparmor (4.1.0~beta5-0ubuntu11) ... 613s Reloading AppArmor profiles 615s Setting up libdpkg-perl (1.22.18ubuntu2) ... 615s Setting up ubuntu-pro-client (35) ... 615s Installing new version of config file /etc/apparmor.d/ubuntu_pro_apt_news ... 615s Installing new version of config file /etc/apt/apt.conf.d/20apt-esm-hook.conf ... 616s Setting up libldap2:s390x (2.6.9+dfsg-2ubuntu1) ... 616s Setting up fwupd (2.0.6-7) ... 616s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 616s fwupd.service is a disabled or a static unit not running, not starting it. 616s Setting up ubuntu-pro-client-l10n (35) ... 616s Setting up dpkg-dev (1.22.18ubuntu2) ... 616s Processing triggers for libc-bin (2.41-1ubuntu2) ... 616s Processing triggers for systemd (257.4-1ubuntu1) ... 616s Processing triggers for man-db (2.13.0-1) ... 618s Processing triggers for dbus (1.16.2-2ubuntu1) ... 619s Reading package lists... 619s Building dependency tree... 619s Reading state information... 619s Starting pkgProblemResolver with broken count: 0 619s Starting 2 pkgProblemResolver with broken count: 0 619s Done 619s Solving dependencies... 619s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 619s autopkgtest [13:16:19]: rebooting testbed after setup commands that affected boot 638s autopkgtest [13:16:38]: testbed running kernel: Linux 6.14.0-11-generic #11-Ubuntu SMP Mon Mar 17 11:24:17 UTC 2025 641s autopkgtest [13:16:41]: @@@@@@@@@@@@@@@@@@@@ apt-source cctbx 649s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe cctbx 2024.10+ds2+~3.22.1+ds1-4build2 (dsc) [4106 B] 649s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe cctbx 2024.10+ds2+~3.22.1+ds1-4build2 (tar) [378 kB] 649s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe cctbx 2024.10+ds2+~3.22.1+ds1-4build2 (tar) [23.9 MB] 649s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe cctbx 2024.10+ds2+~3.22.1+ds1-4build2 (diff) [418 kB] 649s gpgv: Signature made Tue Mar 4 14:45:06 2025 UTC 649s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 649s gpgv: Can't check signature: No public key 649s dpkg-source: warning: cannot verify inline signature for ./cctbx_2024.10+ds2+~3.22.1+ds1-4build2.dsc: no acceptable signature found 651s autopkgtest [13:16:51]: testing package cctbx version 2024.10+ds2+~3.22.1+ds1-4build2 653s autopkgtest [13:16:53]: build not needed 659s autopkgtest [13:16:59]: test cctbx: preparing testbed 659s Reading package lists... 660s Building dependency tree... 660s Reading state information... 660s Starting pkgProblemResolver with broken count: 0 660s Starting 2 pkgProblemResolver with broken count: 0 660s Done 660s The following NEW packages will be installed: 660s adwaita-icon-theme at-spi2-common blt cpp cpp-14 cpp-14-s390x-linux-gnu 660s cpp-s390x-linux-gnu dconf-gsettings-backend dconf-service fontconfig 660s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 660s fonts-lato fonts-lyx g++ g++-14 g++-14-s390x-linux-gnu g++-s390x-linux-gnu 660s gcc gcc-14 gcc-14-s390x-linux-gnu gcc-s390x-linux-gnu gtk-update-icon-cache 660s hicolor-icon-theme libaec0 libann-cctbx-dev libann-cctbx0 libantlr3c-3.4-0 660s libasan8 libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 660s libavahi-client3 libavahi-common-data libavahi-common3 libblas3 660s libboost-numpy1.83.0 libboost-python-dev libboost-python1.83-dev 660s libboost-python1.83.0 libboost-thread1.83.0 libboost-timer1.83.0 660s libboost1.83-dev libcairo-gobject2 libcairo2 libcbf1t64 libcc1-0 660s libccp4-data libccp4-dev libccp4c0t64 libccp4f0t64 libcctbx-dev libcctbx0 660s libcolord2 libcups2t64 libdatrie1 libdconf1 libdeflate0 660s libdouble-conversion3 libegl-mesa0 libegl1 libepoxy0 libexpat1-dev 660s libfontconfig1 libfreetype6 libgbm1 libgcc-14-dev libgdk-pixbuf-2.0-0 660s libgdk-pixbuf2.0-common libgfortran5 libgl1 libgl1-mesa-dri libglew2.2 660s libglu1-mesa libglut3.12 libglvnd0 libglx-mesa0 libglx0 libgomp1 660s libgraphite2-3 libgtk-3-0t64 libgtk-3-common libharfbuzz0b libhdf5-310 660s libhdf5-hl-310 libice6 libimagequant0 libinput-bin libinput10 libisl23 660s libitm1 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 660s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 liblzf1 660s libmd4c0 libmmdb2-0 libmpc3 libmtdev1t64 libnetcdf22 libnotify4 libopengl0 660s libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 660s libpcre2-16-0 libpcre2-32-0 libpixman-1-0 libpython3-dev libpython3.13-dev 660s libqhull-r8.0 libqt5core5t64 libqt5dbus5t64 libqt5designer5 libqt5gui5t64 660s libqt5help5 libqt5network5t64 libqt5opengl5t64 libqt5printsupport5t64 660s libqt5sql5t64 libqt5test5t64 libqt5widgets5t64 libqt5xml5t64 libraqm0 660s libsharpyuv0 libsm6 libssm2 libstdc++-14-dev libsz2 libtcl8.6 libthai-data 660s libthai0 libtiff6 libtk8.6 libubsan1 libvulkan1 libwacom-common libwacom9 660s libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 660s libwebp7 libwebpdemux2 libwebpmux3 libwxbase3.2-1t64 libwxgtk-gl3.2-1t64 660s libwxgtk3.2-1t64 libx11-xcb1 libxcb-dri3-0 libxcb-glx0 libxcb-icccm4 660s libxcb-image0 libxcb-keysyms1 libxcb-present0 libxcb-randr0 660s libxcb-render-util0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 660s libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 660s libxcomposite1 libxcursor1 libxdamage1 libxfixes3 libxft2 libxi6 660s libxinerama1 libxkbcommon-x11-0 libxrandr2 libxrender1 libxshmfence1 660s libxslt1.1 libxss1 libxtst6 libxxf86vm1 mesa-libgallium pymol-data 660s python-matplotlib-data python3-all python3-brotli python3-cctbx 660s python3-contourpy python3-cycler python3-dateutil python3-decorator 660s python3-dev python3-flexcache python3-flexparser python3-fonttools 660s python3-fs python3-h5py python3-h5py-serial python3-hdf5plugin 660s python3-iniconfig python3-kiwisolver python3-legacy-cgi python3-lxml 660s python3-lz4 python3-matplotlib python3-mpmath python3-mrcfile 660s python3-natsort python3-numpy python3-numpy-dev python3-nxmx python3-opengl 660s python3-ordered-set python3-packaging python3-pil python3-pil.imagetk 660s python3-pint python3-platformdirs python3-pluggy python3-procrunner 660s python3-pycbf python3-pymol python3-pyqt5 python3-pyqt5.qtopengl 660s python3-pyqt5.sip python3-pytest python3-scipy python3-six python3-sympy 660s python3-tk python3-tqdm python3-ufolib2 python3-wxgtk4.0 python3.13-dev 660s python3.13-tk sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data x11-common 660s zlib1g-dev 660s 0 upgraded, 250 newly installed, 0 to remove and 0 not upgraded. 660s Need to get 237 MB of archives. 660s After this operation, 1112 MB of additional disk space will be used. 660s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-lato all 2.015-1 [2781 kB] 664s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy-dev s390x 1:2.2.3+ds-5 [147 kB] 665s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 665s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250315-1ubuntu1 [620 kB] 666s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 670s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:2.2.3+ds-5 [4396 kB] 676s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [8004 B] 676s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB] 676s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 676s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 676s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 676s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 676s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 677s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 677s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libgdk-pixbuf-2.0-0 s390x 2.42.12+dfsg-2 [154 kB] 677s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x gtk-update-icon-cache s390x 4.18.2+ds-1 [53.2 kB] 677s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x hicolor-icon-theme all 0.18-2 [13.3 kB] 677s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x adwaita-icon-theme all 48.0-1 [578 kB] 678s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x at-spi2-common all 2.56.0-2 [9108 B] 678s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libtcl8.6 s390x 8.6.16+dfsg-1 [1034 kB] 679s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 680s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 681s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 682s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-2.1ubuntu1 [37.7 kB] 682s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-2.1ubuntu1 [150 kB] 682s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 682s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB] 682s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] 682s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B] 682s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libtk8.6 s390x 8.6.16-1 [830 kB] 683s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x tk8.6-blt2.5 s390x 2.5.3+dfsg-8 [657 kB] 684s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x blt s390x 2.5.3+dfsg-8 [4826 B] 684s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libisl23 s390x 0.27-1 [704 kB] 685s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libmpc3 s390x 1.3.1-1build2 [57.8 kB] 685s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14-s390x-linux-gnu s390x 14.2.0-19ubuntu1 [9571 kB] 698s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14 s390x 14.2.0-19ubuntu1 [1030 B] 698s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [5556 B] 698s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x cpp s390x 4:14.2.0-1ubuntu1 [22.4 kB] 698s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libdconf1 s390x 0.40.0-5 [40.0 kB] 698s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x dconf-service s390x 0.40.0-5 [28.4 kB] 698s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x dconf-gsettings-backend s390x 0.40.0-5 [22.8 kB] 698s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig s390x 2.15.0-2.1ubuntu1 [191 kB] 699s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 699s Get:44 http://ftpmaster.internal/ubuntu plucky/universe s390x fonts-lyx all 2.4.3-1 [171 kB] 700s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x libcc1-0 s390x 15-20250315-1ubuntu1 [49.0 kB] 700s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250315-1ubuntu1 [151 kB] 700s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x libitm1 s390x 15-20250315-1ubuntu1 [31.1 kB] 700s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x libasan8 s390x 15-20250315-1ubuntu1 [2967 kB] 704s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x libubsan1 s390x 15-20250315-1ubuntu1 [1211 kB] 705s Get:50 http://ftpmaster.internal/ubuntu plucky/main s390x libgcc-14-dev s390x 14.2.0-19ubuntu1 [1037 kB] 706s Get:51 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14-s390x-linux-gnu s390x 14.2.0-19ubuntu1 [18.7 MB] 721s Get:52 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14 s390x 14.2.0-19ubuntu1 [528 kB] 721s Get:53 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1204 B] 721s Get:54 http://ftpmaster.internal/ubuntu plucky/main s390x gcc s390x 4:14.2.0-1ubuntu1 [5004 B] 721s Get:55 http://ftpmaster.internal/ubuntu plucky/main s390x libstdc++-14-dev s390x 14.2.0-19ubuntu1 [2615 kB] 723s Get:56 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14-s390x-linux-gnu s390x 14.2.0-19ubuntu1 [11.0 MB] 734s Get:57 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14 s390x 14.2.0-19ubuntu1 [22.2 kB] 734s Get:58 http://ftpmaster.internal/ubuntu plucky/main s390x g++-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [956 B] 734s Get:59 http://ftpmaster.internal/ubuntu plucky/main s390x g++ s390x 4:14.2.0-1ubuntu1 [1080 B] 734s Get:60 http://ftpmaster.internal/ubuntu plucky/universe s390x libaec0 s390x 1.1.3-1 [25.7 kB] 734s Get:61 http://ftpmaster.internal/ubuntu plucky/universe s390x libann-cctbx0 s390x 1.1.2+doc-9build1 [36.2 kB] 734s Get:62 http://ftpmaster.internal/ubuntu plucky/universe s390x libann-cctbx-dev s390x 1.1.2+doc-9build1 [48.1 kB] 734s Get:63 http://ftpmaster.internal/ubuntu plucky/universe s390x libantlr3c-3.4-0 s390x 3.4+dfsg-4build2 [51.3 kB] 735s Get:64 http://ftpmaster.internal/ubuntu plucky/main s390x libatk1.0-0t64 s390x 2.56.0-2 [54.9 kB] 735s Get:65 http://ftpmaster.internal/ubuntu plucky/main s390x libxi6 s390x 2:1.8.2-1 [35.4 kB] 735s Get:66 http://ftpmaster.internal/ubuntu plucky/main s390x libatspi2.0-0t64 s390x 2.56.0-2 [84.0 kB] 735s Get:67 http://ftpmaster.internal/ubuntu plucky/main s390x libatk-bridge2.0-0t64 s390x 2.56.0-2 [66.7 kB] 735s Get:68 http://ftpmaster.internal/ubuntu plucky/main s390x libavahi-common-data s390x 0.8-16ubuntu2 [31.0 kB] 735s Get:69 http://ftpmaster.internal/ubuntu plucky/main s390x libavahi-common3 s390x 0.8-16ubuntu2 [23.5 kB] 735s Get:70 http://ftpmaster.internal/ubuntu plucky/main s390x libavahi-client3 s390x 0.8-16ubuntu2 [26.3 kB] 735s Get:71 http://ftpmaster.internal/ubuntu plucky/main s390x libboost-python1.83.0 s390x 1.83.0-4.1ubuntu2 [313 kB] 736s Get:72 http://ftpmaster.internal/ubuntu plucky/universe s390x libboost-numpy1.83.0 s390x 1.83.0-4.1ubuntu2 [243 kB] 736s Get:73 http://ftpmaster.internal/ubuntu plucky/main s390x libboost1.83-dev s390x 1.83.0-4.1ubuntu2 [10.7 MB] 747s Get:74 http://ftpmaster.internal/ubuntu plucky/main s390x libexpat1-dev s390x 2.6.4-1 [146 kB] 747s Get:75 http://ftpmaster.internal/ubuntu plucky/main s390x zlib1g-dev s390x 1:1.3.dfsg+really1.3.1-1ubuntu1 [898 kB] 748s Get:76 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-dev s390x 3.13.2-2 [5597 kB] 754s Get:77 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3-dev s390x 3.13.2-2 [10.7 kB] 754s Get:78 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-dev s390x 3.13.2-2 [513 kB] 755s Get:79 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 755s Get:80 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 756s Get:81 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 756s Get:82 http://ftpmaster.internal/ubuntu plucky/main s390x python3-dev s390x 3.13.2-2 [26.7 kB] 756s Get:83 http://ftpmaster.internal/ubuntu plucky/universe s390x libboost-python1.83-dev s390x 1.83.0-4.1ubuntu2 [335 kB] 756s Get:84 http://ftpmaster.internal/ubuntu plucky/universe s390x libboost-python-dev s390x 1.83.0.2ubuntu1 [4518 B] 756s Get:85 http://ftpmaster.internal/ubuntu plucky/main s390x libboost-thread1.83.0 s390x 1.83.0-4.1ubuntu2 [279 kB] 757s Get:86 http://ftpmaster.internal/ubuntu plucky/universe s390x libboost-timer1.83.0 s390x 1.83.0-4.1ubuntu2 [241 kB] 757s Get:87 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 757s Get:88 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 757s Get:89 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 757s Get:90 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.4-1 [580 kB] 758s Get:91 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo-gobject2 s390x 1.18.4-1 [127 kB] 758s Get:92 http://ftpmaster.internal/ubuntu plucky/universe s390x libsz2 s390x 1.1.3-1 [5442 B] 758s Get:93 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-310 s390x 1.14.5+repack-3 [1477 kB] 759s Get:94 http://ftpmaster.internal/ubuntu plucky/universe s390x libcbf1t64 s390x 0.9.7+dfsg1-5build1 [391 kB] 760s Get:95 http://ftpmaster.internal/ubuntu plucky/universe s390x libccp4-data all 8.0.0-4 [65.2 kB] 760s Get:96 http://ftpmaster.internal/ubuntu plucky/universe s390x libccp4c0t64 s390x 8.0.0-4 [104 kB] 760s Get:97 http://ftpmaster.internal/ubuntu plucky/universe s390x libmmdb2-0 s390x 2.0.22-1 [351 kB] 760s Get:98 http://ftpmaster.internal/ubuntu plucky/universe s390x libccp4f0t64 s390x 8.0.0-4 [224 kB] 760s Get:99 http://ftpmaster.internal/ubuntu plucky/universe s390x libccp4-dev s390x 8.0.0-4 [42.4 kB] 761s Get:100 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x libcctbx0 s390x 2024.10+ds2+~3.22.1+ds1-4build2 [2003 kB] 763s Get:101 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x libcctbx-dev s390x 2024.10+ds2+~3.22.1+ds1-4build2 [1192 kB] 764s Get:102 http://ftpmaster.internal/ubuntu plucky/main s390x liblcms2-2 s390x 2.16-2 [175 kB] 764s Get:103 http://ftpmaster.internal/ubuntu plucky/main s390x libcolord2 s390x 1.4.7-3 [149 kB] 764s Get:104 http://ftpmaster.internal/ubuntu plucky/main s390x libcups2t64 s390x 2.4.11-0ubuntu2 [282 kB] 765s Get:105 http://ftpmaster.internal/ubuntu plucky/main s390x libdatrie1 s390x 0.2.13-3build1 [20.6 kB] 765s Get:106 http://ftpmaster.internal/ubuntu plucky/universe s390x libdouble-conversion3 s390x 3.3.1-1 [43.3 kB] 765s Get:107 http://ftpmaster.internal/ubuntu plucky/main s390x libwayland-server0 s390x 1.23.1-3 [37.3 kB] 765s Get:108 http://ftpmaster.internal/ubuntu plucky/main s390x libx11-xcb1 s390x 2:1.8.10-2 [7954 B] 765s Get:109 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-dri3-0 s390x 1.17.0-2 [7616 B] 765s Get:110 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-present0 s390x 1.17.0-2 [6244 B] 765s Get:111 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-randr0 s390x 1.17.0-2 [19.2 kB] 765s Get:112 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-sync1 s390x 1.17.0-2 [9488 B] 765s Get:113 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-xfixes0 s390x 1.17.0-2 [10.5 kB] 766s Get:114 http://ftpmaster.internal/ubuntu plucky/main s390x libxshmfence1 s390x 1.3-1build5 [4772 B] 766s Get:115 http://ftpmaster.internal/ubuntu plucky/main s390x mesa-libgallium s390x 25.0.1-2ubuntu2 [8056 kB] 772s Get:116 http://ftpmaster.internal/ubuntu plucky/main s390x libgbm1 s390x 25.0.1-2ubuntu2 [34.5 kB] 772s Get:117 http://ftpmaster.internal/ubuntu plucky/main s390x libwayland-client0 s390x 1.23.1-3 [28.2 kB] 772s Get:118 http://ftpmaster.internal/ubuntu plucky/main s390x libegl-mesa0 s390x 25.0.1-2ubuntu2 [126 kB] 773s Get:119 http://ftpmaster.internal/ubuntu plucky/main s390x libepoxy0 s390x 1.5.10-2 [222 kB] 773s Get:120 http://ftpmaster.internal/ubuntu plucky/main s390x libvulkan1 s390x 1.4.304.0-1 [147 kB] 773s Get:121 http://ftpmaster.internal/ubuntu plucky/main s390x libgl1-mesa-dri s390x 25.0.1-2ubuntu2 [35.4 kB] 773s Get:122 http://ftpmaster.internal/ubuntu plucky/main s390x libglvnd0 s390x 1.7.0-1build1 [110 kB] 773s Get:123 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-glx0 s390x 1.17.0-2 [26.0 kB] 774s Get:124 http://ftpmaster.internal/ubuntu plucky/main s390x libxxf86vm1 s390x 1:1.1.4-1build4 [9630 B] 774s Get:125 http://ftpmaster.internal/ubuntu plucky/main s390x libglx-mesa0 s390x 25.0.1-2ubuntu2 [161 kB] 774s Get:126 http://ftpmaster.internal/ubuntu plucky/main s390x libglx0 s390x 1.7.0-1build1 [32.2 kB] 774s Get:127 http://ftpmaster.internal/ubuntu plucky/main s390x libgl1 s390x 1.7.0-1build1 [142 kB] 774s Get:128 http://ftpmaster.internal/ubuntu plucky/universe s390x libglew2.2 s390x 2.2.0-4build1 [195 kB] 774s Get:129 http://ftpmaster.internal/ubuntu plucky/universe s390x libglut3.12 s390x 3.4.0-4 [99.3 kB] 775s Get:130 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 775s Get:131 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB] 775s Get:132 http://ftpmaster.internal/ubuntu plucky/main s390x libthai-data all 0.1.29-2build1 [158 kB] 776s Get:133 http://ftpmaster.internal/ubuntu plucky/main s390x libthai0 s390x 0.1.29-2build1 [20.7 kB] 776s Get:134 http://ftpmaster.internal/ubuntu plucky/main s390x libpango-1.0-0 s390x 1.56.3-1 [254 kB] 776s Get:135 http://ftpmaster.internal/ubuntu plucky/main s390x libpangoft2-1.0-0 s390x 1.56.3-1 [50.5 kB] 776s Get:136 http://ftpmaster.internal/ubuntu plucky/main s390x libpangocairo-1.0-0 s390x 1.56.3-1 [28.2 kB] 776s Get:137 http://ftpmaster.internal/ubuntu plucky/main s390x libwayland-cursor0 s390x 1.23.1-3 [11.5 kB] 776s Get:138 http://ftpmaster.internal/ubuntu plucky/main s390x libwayland-egl1 s390x 1.23.1-3 [6078 B] 776s Get:139 http://ftpmaster.internal/ubuntu plucky/main s390x libxcomposite1 s390x 1:0.4.6-1 [6588 B] 777s Get:140 http://ftpmaster.internal/ubuntu plucky/main s390x libxfixes3 s390x 1:6.0.0-2build1 [11.3 kB] 777s Get:141 http://ftpmaster.internal/ubuntu plucky/main s390x libxcursor1 s390x 1:1.2.3-1 [23.4 kB] 777s Get:142 http://ftpmaster.internal/ubuntu plucky/main s390x libxdamage1 s390x 1:1.1.6-1build1 [6156 B] 777s Get:143 http://ftpmaster.internal/ubuntu plucky/main s390x libxinerama1 s390x 2:1.1.4-3build1 [6476 B] 777s Get:144 http://ftpmaster.internal/ubuntu plucky/main s390x libxrandr2 s390x 2:1.5.4-1 [20.8 kB] 777s Get:145 http://ftpmaster.internal/ubuntu plucky/main s390x libgtk-3-common all 3.24.49-2ubuntu1 [1424 kB] 778s Get:146 http://ftpmaster.internal/ubuntu plucky/main s390x libgtk-3-0t64 s390x 3.24.49-2ubuntu1 [2950 kB] 781s Get:147 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-hl-310 s390x 1.14.5+repack-3 [61.0 kB] 781s Get:148 http://ftpmaster.internal/ubuntu plucky/main s390x libice6 s390x 2:1.1.1-1 [45.4 kB] 781s Get:149 http://ftpmaster.internal/ubuntu plucky/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 781s Get:150 http://ftpmaster.internal/ubuntu plucky/main s390x libwacom-common all 2.14.0-1 [103 kB] 782s Get:151 http://ftpmaster.internal/ubuntu plucky/main s390x libwacom9 s390x 2.14.0-1 [27.1 kB] 782s Get:152 http://ftpmaster.internal/ubuntu plucky/main s390x libinput-bin s390x 1.27.1-1 [23.3 kB] 782s Get:153 http://ftpmaster.internal/ubuntu plucky/main s390x libmtdev1t64 s390x 1.1.7-1 [15.6 kB] 782s Get:154 http://ftpmaster.internal/ubuntu plucky/main s390x libinput10 s390x 1.27.1-1 [139 kB] 782s Get:155 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 782s Get:156 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 783s Get:157 http://ftpmaster.internal/ubuntu plucky/universe s390x liblzf1 s390x 3.6-4 [7020 B] 783s Get:158 http://ftpmaster.internal/ubuntu plucky/universe s390x libmd4c0 s390x 0.5.2-2 [47.7 kB] 783s Get:159 http://ftpmaster.internal/ubuntu plucky/universe s390x libnetcdf22 s390x 1:4.9.3-1 [533 kB] 783s Get:160 http://ftpmaster.internal/ubuntu plucky/main s390x libnotify4 s390x 0.8.4-1 [25.9 kB] 784s Get:161 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-16-0 s390x 10.45-1 [259 kB] 784s Get:162 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-32-0 s390x 10.45-1 [245 kB] 784s Get:163 http://ftpmaster.internal/ubuntu plucky/universe s390x libqhull-r8.0 s390x 2020.2-6build1 [199 kB] 784s Get:164 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5core5t64 s390x 5.15.15+dfsg-4ubuntu1 [2242 kB] 787s Get:165 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5dbus5t64 s390x 5.15.15+dfsg-4ubuntu1 [240 kB] 787s Get:166 http://ftpmaster.internal/ubuntu plucky/main s390x libegl1 s390x 1.7.0-1build1 [31.8 kB] 787s Get:167 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5network5t64 s390x 5.15.15+dfsg-4ubuntu1 [788 kB] 788s Get:168 http://ftpmaster.internal/ubuntu plucky/main s390x libsm6 s390x 2:1.2.4-1 [18.4 kB] 788s Get:169 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-icccm4 s390x 0.4.2-1 [11.4 kB] 788s Get:170 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-util1 s390x 0.4.1-1 [10.7 kB] 788s Get:171 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-image0 s390x 0.4.0-2build1 [12.0 kB] 788s Get:172 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-keysyms1 s390x 0.4.1-1 [8908 B] 788s Get:173 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render-util0 s390x 0.3.10-1 [10.3 kB] 788s Get:174 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shape0 s390x 1.17.0-2 [6202 B] 788s Get:175 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-xinerama0 s390x 1.17.0-2 [5430 B] 788s Get:176 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-xinput0 s390x 1.17.0-2 [35.8 kB] 789s Get:177 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-xkb1 s390x 1.17.0-2 [34.5 kB] 789s Get:178 http://ftpmaster.internal/ubuntu plucky/main s390x libxkbcommon-x11-0 s390x 1.7.0-2 [14.8 kB] 789s Get:179 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5gui5t64 s390x 5.15.15+dfsg-4ubuntu1 [4187 kB] 793s Get:180 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5widgets5t64 s390x 5.15.15+dfsg-4ubuntu1 [2718 kB] 795s Get:181 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5xml5t64 s390x 5.15.15+dfsg-4ubuntu1 [129 kB] 795s Get:182 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5designer5 s390x 5.15.15-6build1 [2900 kB] 798s Get:183 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5sql5t64 s390x 5.15.15+dfsg-4ubuntu1 [130 kB] 798s Get:184 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5help5 s390x 5.15.15-6build1 [172 kB] 798s Get:185 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5opengl5t64 s390x 5.15.15+dfsg-4ubuntu1 [156 kB] 798s Get:186 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5printsupport5t64 s390x 5.15.15+dfsg-4ubuntu1 [218 kB] 799s Get:187 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5test5t64 s390x 5.15.15+dfsg-4ubuntu1 [156 kB] 799s Get:188 http://ftpmaster.internal/ubuntu plucky/main s390x libraqm0 s390x 0.10.2-1 [15.8 kB] 799s Get:189 http://ftpmaster.internal/ubuntu plucky/universe s390x libssm2 s390x 1.4.0-2build1 [97.8 kB] 799s Get:190 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpdemux2 s390x 1.5.0-0.1 [12.6 kB] 799s Get:191 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpmux3 s390x 1.5.0-0.1 [25.8 kB] 799s Get:192 http://ftpmaster.internal/ubuntu plucky/universe s390x libwxbase3.2-1t64 s390x 3.2.6+dfsg-2ubuntu1 [915 kB] 800s Get:193 http://ftpmaster.internal/ubuntu plucky/main s390x libxtst6 s390x 2:1.2.5-1 [13.5 kB] 800s Get:194 http://ftpmaster.internal/ubuntu plucky/universe s390x libwxgtk3.2-1t64 s390x 3.2.6+dfsg-2ubuntu1 [4737 kB] 804s Get:195 http://ftpmaster.internal/ubuntu plucky/universe s390x libwxgtk-gl3.2-1t64 s390x 3.2.6+dfsg-2ubuntu1 [52.9 kB] 804s Get:196 http://ftpmaster.internal/ubuntu plucky/main s390x libxslt1.1 s390x 1.1.39-0exp1ubuntu4 [170 kB] 804s Get:197 http://ftpmaster.internal/ubuntu plucky/universe s390x pymol-data all 3.1.0+dfsg-1 [1394 kB] 805s Get:198 http://ftpmaster.internal/ubuntu plucky/universe s390x python-matplotlib-data all 3.8.3-7build1 [2934 kB] 808s Get:199 http://ftpmaster.internal/ubuntu plucky/main s390x python3-all s390x 3.13.2-2 [886 B] 808s Get:200 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-brotli s390x 1.1.0-2build4 [380 kB] 808s Get:201 http://ftpmaster.internal/ubuntu plucky/main s390x python3-legacy-cgi all 2.6.2-1 [16.6 kB] 808s Get:202 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pycbf s390x 0.9.7+dfsg1-5build1 [152 kB] 808s Get:203 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py-serial s390x 3.13.0-1 [1185 kB] 810s Get:204 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py all 3.13.0-1 [7978 B] 810s Get:205 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-hdf5plugin all 5.0.0-1 [23.1 kB] 810s Get:206 http://ftpmaster.internal/ubuntu plucky/main s390x python3-dateutil all 2.9.0-4 [80.3 kB] 810s Get:207 http://ftpmaster.internal/ubuntu plucky/main s390x libopenjp2-7 s390x 2.5.3-2 [207 kB] 814s Get:208 http://ftpmaster.internal/ubuntu plucky/main s390x python3-pil s390x 11.1.0-5build1 [498 kB] 814s Get:209 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-tk s390x 3.13.2-2 [108 kB] 814s Get:210 http://ftpmaster.internal/ubuntu plucky/main s390x python3-tk s390x 3.13.2-1 [9820 B] 814s Get:211 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pil.imagetk s390x 11.1.0-5build1 [9668 B] 814s Get:212 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-contourpy s390x 1.3.1-1build1 [197 kB] 814s Get:213 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-cycler all 0.12.1-1 [9716 B] 814s Get:214 http://ftpmaster.internal/ubuntu plucky/main s390x python3-platformdirs all 4.3.6-1 [16.8 kB] 814s Get:215 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-fs all 2.4.16-7 [90.8 kB] 814s Get:216 http://ftpmaster.internal/ubuntu plucky/main s390x python3-lxml s390x 5.3.1-1build1 [1370 kB] 814s Get:217 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-lz4 s390x 4.4.0+dfsg-1build1 [26.6 kB] 814s Get:218 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 814s Get:219 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.14.1-4ubuntu2 [18.0 MB] 825s Get:220 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-mpmath all 1.3.0-1 [425 kB] 825s Get:221 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-sympy all 1.13.3-5 [4229 kB] 828s Get:222 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 828s Get:223 http://ftpmaster.internal/ubuntu plucky/universe s390x unicode-data all 15.1.0-1 [8878 kB] 833s Get:224 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-fonttools s390x 4.55.3-2build1 [1496 kB] 835s Get:225 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-kiwisolver s390x 1.4.7-3build1 [55.0 kB] 835s Get:226 http://ftpmaster.internal/ubuntu plucky/main s390x python3-packaging all 24.2-1 [51.5 kB] 835s Get:227 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-matplotlib s390x 3.8.3-7build1 [17.3 MB] 848s Get:228 http://ftpmaster.internal/ubuntu plucky/main s390x sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 848s Get:229 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-mrcfile all 1.5.4-2 [116 kB] 849s Get:230 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-natsort all 8.0.2-2 [33.8 kB] 849s Get:231 http://ftpmaster.internal/ubuntu plucky/main s390x python3-flexcache all 0.3-2 [13.4 kB] 849s Get:232 http://ftpmaster.internal/ubuntu plucky/main s390x python3-flexparser all 0.4-1 [43.8 kB] 849s Get:233 http://ftpmaster.internal/ubuntu plucky/main s390x python3-pint all 0.24.4-1 [203 kB] 849s Get:234 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-nxmx all 0.0.4-1 [16.4 kB] 849s Get:235 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-ordered-set all 4.1.0-1 [9778 B] 849s Get:236 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-procrunner all 2.3.3-2 [12.0 kB] 850s Get:237 http://ftpmaster.internal/ubuntu plucky/main s390x libopengl0 s390x 1.7.0-1build1 [48.0 kB] 850s Get:238 http://ftpmaster.internal/ubuntu plucky/main s390x libglu1-mesa s390x 9.0.2-1.1build1 [176 kB] 850s Get:239 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-opengl all 3.1.9+dfsg-1syncable1 [631 kB] 851s Get:240 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pyqt5.sip s390x 12.17.0-1build1 [66.5 kB] 851s Get:241 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pyqt5 s390x 5.15.11+dfsg-2 [2880 kB] 853s Get:242 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pyqt5.qtopengl s390x 5.15.11+dfsg-2 [140 kB] 854s Get:243 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pymol s390x 3.1.0+dfsg-1 [4292 kB] 857s Get:244 http://ftpmaster.internal/ubuntu plucky/main s390x python3-six all 1.17.0-1 [13.2 kB] 857s Get:245 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-tqdm all 4.67.1-2 [92.5 kB] 857s Get:246 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-wxgtk4.0 s390x 4.2.2+dfsg-3build1 [7757 kB] 863s Get:247 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x python3-cctbx s390x 2024.10+ds2+~3.22.1+ds1-4build2 [28.1 MB] 885s Get:248 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-iniconfig all 1.1.1-2 [6024 B] 885s Get:249 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pluggy all 1.5.0-1 [21.0 kB] 885s Get:250 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pytest all 8.3.5-1 [252 kB] 886s Fetched 237 MB in 3min 45s (1055 kB/s) 886s Selecting previously unselected package fonts-lato. 886s (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 ... 81447 files and directories currently installed.) 886s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ... 886s Unpacking fonts-lato (2.015-1) ... 886s Selecting previously unselected package python3-numpy-dev:s390x. 886s Preparing to unpack .../001-python3-numpy-dev_1%3a2.2.3+ds-5_s390x.deb ... 886s Unpacking python3-numpy-dev:s390x (1:2.2.3+ds-5) ... 886s Selecting previously unselected package libblas3:s390x. 886s Preparing to unpack .../002-libblas3_3.12.1-2_s390x.deb ... 886s Unpacking libblas3:s390x (3.12.1-2) ... 886s Selecting previously unselected package libgfortran5:s390x. 886s Preparing to unpack .../003-libgfortran5_15-20250315-1ubuntu1_s390x.deb ... 886s Unpacking libgfortran5:s390x (15-20250315-1ubuntu1) ... 886s Selecting previously unselected package liblapack3:s390x. 886s Preparing to unpack .../004-liblapack3_3.12.1-2_s390x.deb ... 886s Unpacking liblapack3:s390x (3.12.1-2) ... 886s Selecting previously unselected package python3-numpy. 886s Preparing to unpack .../005-python3-numpy_1%3a2.2.3+ds-5_s390x.deb ... 886s Unpacking python3-numpy (1:2.2.3+ds-5) ... 886s Selecting previously unselected package libgdk-pixbuf2.0-common. 886s Preparing to unpack .../006-libgdk-pixbuf2.0-common_2.42.12+dfsg-2_all.deb ... 886s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... 886s Selecting previously unselected package libjpeg-turbo8:s390x. 886s Preparing to unpack .../007-libjpeg-turbo8_2.1.5-3ubuntu2_s390x.deb ... 886s Unpacking libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 886s Selecting previously unselected package libjpeg8:s390x. 886s Preparing to unpack .../008-libjpeg8_8c-2ubuntu11_s390x.deb ... 886s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 886s Selecting previously unselected package libdeflate0:s390x. 886s Preparing to unpack .../009-libdeflate0_1.23-1_s390x.deb ... 886s Unpacking libdeflate0:s390x (1.23-1) ... 886s Selecting previously unselected package libjbig0:s390x. 886s Preparing to unpack .../010-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 886s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 886s Selecting previously unselected package libsharpyuv0:s390x. 886s Preparing to unpack .../011-libsharpyuv0_1.5.0-0.1_s390x.deb ... 886s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ... 886s Selecting previously unselected package libwebp7:s390x. 886s Preparing to unpack .../012-libwebp7_1.5.0-0.1_s390x.deb ... 886s Unpacking libwebp7:s390x (1.5.0-0.1) ... 886s Selecting previously unselected package libtiff6:s390x. 886s Preparing to unpack .../013-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ... 886s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 886s Selecting previously unselected package libgdk-pixbuf-2.0-0:s390x. 886s Preparing to unpack .../014-libgdk-pixbuf-2.0-0_2.42.12+dfsg-2_s390x.deb ... 886s Unpacking libgdk-pixbuf-2.0-0:s390x (2.42.12+dfsg-2) ... 886s Selecting previously unselected package gtk-update-icon-cache. 886s Preparing to unpack .../015-gtk-update-icon-cache_4.18.2+ds-1_s390x.deb ... 886s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 886s 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. 886s Unpacking gtk-update-icon-cache (4.18.2+ds-1) ... 886s Selecting previously unselected package hicolor-icon-theme. 886s Preparing to unpack .../016-hicolor-icon-theme_0.18-2_all.deb ... 886s Unpacking hicolor-icon-theme (0.18-2) ... 886s Selecting previously unselected package adwaita-icon-theme. 886s Preparing to unpack .../017-adwaita-icon-theme_48.0-1_all.deb ... 886s Unpacking adwaita-icon-theme (48.0-1) ... 886s Selecting previously unselected package at-spi2-common. 886s Preparing to unpack .../018-at-spi2-common_2.56.0-2_all.deb ... 886s Unpacking at-spi2-common (2.56.0-2) ... 886s Selecting previously unselected package libtcl8.6:s390x. 886s Preparing to unpack .../019-libtcl8.6_8.6.16+dfsg-1_s390x.deb ... 886s Unpacking libtcl8.6:s390x (8.6.16+dfsg-1) ... 886s Selecting previously unselected package libfreetype6:s390x. 886s Preparing to unpack .../020-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 886s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 887s Selecting previously unselected package fonts-dejavu-mono. 887s Preparing to unpack .../021-fonts-dejavu-mono_2.37-8_all.deb ... 887s Unpacking fonts-dejavu-mono (2.37-8) ... 887s Selecting previously unselected package fonts-dejavu-core. 887s Preparing to unpack .../022-fonts-dejavu-core_2.37-8_all.deb ... 887s Unpacking fonts-dejavu-core (2.37-8) ... 887s Selecting previously unselected package fontconfig-config. 887s Preparing to unpack .../023-fontconfig-config_2.15.0-2.1ubuntu1_s390x.deb ... 887s Unpacking fontconfig-config (2.15.0-2.1ubuntu1) ... 887s Selecting previously unselected package libfontconfig1:s390x. 887s Preparing to unpack .../024-libfontconfig1_2.15.0-2.1ubuntu1_s390x.deb ... 887s Unpacking libfontconfig1:s390x (2.15.0-2.1ubuntu1) ... 887s Selecting previously unselected package libxrender1:s390x. 887s Preparing to unpack .../025-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 887s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 887s Selecting previously unselected package libxft2:s390x. 887s Preparing to unpack .../026-libxft2_2.3.6-1build1_s390x.deb ... 887s Unpacking libxft2:s390x (2.3.6-1build1) ... 887s Selecting previously unselected package x11-common. 887s Preparing to unpack .../027-x11-common_1%3a7.7+23ubuntu3_all.deb ... 887s Unpacking x11-common (1:7.7+23ubuntu3) ... 887s Selecting previously unselected package libxss1:s390x. 887s Preparing to unpack .../028-libxss1_1%3a1.2.3-1build3_s390x.deb ... 887s Unpacking libxss1:s390x (1:1.2.3-1build3) ... 887s Selecting previously unselected package libtk8.6:s390x. 887s Preparing to unpack .../029-libtk8.6_8.6.16-1_s390x.deb ... 887s Unpacking libtk8.6:s390x (8.6.16-1) ... 887s Selecting previously unselected package tk8.6-blt2.5. 887s Preparing to unpack .../030-tk8.6-blt2.5_2.5.3+dfsg-8_s390x.deb ... 887s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 887s Selecting previously unselected package blt. 887s Preparing to unpack .../031-blt_2.5.3+dfsg-8_s390x.deb ... 887s Unpacking blt (2.5.3+dfsg-8) ... 887s Selecting previously unselected package libisl23:s390x. 887s Preparing to unpack .../032-libisl23_0.27-1_s390x.deb ... 887s Unpacking libisl23:s390x (0.27-1) ... 887s Selecting previously unselected package libmpc3:s390x. 887s Preparing to unpack .../033-libmpc3_1.3.1-1build2_s390x.deb ... 887s Unpacking libmpc3:s390x (1.3.1-1build2) ... 887s Selecting previously unselected package cpp-14-s390x-linux-gnu. 887s Preparing to unpack .../034-cpp-14-s390x-linux-gnu_14.2.0-19ubuntu1_s390x.deb ... 887s Unpacking cpp-14-s390x-linux-gnu (14.2.0-19ubuntu1) ... 887s Selecting previously unselected package cpp-14. 887s Preparing to unpack .../035-cpp-14_14.2.0-19ubuntu1_s390x.deb ... 887s Unpacking cpp-14 (14.2.0-19ubuntu1) ... 887s Selecting previously unselected package cpp-s390x-linux-gnu. 887s Preparing to unpack .../036-cpp-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 887s Unpacking cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 887s Selecting previously unselected package cpp. 887s Preparing to unpack .../037-cpp_4%3a14.2.0-1ubuntu1_s390x.deb ... 887s Unpacking cpp (4:14.2.0-1ubuntu1) ... 887s Selecting previously unselected package libdconf1:s390x. 887s Preparing to unpack .../038-libdconf1_0.40.0-5_s390x.deb ... 887s Unpacking libdconf1:s390x (0.40.0-5) ... 887s Selecting previously unselected package dconf-service. 887s Preparing to unpack .../039-dconf-service_0.40.0-5_s390x.deb ... 887s Unpacking dconf-service (0.40.0-5) ... 887s Selecting previously unselected package dconf-gsettings-backend:s390x. 887s Preparing to unpack .../040-dconf-gsettings-backend_0.40.0-5_s390x.deb ... 887s Unpacking dconf-gsettings-backend:s390x (0.40.0-5) ... 887s Selecting previously unselected package fontconfig. 887s Preparing to unpack .../041-fontconfig_2.15.0-2.1ubuntu1_s390x.deb ... 887s Unpacking fontconfig (2.15.0-2.1ubuntu1) ... 887s Selecting previously unselected package fonts-font-awesome. 887s Preparing to unpack .../042-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 887s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 887s Selecting previously unselected package fonts-lyx. 887s Preparing to unpack .../043-fonts-lyx_2.4.3-1_all.deb ... 887s Unpacking fonts-lyx (2.4.3-1) ... 887s Selecting previously unselected package libcc1-0:s390x. 887s Preparing to unpack .../044-libcc1-0_15-20250315-1ubuntu1_s390x.deb ... 887s Unpacking libcc1-0:s390x (15-20250315-1ubuntu1) ... 887s Selecting previously unselected package libgomp1:s390x. 887s Preparing to unpack .../045-libgomp1_15-20250315-1ubuntu1_s390x.deb ... 887s Unpacking libgomp1:s390x (15-20250315-1ubuntu1) ... 887s Selecting previously unselected package libitm1:s390x. 887s Preparing to unpack .../046-libitm1_15-20250315-1ubuntu1_s390x.deb ... 887s Unpacking libitm1:s390x (15-20250315-1ubuntu1) ... 887s Selecting previously unselected package libasan8:s390x. 887s Preparing to unpack .../047-libasan8_15-20250315-1ubuntu1_s390x.deb ... 887s Unpacking libasan8:s390x (15-20250315-1ubuntu1) ... 887s Selecting previously unselected package libubsan1:s390x. 887s Preparing to unpack .../048-libubsan1_15-20250315-1ubuntu1_s390x.deb ... 887s Unpacking libubsan1:s390x (15-20250315-1ubuntu1) ... 887s Selecting previously unselected package libgcc-14-dev:s390x. 887s Preparing to unpack .../049-libgcc-14-dev_14.2.0-19ubuntu1_s390x.deb ... 887s Unpacking libgcc-14-dev:s390x (14.2.0-19ubuntu1) ... 887s Selecting previously unselected package gcc-14-s390x-linux-gnu. 887s Preparing to unpack .../050-gcc-14-s390x-linux-gnu_14.2.0-19ubuntu1_s390x.deb ... 887s Unpacking gcc-14-s390x-linux-gnu (14.2.0-19ubuntu1) ... 888s Selecting previously unselected package gcc-14. 888s Preparing to unpack .../051-gcc-14_14.2.0-19ubuntu1_s390x.deb ... 888s Unpacking gcc-14 (14.2.0-19ubuntu1) ... 888s Selecting previously unselected package gcc-s390x-linux-gnu. 888s Preparing to unpack .../052-gcc-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 888s Unpacking gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 888s Selecting previously unselected package gcc. 888s Preparing to unpack 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888s Unpacking libatk1.0-0t64:s390x (2.56.0-2) ... 888s Selecting previously unselected package libxi6:s390x. 888s Preparing to unpack .../064-libxi6_2%3a1.8.2-1_s390x.deb ... 888s Unpacking libxi6:s390x (2:1.8.2-1) ... 888s Selecting previously unselected package libatspi2.0-0t64:s390x. 888s Preparing to unpack .../065-libatspi2.0-0t64_2.56.0-2_s390x.deb ... 888s Unpacking libatspi2.0-0t64:s390x (2.56.0-2) ... 888s Selecting previously unselected package libatk-bridge2.0-0t64:s390x. 888s Preparing to unpack .../066-libatk-bridge2.0-0t64_2.56.0-2_s390x.deb ... 888s Unpacking libatk-bridge2.0-0t64:s390x (2.56.0-2) ... 888s Selecting previously unselected package libavahi-common-data:s390x. 888s Preparing to unpack .../067-libavahi-common-data_0.8-16ubuntu2_s390x.deb ... 888s Unpacking libavahi-common-data:s390x (0.8-16ubuntu2) ... 888s Selecting previously unselected package libavahi-common3:s390x. 888s Preparing to unpack .../068-libavahi-common3_0.8-16ubuntu2_s390x.deb ... 888s Unpacking libavahi-common3:s390x (0.8-16ubuntu2) ... 888s Selecting previously unselected package libavahi-client3:s390x. 888s Preparing to unpack .../069-libavahi-client3_0.8-16ubuntu2_s390x.deb ... 888s Unpacking libavahi-client3:s390x (0.8-16ubuntu2) ... 888s Selecting previously unselected package libboost-python1.83.0. 888s Preparing to unpack .../070-libboost-python1.83.0_1.83.0-4.1ubuntu2_s390x.deb ... 888s Unpacking libboost-python1.83.0 (1.83.0-4.1ubuntu2) ... 888s Selecting previously unselected package libboost-numpy1.83.0. 888s Preparing to unpack .../071-libboost-numpy1.83.0_1.83.0-4.1ubuntu2_s390x.deb ... 888s Unpacking libboost-numpy1.83.0 (1.83.0-4.1ubuntu2) ... 888s Selecting previously unselected package libboost1.83-dev:s390x. 888s Preparing to unpack .../072-libboost1.83-dev_1.83.0-4.1ubuntu2_s390x.deb ... 888s Unpacking libboost1.83-dev:s390x (1.83.0-4.1ubuntu2) ... 889s Selecting previously unselected package libexpat1-dev:s390x. 889s Preparing to unpack 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.../083-libboost-python-dev_1.83.0.2ubuntu1_s390x.deb ... 889s Unpacking libboost-python-dev (1.83.0.2ubuntu1) ... 889s Selecting previously unselected package libboost-thread1.83.0:s390x. 889s Preparing to unpack .../084-libboost-thread1.83.0_1.83.0-4.1ubuntu2_s390x.deb ... 889s Unpacking libboost-thread1.83.0:s390x (1.83.0-4.1ubuntu2) ... 889s Selecting previously unselected package libboost-timer1.83.0:s390x. 889s Preparing to unpack .../085-libboost-timer1.83.0_1.83.0-4.1ubuntu2_s390x.deb ... 889s Unpacking libboost-timer1.83.0:s390x (1.83.0-4.1ubuntu2) ... 889s Selecting previously unselected package libpixman-1-0:s390x. 889s Preparing to unpack .../086-libpixman-1-0_0.44.0-3_s390x.deb ... 889s Unpacking libpixman-1-0:s390x (0.44.0-3) ... 889s Selecting previously unselected package libxcb-render0:s390x. 889s Preparing to unpack .../087-libxcb-render0_1.17.0-2_s390x.deb ... 889s Unpacking libxcb-render0:s390x (1.17.0-2) ... 889s Selecting previously unselected package libxcb-shm0:s390x. 889s Preparing to unpack .../088-libxcb-shm0_1.17.0-2_s390x.deb ... 889s Unpacking libxcb-shm0:s390x (1.17.0-2) ... 889s Selecting previously unselected package libcairo2:s390x. 889s Preparing to unpack .../089-libcairo2_1.18.4-1_s390x.deb ... 889s Unpacking libcairo2:s390x (1.18.4-1) ... 889s Selecting previously unselected package libcairo-gobject2:s390x. 889s Preparing to unpack .../090-libcairo-gobject2_1.18.4-1_s390x.deb ... 889s Unpacking libcairo-gobject2:s390x (1.18.4-1) ... 889s Selecting previously unselected package libsz2:s390x. 889s Preparing to unpack .../091-libsz2_1.1.3-1_s390x.deb ... 889s Unpacking libsz2:s390x (1.1.3-1) ... 889s Selecting previously unselected package libhdf5-310:s390x. 889s Preparing to unpack .../092-libhdf5-310_1.14.5+repack-3_s390x.deb ... 889s Unpacking libhdf5-310:s390x (1.14.5+repack-3) ... 890s Selecting previously unselected package libcbf1t64:s390x. 890s Preparing to unpack .../093-libcbf1t64_0.9.7+dfsg1-5build1_s390x.deb ... 890s Unpacking libcbf1t64:s390x (0.9.7+dfsg1-5build1) ... 890s Selecting previously unselected package libccp4-data. 890s Preparing to unpack .../094-libccp4-data_8.0.0-4_all.deb ... 890s Unpacking libccp4-data (8.0.0-4) ... 890s Selecting previously unselected package libccp4c0t64:s390x. 890s Preparing to unpack .../095-libccp4c0t64_8.0.0-4_s390x.deb ... 890s Unpacking libccp4c0t64:s390x (8.0.0-4) ... 890s Selecting previously unselected package libmmdb2-0:s390x. 890s Preparing to unpack .../096-libmmdb2-0_2.0.22-1_s390x.deb ... 890s Unpacking libmmdb2-0:s390x (2.0.22-1) ... 890s Selecting previously unselected package libccp4f0t64:s390x. 890s Preparing to unpack .../097-libccp4f0t64_8.0.0-4_s390x.deb ... 890s Unpacking libccp4f0t64:s390x (8.0.0-4) ... 890s Selecting previously unselected package libccp4-dev:s390x. 890s Preparing to unpack .../098-libccp4-dev_8.0.0-4_s390x.deb ... 890s Unpacking libccp4-dev:s390x (8.0.0-4) ... 890s Selecting previously unselected package libcctbx0. 890s Preparing to unpack .../099-libcctbx0_2024.10+ds2+~3.22.1+ds1-4build2_s390x.deb ... 890s Unpacking libcctbx0 (2024.10+ds2+~3.22.1+ds1-4build2) ... 890s Selecting previously unselected package libcctbx-dev. 890s Preparing to unpack .../100-libcctbx-dev_2024.10+ds2+~3.22.1+ds1-4build2_s390x.deb ... 890s Unpacking libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4build2) ... 890s Selecting previously unselected package liblcms2-2:s390x. 890s Preparing to unpack .../101-liblcms2-2_2.16-2_s390x.deb ... 890s Unpacking liblcms2-2:s390x (2.16-2) ... 890s Selecting previously unselected package libcolord2:s390x. 890s Preparing to unpack .../102-libcolord2_1.4.7-3_s390x.deb ... 890s Unpacking libcolord2:s390x (1.4.7-3) ... 890s Selecting previously unselected package libcups2t64:s390x. 890s Preparing to unpack .../103-libcups2t64_2.4.11-0ubuntu2_s390x.deb ... 890s Unpacking libcups2t64:s390x (2.4.11-0ubuntu2) ... 890s Selecting previously unselected package libdatrie1:s390x. 890s Preparing to unpack .../104-libdatrie1_0.2.13-3build1_s390x.deb ... 890s Unpacking libdatrie1:s390x (0.2.13-3build1) ... 890s Selecting previously unselected package libdouble-conversion3:s390x. 890s Preparing to unpack .../105-libdouble-conversion3_3.3.1-1_s390x.deb ... 890s Unpacking libdouble-conversion3:s390x (3.3.1-1) ... 890s Selecting previously unselected package libwayland-server0:s390x. 890s Preparing to unpack .../106-libwayland-server0_1.23.1-3_s390x.deb ... 890s Unpacking libwayland-server0:s390x (1.23.1-3) ... 890s Selecting previously unselected package libx11-xcb1:s390x. 890s Preparing to unpack .../107-libx11-xcb1_2%3a1.8.10-2_s390x.deb ... 890s Unpacking libx11-xcb1:s390x (2:1.8.10-2) ... 890s Selecting previously unselected package libxcb-dri3-0:s390x. 890s Preparing to unpack .../108-libxcb-dri3-0_1.17.0-2_s390x.deb ... 890s Unpacking libxcb-dri3-0:s390x (1.17.0-2) ... 890s Selecting previously unselected package libxcb-present0:s390x. 890s Preparing to unpack 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Unpacking mesa-libgallium:s390x (25.0.1-2ubuntu2) ... 890s Selecting previously unselected package libgbm1:s390x. 890s Preparing to unpack .../115-libgbm1_25.0.1-2ubuntu2_s390x.deb ... 890s Unpacking libgbm1:s390x (25.0.1-2ubuntu2) ... 890s Selecting previously unselected package libwayland-client0:s390x. 890s Preparing to unpack .../116-libwayland-client0_1.23.1-3_s390x.deb ... 890s Unpacking libwayland-client0:s390x (1.23.1-3) ... 890s Selecting previously unselected package libegl-mesa0:s390x. 890s Preparing to unpack .../117-libegl-mesa0_25.0.1-2ubuntu2_s390x.deb ... 890s Unpacking libegl-mesa0:s390x (25.0.1-2ubuntu2) ... 890s Selecting previously unselected package libepoxy0:s390x. 890s Preparing to unpack .../118-libepoxy0_1.5.10-2_s390x.deb ... 890s Unpacking libepoxy0:s390x (1.5.10-2) ... 890s Selecting previously unselected package libvulkan1:s390x. 890s Preparing to unpack .../119-libvulkan1_1.4.304.0-1_s390x.deb ... 890s Unpacking libvulkan1:s390x (1.4.304.0-1) ... 890s Selecting previously unselected package libgl1-mesa-dri:s390x. 890s Preparing to unpack .../120-libgl1-mesa-dri_25.0.1-2ubuntu2_s390x.deb ... 890s Unpacking libgl1-mesa-dri:s390x (25.0.1-2ubuntu2) ... 890s Selecting previously unselected package libglvnd0:s390x. 890s Preparing to unpack .../121-libglvnd0_1.7.0-1build1_s390x.deb ... 890s Unpacking libglvnd0:s390x (1.7.0-1build1) ... 890s Selecting previously unselected package libxcb-glx0:s390x. 890s Preparing to unpack .../122-libxcb-glx0_1.17.0-2_s390x.deb ... 890s Unpacking libxcb-glx0:s390x (1.17.0-2) ... 890s Selecting previously unselected package libxxf86vm1:s390x. 890s Preparing to unpack .../123-libxxf86vm1_1%3a1.1.4-1build4_s390x.deb ... 890s Unpacking libxxf86vm1:s390x (1:1.1.4-1build4) ... 890s Selecting previously unselected package libglx-mesa0:s390x. 890s Preparing to unpack .../124-libglx-mesa0_25.0.1-2ubuntu2_s390x.deb ... 890s Unpacking libglx-mesa0:s390x (25.0.1-2ubuntu2) ... 890s Selecting previously unselected package libglx0:s390x. 890s Preparing to unpack .../125-libglx0_1.7.0-1build1_s390x.deb ... 890s Unpacking libglx0:s390x (1.7.0-1build1) ... 890s Selecting previously unselected package libgl1:s390x. 890s Preparing to unpack .../126-libgl1_1.7.0-1build1_s390x.deb ... 890s Unpacking libgl1:s390x (1.7.0-1build1) ... 890s Selecting previously unselected package libglew2.2:s390x. 890s Preparing to unpack .../127-libglew2.2_2.2.0-4build1_s390x.deb ... 890s Unpacking libglew2.2:s390x (2.2.0-4build1) ... 890s Selecting previously unselected package libglut3.12:s390x. 890s Preparing to unpack .../128-libglut3.12_3.4.0-4_s390x.deb ... 890s Unpacking libglut3.12:s390x (3.4.0-4) ... 890s Selecting previously unselected package libgraphite2-3:s390x. 890s Preparing to unpack .../129-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 890s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 890s Selecting previously unselected package libharfbuzz0b:s390x. 890s Preparing to unpack .../130-libharfbuzz0b_10.2.0-1_s390x.deb ... 890s Unpacking libharfbuzz0b:s390x (10.2.0-1) ... 890s Selecting previously unselected package libthai-data. 890s Preparing to unpack .../131-libthai-data_0.1.29-2build1_all.deb ... 890s Unpacking libthai-data (0.1.29-2build1) ... 890s Selecting previously unselected package libthai0:s390x. 890s Preparing to unpack .../132-libthai0_0.1.29-2build1_s390x.deb ... 890s Unpacking libthai0:s390x (0.1.29-2build1) ... 890s Selecting previously unselected package libpango-1.0-0:s390x. 890s Preparing to unpack .../133-libpango-1.0-0_1.56.3-1_s390x.deb ... 890s Unpacking libpango-1.0-0:s390x (1.56.3-1) ... 890s Selecting previously unselected package libpangoft2-1.0-0:s390x. 890s Preparing to unpack .../134-libpangoft2-1.0-0_1.56.3-1_s390x.deb ... 890s Unpacking libpangoft2-1.0-0:s390x (1.56.3-1) ... 890s Selecting previously unselected package libpangocairo-1.0-0:s390x. 890s Preparing to unpack .../135-libpangocairo-1.0-0_1.56.3-1_s390x.deb ... 890s Unpacking libpangocairo-1.0-0:s390x (1.56.3-1) ... 890s Selecting previously unselected package libwayland-cursor0:s390x. 890s Preparing to unpack .../136-libwayland-cursor0_1.23.1-3_s390x.deb ... 890s Unpacking libwayland-cursor0:s390x (1.23.1-3) ... 890s Selecting previously unselected package libwayland-egl1:s390x. 890s Preparing to unpack .../137-libwayland-egl1_1.23.1-3_s390x.deb ... 890s Unpacking libwayland-egl1:s390x (1.23.1-3) ... 890s Selecting previously unselected package libxcomposite1:s390x. 890s Preparing to unpack .../138-libxcomposite1_1%3a0.4.6-1_s390x.deb ... 890s Unpacking libxcomposite1:s390x (1:0.4.6-1) ... 890s Selecting previously unselected package libxfixes3:s390x. 890s Preparing to unpack .../139-libxfixes3_1%3a6.0.0-2build1_s390x.deb ... 890s Unpacking libxfixes3:s390x (1:6.0.0-2build1) ... 890s Selecting previously unselected package libxcursor1:s390x. 890s Preparing to unpack .../140-libxcursor1_1%3a1.2.3-1_s390x.deb ... 890s Unpacking libxcursor1:s390x (1:1.2.3-1) ... 890s Selecting previously unselected package libxdamage1:s390x. 890s Preparing to unpack .../141-libxdamage1_1%3a1.1.6-1build1_s390x.deb ... 890s Unpacking libxdamage1:s390x (1:1.1.6-1build1) ... 891s Selecting previously unselected package libxinerama1:s390x. 891s Preparing to unpack .../142-libxinerama1_2%3a1.1.4-3build1_s390x.deb ... 891s Unpacking libxinerama1:s390x (2:1.1.4-3build1) ... 891s Selecting previously unselected package libxrandr2:s390x. 891s Preparing to unpack .../143-libxrandr2_2%3a1.5.4-1_s390x.deb ... 891s Unpacking libxrandr2:s390x (2:1.5.4-1) ... 891s Selecting previously unselected package libgtk-3-common. 891s Preparing to unpack .../144-libgtk-3-common_3.24.49-2ubuntu1_all.deb ... 891s Unpacking libgtk-3-common (3.24.49-2ubuntu1) ... 891s Selecting previously unselected package libgtk-3-0t64:s390x. 891s Preparing to unpack .../145-libgtk-3-0t64_3.24.49-2ubuntu1_s390x.deb ... 891s Unpacking libgtk-3-0t64:s390x (3.24.49-2ubuntu1) ... 891s Selecting previously unselected package libhdf5-hl-310:s390x. 891s Preparing to unpack .../146-libhdf5-hl-310_1.14.5+repack-3_s390x.deb ... 891s Unpacking libhdf5-hl-310:s390x (1.14.5+repack-3) ... 891s Selecting previously unselected package libice6:s390x. 891s Preparing to unpack .../147-libice6_2%3a1.1.1-1_s390x.deb ... 891s Unpacking libice6:s390x (2:1.1.1-1) ... 891s Selecting previously unselected package libimagequant0:s390x. 891s Preparing to unpack .../148-libimagequant0_2.18.0-1build1_s390x.deb ... 891s Unpacking libimagequant0:s390x (2.18.0-1build1) ... 891s Selecting previously unselected package libwacom-common. 891s Preparing to unpack .../149-libwacom-common_2.14.0-1_all.deb ... 891s Unpacking libwacom-common (2.14.0-1) ... 891s Selecting previously unselected package libwacom9:s390x. 891s Preparing to unpack .../150-libwacom9_2.14.0-1_s390x.deb ... 891s Unpacking libwacom9:s390x (2.14.0-1) ... 891s Selecting previously unselected package libinput-bin. 891s Preparing to unpack .../151-libinput-bin_1.27.1-1_s390x.deb ... 891s Unpacking libinput-bin (1.27.1-1) ... 891s Selecting previously unselected package libmtdev1t64:s390x. 891s Preparing to unpack .../152-libmtdev1t64_1.1.7-1_s390x.deb ... 891s Unpacking libmtdev1t64:s390x (1.1.7-1) ... 891s Selecting previously unselected package libinput10:s390x. 891s Preparing to unpack .../153-libinput10_1.27.1-1_s390x.deb ... 891s Unpacking libinput10:s390x (1.27.1-1) ... 891s Selecting previously unselected package libjs-jquery-ui. 891s Preparing to unpack .../154-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 891s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 891s Selecting previously unselected package liblbfgsb0:s390x. 891s Preparing to unpack .../155-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 891s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 891s Selecting previously unselected package liblzf1:s390x. 891s Preparing to unpack .../156-liblzf1_3.6-4_s390x.deb ... 891s Unpacking liblzf1:s390x (3.6-4) ... 891s Selecting previously unselected package libmd4c0:s390x. 891s Preparing to unpack .../157-libmd4c0_0.5.2-2_s390x.deb ... 891s Unpacking libmd4c0:s390x (0.5.2-2) ... 891s Selecting previously unselected package libnetcdf22:s390x. 891s Preparing to unpack .../158-libnetcdf22_1%3a4.9.3-1_s390x.deb ... 891s Unpacking libnetcdf22:s390x (1:4.9.3-1) ... 891s Selecting previously unselected package libnotify4:s390x. 891s Preparing to unpack .../159-libnotify4_0.8.4-1_s390x.deb ... 891s Unpacking libnotify4:s390x (0.8.4-1) ... 891s Selecting previously unselected package libpcre2-16-0:s390x. 891s Preparing to unpack .../160-libpcre2-16-0_10.45-1_s390x.deb ... 891s Unpacking libpcre2-16-0:s390x (10.45-1) ... 891s Selecting previously unselected package libpcre2-32-0:s390x. 891s Preparing to unpack .../161-libpcre2-32-0_10.45-1_s390x.deb ... 891s Unpacking libpcre2-32-0:s390x (10.45-1) ... 891s Selecting previously unselected package libqhull-r8.0:s390x. 891s Preparing to unpack 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891s Preparing to unpack .../167-libsm6_2%3a1.2.4-1_s390x.deb ... 891s Unpacking libsm6:s390x (2:1.2.4-1) ... 891s Selecting previously unselected package libxcb-icccm4:s390x. 891s Preparing to unpack .../168-libxcb-icccm4_0.4.2-1_s390x.deb ... 891s Unpacking libxcb-icccm4:s390x (0.4.2-1) ... 891s Selecting previously unselected package libxcb-util1:s390x. 891s Preparing to unpack .../169-libxcb-util1_0.4.1-1_s390x.deb ... 891s Unpacking libxcb-util1:s390x (0.4.1-1) ... 891s Selecting previously unselected package libxcb-image0:s390x. 891s Preparing to unpack .../170-libxcb-image0_0.4.0-2build1_s390x.deb ... 891s Unpacking libxcb-image0:s390x (0.4.0-2build1) ... 891s Selecting previously unselected package libxcb-keysyms1:s390x. 891s Preparing to unpack .../171-libxcb-keysyms1_0.4.1-1_s390x.deb ... 891s Unpacking libxcb-keysyms1:s390x (0.4.1-1) ... 891s Selecting previously unselected package libxcb-render-util0:s390x. 891s Preparing to unpack .../172-libxcb-render-util0_0.3.10-1_s390x.deb ... 891s Unpacking libxcb-render-util0:s390x (0.3.10-1) ... 891s Selecting previously unselected package libxcb-shape0:s390x. 891s Preparing to unpack .../173-libxcb-shape0_1.17.0-2_s390x.deb ... 891s Unpacking libxcb-shape0:s390x (1.17.0-2) ... 891s Selecting previously unselected package libxcb-xinerama0:s390x. 891s Preparing to unpack .../174-libxcb-xinerama0_1.17.0-2_s390x.deb ... 891s Unpacking libxcb-xinerama0:s390x (1.17.0-2) ... 891s Selecting previously unselected package libxcb-xinput0:s390x. 891s Preparing to unpack .../175-libxcb-xinput0_1.17.0-2_s390x.deb ... 891s Unpacking libxcb-xinput0:s390x (1.17.0-2) ... 891s Selecting previously unselected package libxcb-xkb1:s390x. 891s Preparing to unpack .../176-libxcb-xkb1_1.17.0-2_s390x.deb ... 891s Unpacking libxcb-xkb1:s390x (1.17.0-2) ... 891s Selecting previously unselected package libxkbcommon-x11-0:s390x. 891s Preparing to unpack .../177-libxkbcommon-x11-0_1.7.0-2_s390x.deb 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unpack .../182-libqt5sql5t64_5.15.15+dfsg-4ubuntu1_s390x.deb ... 891s Unpacking libqt5sql5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 891s Selecting previously unselected package libqt5help5:s390x. 892s Preparing to unpack .../183-libqt5help5_5.15.15-6build1_s390x.deb ... 892s Unpacking libqt5help5:s390x (5.15.15-6build1) ... 892s Selecting previously unselected package libqt5opengl5t64:s390x. 892s Preparing to unpack .../184-libqt5opengl5t64_5.15.15+dfsg-4ubuntu1_s390x.deb ... 892s Unpacking libqt5opengl5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 892s Selecting previously unselected package libqt5printsupport5t64:s390x. 892s Preparing to unpack .../185-libqt5printsupport5t64_5.15.15+dfsg-4ubuntu1_s390x.deb ... 892s Unpacking libqt5printsupport5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 892s Selecting previously unselected package libqt5test5t64:s390x. 892s Preparing to unpack .../186-libqt5test5t64_5.15.15+dfsg-4ubuntu1_s390x.deb ... 892s Unpacking libqt5test5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 892s Selecting previously unselected package libraqm0:s390x. 892s Preparing to unpack .../187-libraqm0_0.10.2-1_s390x.deb ... 892s Unpacking libraqm0:s390x (0.10.2-1) ... 892s Selecting previously unselected package libssm2:s390x. 892s Preparing to unpack .../188-libssm2_1.4.0-2build1_s390x.deb ... 892s Unpacking libssm2:s390x (1.4.0-2build1) ... 892s Selecting previously unselected package libwebpdemux2:s390x. 892s Preparing to unpack .../189-libwebpdemux2_1.5.0-0.1_s390x.deb ... 892s Unpacking libwebpdemux2:s390x (1.5.0-0.1) ... 892s Selecting previously unselected package libwebpmux3:s390x. 892s Preparing to unpack .../190-libwebpmux3_1.5.0-0.1_s390x.deb ... 892s Unpacking libwebpmux3:s390x (1.5.0-0.1) ... 892s Selecting previously unselected package libwxbase3.2-1t64:s390x. 892s Preparing to unpack .../191-libwxbase3.2-1t64_3.2.6+dfsg-2ubuntu1_s390x.deb ... 892s Unpacking libwxbase3.2-1t64:s390x (3.2.6+dfsg-2ubuntu1) ... 892s Selecting previously unselected package libxtst6:s390x. 892s Preparing to unpack .../192-libxtst6_2%3a1.2.5-1_s390x.deb ... 892s Unpacking libxtst6:s390x (2:1.2.5-1) ... 892s Selecting previously unselected package libwxgtk3.2-1t64:s390x. 892s Preparing to unpack .../193-libwxgtk3.2-1t64_3.2.6+dfsg-2ubuntu1_s390x.deb ... 892s Unpacking libwxgtk3.2-1t64:s390x (3.2.6+dfsg-2ubuntu1) ... 892s Selecting previously unselected package libwxgtk-gl3.2-1t64:s390x. 892s Preparing to unpack .../194-libwxgtk-gl3.2-1t64_3.2.6+dfsg-2ubuntu1_s390x.deb ... 892s Unpacking libwxgtk-gl3.2-1t64:s390x (3.2.6+dfsg-2ubuntu1) ... 892s Selecting previously unselected package libxslt1.1:s390x. 892s Preparing to unpack .../195-libxslt1.1_1.1.39-0exp1ubuntu4_s390x.deb ... 892s Unpacking libxslt1.1:s390x (1.1.39-0exp1ubuntu4) ... 892s Selecting previously unselected package pymol-data. 892s Preparing to unpack .../196-pymol-data_3.1.0+dfsg-1_all.deb ... 892s Unpacking pymol-data (3.1.0+dfsg-1) ... 892s Selecting previously unselected package python-matplotlib-data. 892s Preparing to unpack .../197-python-matplotlib-data_3.8.3-7build1_all.deb ... 892s Unpacking python-matplotlib-data (3.8.3-7build1) ... 892s Selecting previously unselected package python3-all. 892s Preparing to unpack .../198-python3-all_3.13.2-2_s390x.deb ... 892s Unpacking python3-all (3.13.2-2) ... 892s Selecting previously unselected package python3-brotli. 892s Preparing to unpack .../199-python3-brotli_1.1.0-2build4_s390x.deb ... 892s Unpacking python3-brotli (1.1.0-2build4) ... 892s Selecting previously unselected package python3-legacy-cgi. 892s Preparing to unpack .../200-python3-legacy-cgi_2.6.2-1_all.deb ... 892s Unpacking python3-legacy-cgi (2.6.2-1) ... 892s Selecting previously unselected package python3-pycbf. 892s Preparing to unpack .../201-python3-pycbf_0.9.7+dfsg1-5build1_s390x.deb ... 892s Unpacking python3-pycbf (0.9.7+dfsg1-5build1) ... 892s Selecting previously unselected package python3-h5py-serial. 892s Preparing to unpack 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package python3-platformdirs. 892s Preparing to unpack .../213-python3-platformdirs_4.3.6-1_all.deb ... 892s Unpacking python3-platformdirs (4.3.6-1) ... 892s Selecting previously unselected package python3-fs. 892s Preparing to unpack .../214-python3-fs_2.4.16-7_all.deb ... 892s Unpacking python3-fs (2.4.16-7) ... 892s Selecting previously unselected package python3-lxml:s390x. 892s Preparing to unpack .../215-python3-lxml_5.3.1-1build1_s390x.deb ... 892s Unpacking python3-lxml:s390x (5.3.1-1build1) ... 892s Selecting previously unselected package python3-lz4. 892s Preparing to unpack .../216-python3-lz4_4.4.0+dfsg-1build1_s390x.deb ... 892s Unpacking python3-lz4 (4.4.0+dfsg-1build1) ... 892s Selecting previously unselected package python3-decorator. 892s Preparing to unpack .../217-python3-decorator_5.1.1-5_all.deb ... 892s Unpacking python3-decorator (5.1.1-5) ... 892s Selecting previously unselected package python3-scipy. 892s Preparing to unpack .../218-python3-scipy_1.14.1-4ubuntu2_s390x.deb ... 892s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 893s Selecting previously unselected package python3-mpmath. 893s Preparing to unpack .../219-python3-mpmath_1.3.0-1_all.deb ... 893s Unpacking python3-mpmath (1.3.0-1) ... 893s Selecting previously unselected package python3-sympy. 893s Preparing to unpack .../220-python3-sympy_1.13.3-5_all.deb ... 893s Unpacking python3-sympy (1.13.3-5) ... 893s Selecting previously unselected package python3-ufolib2. 893s Preparing to unpack .../221-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 893s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 893s Selecting previously unselected package unicode-data. 893s Preparing to unpack .../222-unicode-data_15.1.0-1_all.deb ... 893s Unpacking unicode-data (15.1.0-1) ... 893s Selecting previously unselected package python3-fonttools. 893s Preparing to unpack .../223-python3-fonttools_4.55.3-2build1_s390x.deb ... 893s Unpacking python3-fonttools (4.55.3-2build1) ... 893s Selecting previously unselected package python3-kiwisolver. 893s Preparing to unpack .../224-python3-kiwisolver_1.4.7-3build1_s390x.deb ... 893s Unpacking python3-kiwisolver (1.4.7-3build1) ... 893s Selecting previously unselected package python3-packaging. 893s Preparing to unpack .../225-python3-packaging_24.2-1_all.deb ... 893s Unpacking python3-packaging (24.2-1) ... 893s Selecting previously unselected package python3-matplotlib. 893s Preparing to unpack .../226-python3-matplotlib_3.8.3-7build1_s390x.deb ... 893s Unpacking python3-matplotlib (3.8.3-7build1) ... 893s Selecting previously unselected package sphinx-rtd-theme-common. 893s Preparing to unpack .../227-sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb ... 893s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 893s Selecting previously unselected package python3-mrcfile. 893s Preparing to unpack .../228-python3-mrcfile_1.5.4-2_all.deb ... 893s Unpacking python3-mrcfile (1.5.4-2) ... 893s Selecting previously unselected package python3-natsort. 893s Preparing to unpack .../229-python3-natsort_8.0.2-2_all.deb ... 893s Unpacking python3-natsort (8.0.2-2) ... 893s Selecting previously unselected package python3-flexcache. 893s Preparing to unpack .../230-python3-flexcache_0.3-2_all.deb ... 893s Unpacking python3-flexcache (0.3-2) ... 893s Selecting previously unselected package python3-flexparser. 893s Preparing to unpack .../231-python3-flexparser_0.4-1_all.deb ... 893s Unpacking python3-flexparser (0.4-1) ... 893s Selecting previously unselected package python3-pint. 893s Preparing to unpack .../232-python3-pint_0.24.4-1_all.deb ... 893s Unpacking python3-pint (0.24.4-1) ... 894s Selecting previously unselected package python3-nxmx. 894s Preparing to unpack .../233-python3-nxmx_0.0.4-1_all.deb ... 894s Unpacking python3-nxmx (0.0.4-1) ... 894s Selecting previously unselected package python3-ordered-set. 894s Preparing to unpack .../234-python3-ordered-set_4.1.0-1_all.deb ... 894s Unpacking python3-ordered-set (4.1.0-1) ... 894s Selecting previously unselected package python3-procrunner. 894s Preparing to unpack .../235-python3-procrunner_2.3.3-2_all.deb ... 894s Unpacking python3-procrunner (2.3.3-2) ... 894s Selecting previously unselected package libopengl0:s390x. 894s Preparing to unpack .../236-libopengl0_1.7.0-1build1_s390x.deb ... 894s Unpacking libopengl0:s390x (1.7.0-1build1) ... 894s Selecting previously unselected package libglu1-mesa:s390x. 894s Preparing to unpack .../237-libglu1-mesa_9.0.2-1.1build1_s390x.deb ... 894s Unpacking libglu1-mesa:s390x (9.0.2-1.1build1) ... 894s Selecting previously unselected package python3-opengl. 894s Preparing to unpack .../238-python3-opengl_3.1.9+dfsg-1syncable1_all.deb ... 894s Unpacking python3-opengl (3.1.9+dfsg-1syncable1) ... 894s Selecting previously unselected package python3-pyqt5.sip. 894s Preparing to unpack .../239-python3-pyqt5.sip_12.17.0-1build1_s390x.deb ... 894s Unpacking python3-pyqt5.sip (12.17.0-1build1) ... 894s Selecting previously unselected package python3-pyqt5. 894s Preparing to unpack .../240-python3-pyqt5_5.15.11+dfsg-2_s390x.deb ... 894s Unpacking python3-pyqt5 (5.15.11+dfsg-2) ... 894s Selecting previously unselected package python3-pyqt5.qtopengl. 894s Preparing to unpack .../241-python3-pyqt5.qtopengl_5.15.11+dfsg-2_s390x.deb ... 894s Unpacking python3-pyqt5.qtopengl (5.15.11+dfsg-2) ... 894s Selecting previously unselected package python3-pymol. 894s Preparing to unpack .../242-python3-pymol_3.1.0+dfsg-1_s390x.deb ... 894s Unpacking python3-pymol (3.1.0+dfsg-1) ... 894s Selecting previously unselected package python3-six. 894s Preparing to unpack .../243-python3-six_1.17.0-1_all.deb ... 894s Unpacking python3-six (1.17.0-1) ... 894s Selecting previously unselected package python3-tqdm. 894s Preparing to unpack .../244-python3-tqdm_4.67.1-2_all.deb ... 894s Unpacking python3-tqdm (4.67.1-2) ... 894s Selecting previously unselected package python3-wxgtk4.0. 894s Preparing to unpack .../245-python3-wxgtk4.0_4.2.2+dfsg-3build1_s390x.deb ... 894s Unpacking python3-wxgtk4.0 (4.2.2+dfsg-3build1) ... 895s Selecting previously unselected package python3-cctbx. 895s Preparing to unpack .../246-python3-cctbx_2024.10+ds2+~3.22.1+ds1-4build2_s390x.deb ... 895s Unpacking python3-cctbx (2024.10+ds2+~3.22.1+ds1-4build2) ... 895s Selecting previously unselected package python3-iniconfig. 895s Preparing to unpack .../247-python3-iniconfig_1.1.1-2_all.deb ... 895s Unpacking python3-iniconfig (1.1.1-2) ... 895s Selecting previously unselected package python3-pluggy. 895s Preparing to unpack .../248-python3-pluggy_1.5.0-1_all.deb ... 895s Unpacking python3-pluggy (1.5.0-1) ... 895s Selecting previously unselected package python3-pytest. 895s Preparing to unpack .../249-python3-pytest_8.3.5-1_all.deb ... 895s Unpacking python3-pytest (8.3.5-1) ... 895s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 895s Setting up libboost-python1.83.0 (1.83.0-4.1ubuntu2) ... 895s Setting up libxcb-dri3-0:s390x (1.17.0-2) ... 895s Setting up liblcms2-2:s390x (2.16-2) ... 895s Setting up python3-iniconfig (1.1.1-2) ... 895s Setting up libpixman-1-0:s390x (0.44.0-3) ... 895s Setting up libsharpyuv0:s390x (1.5.0-0.1) ... 895s Setting up libwayland-server0:s390x (1.23.1-3) ... 895s Setting up libx11-xcb1:s390x (2:1.8.10-2) ... 895s Setting up libdouble-conversion3:s390x (3.3.1-1) ... 895s Setting up fonts-lato (2.015-1) ... 895s Setting up libxdamage1:s390x (1:1.1.6-1build1) ... 895s Setting up libxcb-xfixes0:s390x (1.17.0-2) ... 895s Setting up libantlr3c-3.4-0:s390x (3.4+dfsg-4build2) ... 895s Setting up hicolor-icon-theme (0.18-2) ... 895s Setting up libxi6:s390x (2:1.8.2-1) ... 895s Setting up libxcb-xinput0:s390x (1.17.0-2) ... 895s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ... 895s Setting up libdatrie1:s390x (0.2.13-3build1) ... 895s Setting up libmmdb2-0:s390x (2.0.22-1) ... 895s Setting up libboost-timer1.83.0:s390x (1.83.0-4.1ubuntu2) ... 895s Setting up python3-lz4 (4.4.0+dfsg-1build1) ... 895s Setting up libxcb-render0:s390x (1.17.0-2) ... 895s Setting up libglvnd0:s390x (1.7.0-1build1) ... 895s Setting up fonts-lyx (2.4.3-1) ... 895s Setting up libxcb-glx0:s390x (1.17.0-2) ... 895s Setting up python3-tqdm (4.67.1-2) ... 896s Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... 896s Setting up libxcb-keysyms1:s390x (0.4.1-1) ... 896s Setting up libxcb-shape0:s390x (1.17.0-2) ... 896s Setting up x11-common (1:7.7+23ubuntu3) ... 896s Setting up libdeflate0:s390x (1.23-1) ... 896s Setting up libboost-thread1.83.0:s390x (1.83.0-4.1ubuntu2) ... 896s Setting up libqhull-r8.0:s390x (2020.2-6build1) ... 896s Setting up libxcb-render-util0:s390x (0.3.10-1) ... 896s Setting up python3-all (3.13.2-2) ... 896s Setting up python3-ordered-set (4.1.0-1) ... 896s Setting up libxcb-shm0:s390x (1.17.0-2) ... 896s Setting up libxcb-icccm4:s390x (0.4.2-1) ... 896s Setting up libccp4-data (8.0.0-4) ... 896s Setting up libgomp1:s390x (15-20250315-1ubuntu1) ... 896s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 896s Setting up libpcre2-16-0:s390x (10.45-1) ... 896s Setting up libaec0:s390x (1.1.3-1) ... 896s Setting up libcolord2:s390x (1.4.7-3) ... 896s Setting up python3-platformdirs (4.3.6-1) ... 896s Setting up libopengl0:s390x (1.7.0-1build1) ... 896s Setting up python3-natsort (8.0.2-2) ... 896s Setting up libxcb-util1:s390x (0.4.1-1) ... 896s Setting up libxxf86vm1:s390x (1:1.1.4-1build4) ... 896s Setting up libxcb-xkb1:s390x (1.17.0-2) ... 896s Setting up libxcb-image0:s390x (0.4.0-2build1) ... 896s Setting up python3-fs (2.4.16-7) ... 896s Setting up libxcb-present0:s390x (1.17.0-2) ... 896s Setting up libdconf1:s390x (0.40.0-5) ... 896s Setting up unicode-data (15.1.0-1) ... 896s Setting up python3-six (1.17.0-1) ... 896s Setting up libqt5core5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 896s Setting up python3-decorator (5.1.1-5) ... 896s Setting up libboost-numpy1.83.0 (1.83.0-4.1ubuntu2) ... 896s Setting up libpcre2-32-0:s390x (10.45-1) ... 896s Setting up libblas3:s390x (3.12.1-2) ... 896s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 896s Setting up python3-packaging (24.2-1) ... 897s Setting up libxcb-xinerama0:s390x (1.17.0-2) ... 897s Setting up python3-flexparser (0.4-1) ... 897s Setting up libexpat1-dev:s390x (2.6.4-1) ... 897s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ... 897s Setting up libann-cctbx0 (1.1.2+doc-9build1) ... 897s Setting up libepoxy0:s390x (1.5.10-2) ... 897s Setting up libxfixes3:s390x (1:6.0.0-2build1) ... 897s Setting up libxcb-sync1:s390x (1.17.0-2) ... 897s Setting up python3-brotli (1.1.0-2build4) ... 897s Setting up libavahi-common-data:s390x (0.8-16ubuntu2) ... 897s Setting up libatspi2.0-0t64:s390x (2.56.0-2) ... 897s Setting up liblzf1:s390x (3.6-4) ... 897s Setting up python3-cycler (0.12.1-1) ... 897s Setting up libxinerama1:s390x (2:1.1.4-3build1) ... 897s Setting up libimagequant0:s390x (2.18.0-1build1) ... 897s Setting up pymol-data (3.1.0+dfsg-1) ... 897s Setting up libxkbcommon-x11-0:s390x (1.7.0-2) ... 897s Setting up fonts-dejavu-mono (2.37-8) ... 897s Setting up python3-kiwisolver (1.4.7-3build1) ... 897s Setting up libmpc3:s390x (1.3.1-1build2) ... 897s Setting up python3-numpy-dev:s390x (1:2.2.3+ds-5) ... 897s Setting up libxrandr2:s390x (2:1.5.4-1) ... 897s Setting up libtcl8.6:s390x (8.6.16+dfsg-1) ... 897s Setting up fonts-dejavu-core (2.37-8) ... 897s Setting up libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 897s Setting up libgfortran5:s390x (15-20250315-1ubuntu1) ... 897s Setting up libvulkan1:s390x (1.4.304.0-1) ... 897s Setting up python3-pluggy (1.5.0-1) ... 897s Setting up libwebp7:s390x (1.5.0-0.1) ... 897s Setting up libubsan1:s390x (15-20250315-1ubuntu1) ... 897s Setting up python3-legacy-cgi (2.6.2-1) ... 897s Setting up zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 897s Setting up python3-pyqt5.sip (12.17.0-1build1) ... 897s Setting up libmtdev1t64:s390x (1.1.7-1) ... 897s Setting up libxshmfence1:s390x (1.3-1build5) ... 897s Setting up at-spi2-common (2.56.0-2) ... 897s Setting up libccp4c0t64:s390x (8.0.0-4) ... 897s Setting up libxcb-randr0:s390x (1.17.0-2) ... 897s Setting up libasan8:s390x (15-20250315-1ubuntu1) ... 897s Setting up libxslt1.1:s390x (1.1.39-0exp1ubuntu4) ... 897s Setting up libqt5sql5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 897s Setting up libmd4c0:s390x (0.5.2-2) ... 897s Setting up libopenjp2-7:s390x (2.5.3-2) ... 897s Setting up libharfbuzz0b:s390x (10.2.0-1) ... 897s Setting up libthai-data (0.1.29-2build1) ... 897s Setting up python3-dateutil (2.9.0-4) ... 897s Setting up python3-flexcache (0.3-2) ... 897s Setting up libglu1-mesa:s390x (9.0.2-1.1build1) ... 897s Setting up libwayland-egl1:s390x (1.23.1-3) ... 897s Setting up libxss1:s390x (1:1.2.3-1build3) ... 897s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 897s Setting up libwxbase3.2-1t64:s390x (3.2.6+dfsg-2ubuntu1) ... 897s Setting up python3-mpmath (1.3.0-1) ... 898s Setting up libisl23:s390x (0.27-1) ... 898s Setting up python-matplotlib-data (3.8.3-7build1) ... 898s Setting up libwebpmux3:s390x (1.5.0-0.1) ... 898s Setting up libxcomposite1:s390x (1:0.4.6-1) ... 898s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 898s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 898s Setting up libcc1-0:s390x (15-20250315-1ubuntu1) ... 898s Setting up python3-procrunner (2.3.3-2) ... 898s Setting up libsz2:s390x (1.1.3-1) ... 898s Setting up libitm1:s390x (15-20250315-1ubuntu1) ... 898s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 898s Setting up libann-cctbx-dev (1.1.2+doc-9build1) ... 898s Setting up libwacom-common (2.14.0-1) ... 898s Setting up libwayland-client0:s390x (1.23.1-3) ... 898s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 898s Setting up python3-sympy (1.13.3-5) ... 903s Setting up libice6:s390x (2:1.1.1-1) ... 903s Setting up mesa-libgallium:s390x (25.0.1-2ubuntu2) ... 903s Setting up liblapack3:s390x (3.12.1-2) ... 903s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 903s Setting up libqt5dbus5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 903s Setting up libssm2:s390x (1.4.0-2build1) ... 903s Setting up libatk1.0-0t64:s390x (2.56.0-2) ... 903s Setting up libgbm1:s390x (25.0.1-2ubuntu2) ... 903s Setting up libwacom9:s390x (2.14.0-1) ... 903s Setting up fontconfig-config (2.15.0-2.1ubuntu1) ... 903s Setting up python3-pytest (8.3.5-1) ... 903s Setting up libxtst6:s390x (2:1.2.5-1) ... 903s Setting up libwebpdemux2:s390x (1.5.0-0.1) ... 903s Setting up libxcursor1:s390x (1:1.2.3-1) ... 903s Setting up libgl1-mesa-dri:s390x (25.0.1-2ubuntu2) ... 903s Setting up libqt5network5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 903s Setting up libavahi-common3:s390x (0.8-16ubuntu2) ... 903s Setting up libqt5xml5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 903s Setting up dconf-service (0.40.0-5) ... 903s Setting up libqt5test5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 903s Setting up libccp4f0t64:s390x (8.0.0-4) ... 903s Setting up libinput-bin (1.27.1-1) ... 903s Setting up python3-pint (0.24.4-1) ... 904s Setting up libthai0:s390x (0.1.29-2build1) ... 904s Setting up libegl-mesa0:s390x (25.0.1-2ubuntu2) ... 904s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 904s Setting up libraqm0:s390x (0.10.2-1) ... 904s Setting up libpython3.13-dev:s390x (3.13.2-2) ... 904s Setting up python3-numpy (1:2.2.3+ds-5) ... 905s Setting up libjs-sphinxdoc (8.1.3-5) ... 905s Setting up cpp-14-s390x-linux-gnu (14.2.0-19ubuntu1) ... 905s Setting up cpp-14 (14.2.0-19ubuntu1) ... 905s Setting up libhdf5-310:s390x (1.14.5+repack-3) ... 905s Setting up python3-lxml:s390x (5.3.1-1build1) ... 905s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 905s Setting up libwayland-cursor0:s390x (1.23.1-3) ... 905s Setting up libegl1:s390x (1.7.0-1build1) ... 905s Setting up libgdk-pixbuf-2.0-0:s390x (2.42.12+dfsg-2) ... 905s Setting up python3-contourpy (1.3.1-1build1) ... 905s Setting up libfontconfig1:s390x (2.15.0-2.1ubuntu1) ... 905s Setting up libgcc-14-dev:s390x (14.2.0-19ubuntu1) ... 905s Setting up libstdc++-14-dev:s390x (14.2.0-19ubuntu1) ... 905s Setting up libsm6:s390x (2:1.2.4-1) ... 905s Setting up libavahi-client3:s390x (0.8-16ubuntu2) ... 905s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 906s Setting up python3-mrcfile (1.5.4-2) ... 906s Setting up libatk-bridge2.0-0t64:s390x (2.56.0-2) ... 906s Setting up libinput10:s390x (1.27.1-1) ... 906s Setting up gtk-update-icon-cache (4.18.2+ds-1) ... 906s Setting up libhdf5-hl-310:s390x (1.14.5+repack-3) ... 906s Setting up fontconfig (2.15.0-2.1ubuntu1) ... 908s Regenerating fonts cache... done. 908s Setting up libxft2:s390x (2.3.6-1build1) ... 908s Setting up libboost1.83-dev:s390x (1.83.0-4.1ubuntu2) ... 908s Setting up libglx-mesa0:s390x (25.0.1-2ubuntu2) ... 908s Setting up python3-scipy (1.14.1-4ubuntu2) ... 911s Setting up libpython3-dev:s390x (3.13.2-2) ... 911s Setting up libcbf1t64:s390x (0.9.7+dfsg1-5build1) ... 911s Setting up libglx0:s390x (1.7.0-1build1) ... 911s Setting up dconf-gsettings-backend:s390x (0.40.0-5) ... 911s Setting up cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 911s Setting up libccp4-dev:s390x (8.0.0-4) ... 911s Setting up python3.13-dev (3.13.2-2) ... 911s Setting up libtk8.6:s390x (8.6.16-1) ... 911s Setting up libpango-1.0-0:s390x (1.56.3-1) ... 911s Setting up libnetcdf22:s390x (1:4.9.3-1) ... 911s Setting up python3-h5py-serial (3.13.0-1) ... 911s Setting up libcairo2:s390x (1.18.4-1) ... 911s Setting up python3.13-tk (3.13.2-2) ... 911s Setting up python3-pil:s390x (11.1.0-5build1) ... 911s Setting up gcc-14-s390x-linux-gnu (14.2.0-19ubuntu1) ... 911s Setting up libgl1:s390x (1.7.0-1build1) ... 911s Setting up gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 911s Setting up adwaita-icon-theme (48.0-1) ... 911s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 911s Setting up libglut3.12:s390x (3.4.0-4) ... 911s Setting up libnotify4:s390x (0.8.4-1) ... 911s Setting up python3-dev (3.13.2-2) ... 911s Setting up libboost-python1.83-dev (1.83.0-4.1ubuntu2) ... 911s Setting up python3-pycbf (0.9.7+dfsg1-5build1) ... 911s Setting up python3-h5py (3.13.0-1) ... 912s Setting up g++-14-s390x-linux-gnu (14.2.0-19ubuntu1) ... 912s Setting up libglew2.2:s390x (2.2.0-4build1) ... 912s Setting up python3-hdf5plugin (5.0.0-1) ... 912s Setting up cpp (4:14.2.0-1ubuntu1) ... 912s Setting up libcairo-gobject2:s390x (1.18.4-1) ... 912s Setting up libpangoft2-1.0-0:s390x (1.56.3-1) ... 912s Setting up python3-nxmx (0.0.4-1) ... 912s Setting up libcups2t64:s390x (2.4.11-0ubuntu2) ... 912s Setting up libgtk-3-common (3.24.49-2ubuntu1) ... 912s Setting up libpangocairo-1.0-0:s390x (1.56.3-1) ... 912s Setting up libcctbx0 (2024.10+ds2+~3.22.1+ds1-4build2) ... 912s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 912s Setting up blt (2.5.3+dfsg-8) ... 912s Setting up python3-tk:s390x (3.13.2-1) ... 912s Setting up g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 912s Setting up python3-opengl (3.1.9+dfsg-1syncable1) ... 912s /usr/lib/python3/dist-packages/OpenGL/GL/AMD/vertex_shader_tessellator.py:30: SyntaxWarning: invalid escape sequence '\ ' 912s |\ |\ 913s Setting up gcc-14 (14.2.0-19ubuntu1) ... 913s Setting up libboost-python-dev (1.83.0.2ubuntu1) ... 913s Setting up libqt5gui5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 913s Setting up python3-pil.imagetk:s390x (11.1.0-5build1) ... 913s Setting up g++-14 (14.2.0-19ubuntu1) ... 913s Setting up libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4build2) ... 913s Setting up libqt5widgets5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 913s Setting up libqt5help5:s390x (5.15.15-6build1) ... 913s Setting up gcc (4:14.2.0-1ubuntu1) ... 913s Setting up g++ (4:14.2.0-1ubuntu1) ... 913s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 913s Setting up libqt5opengl5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 913s Setting up libqt5printsupport5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 913s Setting up libqt5designer5:s390x (5.15.15-6build1) ... 913s Setting up python3-pyqt5 (5.15.11+dfsg-2) ... 913s Setting up python3-pyqt5.qtopengl (5.15.11+dfsg-2) ... 913s Setting up python3-pymol (3.1.0+dfsg-1) ... 914s Setting up python3-fonttools (4.55.3-2build1) ... 914s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 914s Setting up python3-matplotlib (3.8.3-7build1) ... 916s Processing triggers for libc-bin (2.41-1ubuntu2) ... 916s Processing triggers for man-db (2.13.0-1) ... 917s Processing triggers for libglib2.0-0t64:s390x (2.84.0-1) ... 917s Setting up libgtk-3-0t64:s390x (3.24.49-2ubuntu1) ... 917s Processing triggers for udev (257.4-1ubuntu1) ... 917s Setting up libwxgtk3.2-1t64:s390x (3.2.6+dfsg-2ubuntu1) ... 917s Setting up libwxgtk-gl3.2-1t64:s390x (3.2.6+dfsg-2ubuntu1) ... 917s Setting up python3-wxgtk4.0 (4.2.2+dfsg-3build1) ... 918s Setting up python3-cctbx (2024.10+ds2+~3.22.1+ds1-4build2) ... 921s /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:18: SyntaxWarning: invalid escape sequence '\{' 921s []_,.;:"&<>()/\{}'`~!@#$%*|+- 921s /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:46: SyntaxWarning: invalid escape sequence '\/' 921s special_characters = """[]_,.;:"&<>()\/\{}'`~!@#$%*|+-""" 931s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:724: SyntaxWarning: invalid escape sequence '\o' 931s width=pairwise_differences_db, label='$\omega_{hkl}$' 931s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:739: SyntaxWarning: invalid escape sequence '\o' 931s axes[0].set_ylabel('Distribution of $\omega_{hbk}$') 931s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:740: SyntaxWarning: invalid escape sequence '\o' 931s axes[0].set_xlabel('Normalized PD ($\omega_{hbk}$)') 931s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:759: SyntaxWarning: invalid escape sequence '\o' 931s axes[1].set_xlabel('Sorted Normalized PD ($\omega_{hbk}$)') 931s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:778: SyntaxWarning: invalid escape sequence '\s' 931s axes[2].set_ylabel('Standard Deviation of $I_{hbk}/\sigma_{hbk}$') 931s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:807: SyntaxWarning: invalid escape sequence '\m' 931s axes_sadd.set_ylabel('$s_{\mathrm{fac}}^2 \\times s_{\mathrm{add}}^2$') 931s Processing triggers for libc-bin (2.41-1ubuntu2) ... 933s autopkgtest [13:21:33]: test cctbx: [----------------------- 933s Testing cctbx with python3.13: 933s Running 546 tests on 2 processors: 933s libtbx.python "/usr/lib/python3/dist-packages/annlib_adaptbx/annlib_adaptbx/sample.py" 933s libtbx.python "/usr/lib/python3/dist-packages/annlib_adaptbx/annlib_adaptbx/self_match.py" 933s "/usr/lib/cctbx/python3.13/boost_adaptbx/tests/tst_optional_copy" 933s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_libc_backtrace.py" 933s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_rational.py" 933s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_optional.py" 933s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_std_pair.py" 933s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_tuple.py" 933s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_stdout.py" 933s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_stderr_stdout.py" 933s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_deprecation_tools.py" 933s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_python_streambuf.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sf_low_res_accuracy.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_double_step_filtration.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_is_periodic.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_reindexing.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_map_to_asu_isym.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_data_manipulation.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_bfgs.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_dev.py" P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry/tests/tst_geometry.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/covariance/tests/tst_covariance.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_goodness_of_symmetry.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_from_map.py" P312 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_aniso_restraints.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/math/boost_python/tst_math.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_targets_fd.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_xray.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray.py" I41/acd 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_r1.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_shelxl_wght_ls.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_f_model.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/array_family/boost_python/tst_flex.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_uctbx.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_crystal_orientation.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_sgtbx.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_N_fold_rot.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_ext.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_distance_based_connectivity.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_super_cell.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adptbx/boost_python/tst_adptbx.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/boost_python/tst_miller.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_chemical_elements.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_xray_scattering.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_henke.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_icsd_radii.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_covalent_radii.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_neutron.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_sasaki.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_tiny_pse.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_wavelengths.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_formula.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_attenuation_coefficient.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/boost_python/tst_maptbx.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_bcr.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_loft.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/dmtbx/boost_python/tst_dmtbx.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/translation_search/boost_python/tst_translation_search.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_ext.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_proxy_registry.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_nonbonded_overlaps.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_process_nonbonded_proxies.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_angle_derivs.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_motif.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adp_restraints/tst_ext.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_math_module.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_krivy_gruber.py" --Quick 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_itvb_2001_table_a1427_hall_symbols.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_space_group_type_tidy_cb_op_t.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_denominators.py" P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_subgroups.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_lattice_symmetry.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints.py" P3 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints_cartesian.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_site_constraints.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reflection_statistics.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_harker.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_special_op_simplifier.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_twin_target.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/symbol_confidence.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/bravais_types.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_lookup_utils.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal.py" I41/acd 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_direct_space_asu.py" I41/acd 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pair_asu_table.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_asu_clusters.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_coordination_sequences.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_close_packing.py" R-3mr 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fourier_transform_real_part_at_x.py" P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller.py" P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem_2.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reciprocal_space_asu.py" P312 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_triplet_generator.py" P41 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_emma.py" P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_expand_to_p1.py" P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_change_basis.py" P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wilson_plot.py" P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_derivatives.py" P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_fast_gradients.py" P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F_sq P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_structure_factors.py" P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_weights_for_symmetry_summation.py" Pmmm 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_real_space_refinement_simple.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation_2.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_loc_res.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_target_and_gradients.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_merge_equivalents.py" P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grouped_data.py" P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_fft_map.py" P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sampled_model_density.py" P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fast_nv1995.py" F222 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_lbfgs.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_2.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grm_pickling.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_french_wilson.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/make_cns_input.py" P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/tst_cns_epsilon.py" P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/tst_cns_hl.py" P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/run_shelx76.py" P31 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pointgroup_tools.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/sub_lattice_tools.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/rational_matrices_point_groups.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/cosets.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_pg_tools.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_twin_laws.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_find_best_cell.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_amplitude_normalisation.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_statistics_graphs.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_web_change_basis.py" 933s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/direct_space_asu/proto/tst_asu.py" 933s libtbx.python 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"/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_molecules.py" 933s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_sparse.py" 933s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_lu_factorization.py" 933s libtbx.python "/usr/lib/python3/dist-packages/scitbx/iso_surface/tst_iso_surface.py" 933s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/simplex.py" 933s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/differential_evolution.py" 933s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/golden_section_search.py" 933s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/direct_search_simulated_annealing.py" 933s libtbx.python "/usr/lib/python3/dist-packages/scitbx/random/tests/tst_random.py" 933s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/tst_normal_equations.py" 933s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/test_problems.py" 933s libtbx.python "/usr/lib/python3/dist-packages/scitbx/glmtbx/tests/tst.py" 933s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_basic.py" 933s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_booth.py" 933s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_twisted.py" 933s libtbx.python "/usr/lib/python3/dist-packages/scitbx/suffixtree/test/tst_single.py" 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/absolute_structure/tests/tst_absolute_structure.py" --fix_random_seeds 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/ab_initio/tests/tst_ab_initio_ext.py" 933s 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" 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/masks/tests/tst_masks.py" 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/structure_factors/direct/tests/tst_standard_xray.py" 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_weighting_schemes.py" --fix_random_seeds 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_lbfgs.py" 933s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_reparametrisation" 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_occupancies.py" 933s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens" 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_same_group.py" 933s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_special_position" 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_reparametrisation.py" 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=naive 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_disorder.py" 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=levenberg-marquardt 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_rigid.py" 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_direction.py" 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_adp_restraints.py" 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_manager.py" 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_restraints.py" --verbose --scatterers=5 --resolution=0.2 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_refine.py" 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py" 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/tests/tst_utils.py" 933s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_least_squares.py" 933s libtbx.python "/usr/lib/python3/dist-packages/rstbx/dps_core/tst_iotbx_converter.py" 933s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_predict.py" 933s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_ewald_sphere.py" 933s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_partial_derivatives.py" 933s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/fastbragg/tst_bragg_minimal.py" 933s libtbx.python "/usr/lib/python3/dist-packages/rstbx/sublattice_support/tst_sublattice.py" 933s libtbx.python -c "from rstbx.run_tests import run; run()" 933s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/core_toolbox/boost_python/tst_small_image.py" 933s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/diffraction/geometry.py" 933s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/math_support/sphere_formulae.py" 933s 933s libtbx.python "/usr/lib/python3/dist-packages/annlib_adaptbx/annlib_adaptbx/self_match.py" [OK] 0.1s 933s Time: 0.13 933s Return code: 0 933s OKs: 1 933s Standard out: 933s OK 933s "/usr/lib/cctbx/python3.13/boost_adaptbx/tests/tst_optional_copy" [OK] 0.0s 933s Time: 0.00 933s Return code: 0 933s OKs: 1 933s Standard out: 933s OK 933s Standard error: 933s show_stack(1): /usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_libc_backtrace.py(9) run 933s show_stack(2): /usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_libc_backtrace.py(15) 933s libc backtrace (21 frames, most recent call last): 933s /usr/bin/python3.13() [0x11fc30a] 933s /lib/s390x-linux-gnu/libc.so.6(__libc_start_main+0xb4) [0x3ffa782be44] 933s /lib/s390x-linux-gnu/libc.so.6(+0x2bd46) [0x3ffa782bd46] 933s /usr/bin/python3.13(Py_BytesMain+0x38) [0x11fd968] 933s /usr/bin/python3.13(Py_RunMain+0x316) [0x1264d06] 933s /usr/bin/python3.13() [0x126758c] 933s /usr/bin/python3.13() [0x1267836] 933s /usr/bin/python3.13() [0x1268108] 933s /usr/bin/python3.13() [0x123e8cc] 933s /usr/bin/python3.13() [0x1245902] 933s /usr/bin/python3.13(PyEval_EvalCode+0x100) [0x1216190] 933s /usr/bin/python3.13(_PyEval_EvalFrameDefault+0x3826) [0x10de166] 933s /usr/bin/python3.13(PyObject_Vectorcall+0x9a) [0x10be61a] 933s /usr/bin/python3.13(_PyObject_MakeTpCall+0x2b2) [0x10b75f2] 933s /lib/s390x-linux-gnu/libboost_python313.so.1.83.0(+0x238f6) [0x3ffa6da38f6] 933s /lib/s390x-linux-gnu/libboost_python313.so.1.83.0(boost::python::handle_exception_impl(boost::function0)+0x88) [0x3ffa6da3648] 933s /lib/s390x-linux-gnu/libboost_python313.so.1.83.0(+0x26e7a) [0x3ffa6da6e7a] 933s /lib/s390x-linux-gnu/libboost_python313.so.1.83.0(boost::python::objects::function::call(_object*, _object*) const+0x80) [0x3ffa6da69b0] 933s /usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-313-s390x-linux-gnu.so(+0x1a406) [0x3ffa6e9a406] 933s /usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-313-s390x-linux-gnu.so(+0x24d2c) [0x3ffa6ea4d2c] 933s /usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-313-s390x-linux-gnu.so(+0x2467e) [0x3ffa6ea467e] 933s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_libc_backtrace.py" [OK] 0.0s 933s Time: 0.04 933s Return code: 0 933s OKs: 1 933s Standard out: 933s OK 933s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_rational.py" [OK] 0.1s 933s Time: 0.08 933s Return code: 0 933s OKs: 1 933s Standard out: 933s OK 933s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_optional.py" [OK] 0.1s 933s Time: 0.06 933s Return code: 0 933s OKs: 1 933s Standard out: 933s exercise_wstring: 933s OK 933s libtbx.python "/usr/lib/python3/dist-packages/annlib_adaptbx/annlib_adaptbx/sample.py" [OK] 0.4s 933s Time: 0.38 933s Return code: 0 933s OKs: 1 933s Standard out: 933s OK 933s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_std_pair.py" [OK] 0.1s 933s Time: 0.07 933s Return code: 0 933s OKs: 1 933s Standard out: 933s OK 933s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_tuple.py" [OK] 0.0s 933s Time: 0.04 933s Return code: 0 933s OKs: 1 933s Standard out: 933s OK 934s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_stderr_stdout.py" [OK] 0.0s 934s Time: 0.04 934s Return code: 0 934s OKs: 1 934s Standard out: 934s OK 934s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_stdout.py" [OK] 0.1s 934s Time: 0.08 934s Return code: 0 934s OKs: 1 934s Standard out: 934s OK 934s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_deprecation_tools.py" [OK] 0.0s 934s Time: 0.04 934s Return code: 0 934s OKs: 1 934s Standard out: 934s OK 935s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 935s 1 935s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 935s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_python_streambuf.py" [EXPECTED FAIL] 1.9s 935s Time: 1.90 935s Return code: 1 935s OKs: 0 935s Standard error: 935s Traceback (most recent call last): 935s File "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_python_streambuf.py", line 7, in 935s import StringIO 935s ModuleNotFoundError: No module named 'StringIO' 937s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 937s 139 937s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 937s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sf_low_res_accuracy.py" [FAIL] 3.3s 937s Time: 3.26 937s Return code: 139 937s OKs: 0 937s Standard error: 937s 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/cctbx/regression/tst_miller_double_step_filtration.py" [FAIL] 4.3s 940s Time: 4.31 940s Return code: 139 940s OKs: 0 940s Standard error: 940s Segmentation fault (core dumped) 943s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 943s 139 943s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 943s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_is_periodic.py" [FAIL] 5.8s 943s Time: 5.77 943s Return code: 139 943s OKs: 0 943s Standard error: 943s Segmentation fault (core dumped) 943s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_map_to_asu_isym.py" [OK] 0.4s 943s Time: 0.42 943s Return code: 0 943s OKs: 1 943s Standard out: 943s OK 945s Standard error: 945s Segmentation fault (core dumped) 945s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 945s 139 945s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 945s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_reindexing.py" [FAIL] 5.6s 945s Time: 5.59 945s Return code: 139 945s OKs: 0 948s Standard error: 948s Segmentation fault (core dumped) 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/cctbx/regression/tst_miller_data_manipulation.py" [FAIL] 5.0s 948s Time: 4.99 948s Return code: 139 948s OKs: 0 950s Standard error: 950s Segmentation fault (core dumped) 950s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 950s 139 950s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 950s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_bfgs.py" [FAIL] 5.0s 950s Time: 4.98 950s Return code: 139 950s OKs: 0 953s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 953s 139 953s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 953s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_dev.py" P31 [FAIL] 5.0s 953s Time: 5.02 953s Return code: 139 953s OKs: 0 953s Standard error: 953s Segmentation fault (core dumped) 956s Standard error: 956s Segmentation fault (core dumped) 956s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 956s 139 956s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 956s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry/tests/tst_geometry.py" [FAIL] 5.5s 956s Time: 5.53 956s Return code: 139 956s OKs: 0 958s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 958s 139 958s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 958s libtbx.python "/usr/lib/python3/dist-packages/cctbx/covariance/tests/tst_covariance.py" [FAIL] 5.4s 958s Time: 5.40 958s Return code: 139 958s OKs: 0 958s Standard error: 958s Segmentation fault (core dumped) 961s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 961s 139 961s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 961s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_goodness_of_symmetry.py" [FAIL] 5.4s 961s Time: 5.43 961s Return code: 139 961s OKs: 0 961s Standard error: 961s Segmentation fault (core dumped) 962s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_aniso_restraints.py" [OK] 0.3s 962s Time: 0.27 962s Return code: 0 962s OKs: 1 962s Standard out: 962s Skipping exercise(): chem_data directory not available 962s OK 962s libtbx.python "/usr/lib/python3/dist-packages/cctbx/math/boost_python/tst_math.py" [OK] 0.1s 962s Time: 0.07 962s Return code: 0 962s OKs: 1 962s Standard out: 962s OK 962s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_targets_fd.py" [OK] 0.3s 962s Time: 0.31 962s Return code: 0 962s OKs: 1 962s Standard out: 962s OK 964s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 964s 139 964s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 964s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_from_map.py" P312 [FAIL] 5.6s 964s Time: 5.63 964s Return code: 139 964s OKs: 0 964s Standard error: 964s Segmentation fault (core dumped) 967s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 967s 139 967s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 967s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_xray.py" [FAIL] 5.2s 967s Time: 5.21 967s Return code: 139 967s OKs: 0 967s Standard error: 967s Segmentation fault (core dumped) 970s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 970s 139 970s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 970s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray.py" I41/acd [FAIL] 5.8s 970s Time: 5.83 970s Return code: 139 970s OKs: 0 970s Standard error: 970s Segmentation fault (core dumped) 973s Standard error: 973s Segmentation fault (core dumped) 973s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 973s 139 973s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 973s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_r1.py" [FAIL] 5.5s 973s Time: 5.47 973s Return code: 139 973s OKs: 0 975s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 975s 139 975s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 975s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_shelxl_wght_ls.py" [FAIL] 5.3s 975s Time: 5.30 975s Return code: 139 975s OKs: 0 975s Standard error: 975s Segmentation fault (core dumped) 978s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 978s 139 978s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 978s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_f_model.py" [FAIL] 5.3s 978s Time: 5.33 978s Return code: 139 978s OKs: 0 978s Standard error: 978s Segmentation fault (core dumped) 981s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 981s 139 981s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 981s libtbx.python "/usr/lib/python3/dist-packages/cctbx/array_family/boost_python/tst_flex.py" [FAIL] 5.4s 981s Time: 5.40 981s Return code: 139 981s OKs: 0 981s Standard error: 981s Segmentation fault (core dumped) 983s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 983s 139 983s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 983s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_uctbx.py" [FAIL] 5.2s 983s Time: 5.17 983s Return code: 139 983s OKs: 0 983s Standard error: 983s Segmentation fault (core dumped) 985s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 985s 139 985s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 985s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_crystal_orientation.py" [FAIL] 4.8s 985s Time: 4.83 985s Return code: 139 985s OKs: 0 985s Standard error: 985s Segmentation fault (core dumped) 986s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_N_fold_rot.py" [OK] 0.2s 986s Time: 0.16 986s Return code: 0 986s OKs: 1 986s Standard out: 986s OK 988s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 988s 139 988s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 988s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_sgtbx.py" [FAIL] 5.1s 988s Time: 5.11 988s Return code: 139 988s OKs: 0 988s Standard error: 988s Segmentation fault (core dumped) 991s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 991s 139 991s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 991s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_ext.py" [FAIL] 5.5s 991s Time: 5.49 991s Return code: 139 991s OKs: 0 991s Standard error: 991s Segmentation fault (core dumped) 993s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 993s 139 993s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 993s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_distance_based_connectivity.py" [FAIL] 5.1s 993s Time: 5.15 993s Return code: 139 993s OKs: 0 993s Standard error: 993s Segmentation fault (core dumped) 997s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 997s 139 997s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 997s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_super_cell.py" [FAIL] 5.9s 997s Time: 5.94 997s Return code: 139 997s OKs: 0 997s Standard error: 997s Segmentation fault (core dumped) 1000s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1000s 139 1000s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1000s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adptbx/boost_python/tst_adptbx.py" [FAIL] 6.4s 1000s Time: 6.43 1000s Return code: 139 1000s OKs: 0 1000s Standard error: 1000s Segmentation fault (core dumped) 1000s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_chemical_elements.py" [OK] 0.1s 1000s Time: 0.08 1000s Return code: 0 1000s OKs: 1 1000s Standard out: 1000s OK 1002s Standard error: 1002s Segmentation fault (core dumped) 1002s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1002s 139 1002s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1002s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/boost_python/tst_miller.py" [FAIL] 5.4s 1002s Time: 5.37 1002s Return code: 139 1002s OKs: 0 1002s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_henke.py" [OK] 0.1s 1002s Time: 0.06 1002s Return code: 0 1002s OKs: 1 1002s Standard out: 1002s OK 1003s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_icsd_radii.py" [OK] 0.1s 1003s Time: 0.07 1003s Return code: 0 1003s OKs: 1 1003s Standard out: 1003s OK 1003s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_covalent_radii.py" [OK] 0.1s 1003s Time: 0.06 1003s Return code: 0 1003s OKs: 1 1003s Standard out: 1003s OK 1003s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_neutron.py" [OK] 0.1s 1003s Time: 0.07 1003s Return code: 0 1003s OKs: 1 1003s Standard out: 1003s OK 1003s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_sasaki.py" [OK] 0.1s 1003s Time: 0.07 1003s Return code: 0 1003s OKs: 1 1003s Standard out: 1003s OK 1003s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_tiny_pse.py" [OK] 0.1s 1003s Time: 0.06 1003s Return code: 0 1003s OKs: 1 1003s Standard out: 1003s OK 1003s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_wavelengths.py" [OK] 0.1s 1003s Time: 0.06 1003s Return code: 0 1003s OKs: 1 1003s Standard out: 1003s OK 1005s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1005s 139 1005s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1005s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_xray_scattering.py" [FAIL] 4.8s 1005s Time: 4.76 1005s Return code: 139 1005s OKs: 0 1005s Standard error: 1005s 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/cctbx/eltbx/tests/tst_formula.py" [FAIL] 4.0s 1007s Time: 3.96 1007s Return code: 139 1007s OKs: 0 1007s Standard error: 1007s Segmentation fault (core dumped) 1009s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1009s 139 1009s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1009s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_attenuation_coefficient.py" [FAIL] 4.4s 1009s Standard error: 1009s Segmentation fault (core dumped) 1009s Time: 4.37 1009s Return code: 139 1009s OKs: 0 1012s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1012s 139 1012s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1012s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/boost_python/tst_maptbx.py" [FAIL] 5.2s 1012s Time: 5.19 1012s Return code: 139 1012s OKs: 0 1012s Standard error: 1012s Segmentation fault (core dumped) 1015s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1015s 139 1015s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1015s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_bcr.py" [FAIL] 6.4s 1015s Standard error: 1015s Segmentation fault (core dumped) 1015s Time: 6.41 1015s Return code: 139 1015s OKs: 0 1018s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1018s 139 1018s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1018s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_loft.py" [FAIL] 6.0s 1018s Time: 5.99 1018s Return code: 139 1018s OKs: 0 1018s Standard error: 1018s Segmentation fault (core dumped) 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/cctbx/dmtbx/boost_python/tst_dmtbx.py" [FAIL] 4.8s 1020s Time: 4.82 1020s Return code: 139 1020s OKs: 0 1020s Standard error: 1020s Segmentation fault (core dumped) 1023s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1023s 139 1023s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1023s libtbx.python "/usr/lib/python3/dist-packages/cctbx/translation_search/boost_python/tst_translation_search.py" [FAIL] 4.6s 1023s Time: 4.60 1023s Return code: 139 1023s OKs: 0 1023s Standard error: 1023s Segmentation fault (core dumped) 1023s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_proxy_registry.py" [OK] 0.2s 1023s Time: 0.17 1023s Return code: 0 1023s OKs: 1 1023s Standard out: 1023s OK 1023s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_nonbonded_overlaps.py" [OK] 0.5s 1023s Time: 0.55 1023s Return code: 0 1023s OKs: 0 1023s Standard out: 1023s chem_data not present, skipping 1024s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_process_nonbonded_proxies.py" [OK] 0.5s 1024s Time: 0.54 1024s Return code: 0 1024s OKs: 0 1024s Standard out: 1024s Test skipped, need monomer library 1025s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1025s 139 1025s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1025s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_ext.py" [FAIL] 5.1s 1025s Time: 5.08 1025s Return code: 139 1025s OKs: 0 1025s Standard error: 1025s Segmentation fault (core dumped) 1025s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_motif.py" [OK] 0.2s 1025s Time: 0.17 1025s Return code: 0 1025s OKs: 0 1025s Standard out: 1025s u+s,u,s: 0.13 0.12 0.01 1028s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1028s 139 1028s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1028s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_angle_derivs.py" [FAIL] 3.8s 1028s Time: 3.83 1028s Return code: 139 1028s OKs: 0 1028s Standard error: 1028s Segmentation fault (core dumped) 1028s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_math_module.py" [OK] 0.1s 1028s Time: 0.07 1028s Return code: 0 1028s OKs: 1 1028s Standard out: 1028s OK 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/cctbx/adp_restraints/tst_ext.py" [FAIL] 4.9s 1030s Time: 4.90 1030s Return code: 139 1030s OKs: 0 1030s Standard error: 1030s Segmentation fault (core dumped) 1033s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1033s 139 1033s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1033s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_krivy_gruber.py" --Quick [FAIL] 5.2s 1033s Time: 5.17 1033s Return code: 139 1033s OKs: 0 1033s Standard error: 1033s Segmentation fault (core dumped) 1033s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_itvb_2001_table_a1427_hall_symbols.py" [OK] 0.2s 1033s Time: 0.16 1033s Return code: 0 1033s OKs: 1 1033s Standard out: 1033s Skipping exercise(): input file not available 1033s OK 1035s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1035s 139 1035s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1035s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx.py" [FAIL] 4.9s 1035s Time: 4.91 1035s Return code: 139 1035s OKs: 0 1035s Standard error: 1035s Segmentation fault (core dumped) 1038s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1038s 139 1038s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1038s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_space_group_type_tidy_cb_op_t.py" [FAIL] 4.6s 1038s Time: 4.57 1038s Return code: 139 1038s OKs: 0 1038s Standard error: 1038s 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/cctbx/regression/tst_sgtbx_denominators.py" P31 [FAIL] 4.6s 1040s Time: 4.56 1040s Return code: 139 1040s OKs: 0 1040s Standard error: 1040s Segmentation fault (core dumped) 1042s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1042s 139 1042s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1042s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_subgroups.py" [FAIL] 4.7s 1042s Time: 4.71 1042s Return code: 139 1042s OKs: 0 1042s Standard error: 1042s Segmentation fault (core dumped) 1045s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1045s 139 1045s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1045s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_lattice_symmetry.py" [FAIL] 4.8s 1045s Time: 4.82 1045s Return code: 139 1045s OKs: 0 1045s Standard error: 1045s 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/cctbx/regression/tst_adp_constraints.py" P3 [FAIL] 4.9s 1047s Time: 4.91 1047s Return code: 139 1047s OKs: 0 1047s Standard error: 1047s Segmentation fault (core dumped) 1048s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_site_constraints.py" [OK] 0.3s 1048s Time: 0.28 1048s Return code: 0 1048s OKs: 0 1048s Standard out: 1048s Skipping process_zeolite_atlas(): input file not available 1048s u+s,u,s: 0.23 0.21 0.02 1050s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1050s 139 1050s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1050s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints_cartesian.py" [FAIL] 4.9s 1050s Time: 4.94 1050s Return code: 139 1050s OKs: 0 1050s Standard error: 1050s Segmentation fault (core dumped) 1052s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1052s 139 1052s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1052s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reflection_statistics.py" [FAIL] 4.6s 1052s Time: 4.58 1052s Return code: 139 1052s OKs: 0 1052s Standard error: 1052s Segmentation fault (core dumped) 1055s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1055s 139 1055s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1055s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_harker.py" [FAIL] 4.9s 1055s Time: 4.92 1055s Return code: 139 1055s OKs: 0 1055s Standard error: 1055s Segmentation fault (core dumped) 1057s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1057s 139 1057s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1057s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_special_op_simplifier.py" [FAIL] 4.9s 1057s Time: 4.89 1057s Return code: 139 1057s OKs: 0 1057s Standard error: 1057s Segmentation fault (core dumped) 1060s Standard error: 1060s Segmentation fault (core dumped) 1060s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1060s 139 1060s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1060s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_twin_target.py" [FAIL] 5.1s 1060s Time: 5.08 1060s Return code: 139 1060s 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/cctbx/sgtbx/symbol_confidence.py" [FAIL] 4.8s 1062s Time: 4.83 1062s Return code: 139 1062s OKs: 0 1062s Standard error: 1062s Segmentation fault (core dumped) 1064s Standard error: 1064s Segmentation fault (core dumped) 1064s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1064s 139 1064s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1064s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/bravais_types.py" [FAIL] 4.4s 1064s Time: 4.44 1064s Return code: 139 1064s OKs: 0 1067s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1067s 139 1067s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1067s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_lookup_utils.py" [FAIL] 4.7s 1067s Time: 4.73 1067s Return code: 139 1067s OKs: 0 1067s Standard error: 1067s Segmentation fault (core dumped) 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/cctbx/regression/tst_crystal.py" I41/acd [FAIL] 5.2s 1069s Standard error: 1069s Segmentation fault (core dumped) 1069s Time: 5.18 1069s Return code: 139 1069s OKs: 0 1072s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1072s 139 1072s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1072s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_direct_space_asu.py" I41/acd [FAIL] 5.1s 1072s Time: 5.15 1072s Return code: 139 1072s OKs: 0 1072s Standard error: 1072s Segmentation fault (core dumped) 1075s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1075s 139 1075s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1075s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pair_asu_table.py" [FAIL] 5.2s 1075s Time: 5.24 1075s Return code: 139 1075s OKs: 0 1075s Standard error: 1075s Segmentation fault (core dumped) 1075s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_coordination_sequences.py" [OK] 0.3s 1075s Time: 0.30 1075s Return code: 0 1075s OKs: 1 1075s Standard out: 1075s Skipping exercise(): input file not available 1075s OK 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/cctbx/regression/tst_crystal_asu_clusters.py" [FAIL] 5.1s 1077s Time: 5.11 1077s Return code: 139 1077s OKs: 0 1077s Standard error: 1077s Segmentation fault (core dumped) 1080s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1080s 139 1080s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1080s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_close_packing.py" R-3mr [FAIL] 4.8s 1080s Time: 4.83 1080s Return code: 139 1080s OKs: 0 1080s Standard error: 1080s Segmentation fault (core dumped) 1082s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1082s 139 1082s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1082s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fourier_transform_real_part_at_x.py" P31 [FAIL] 5.1s 1082s Time: 5.12 1082s Return code: 139 1082s OKs: 0 1082s Standard error: 1082s Segmentation fault (core dumped) 1085s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1085s 139 1085s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1085s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller.py" P31 [FAIL] 5.2s 1085s Time: 5.23 1085s Return code: 139 1085s OKs: 0 1085s Standard error: 1085s Segmentation fault (core dumped) 1085s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem_2.py" [OK] 0.2s 1085s Time: 0.23 1085s Return code: 0 1085s OKs: 0 1085s Standard out: 1085s Skipping test: phenix not available 1087s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1087s 139 1087s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1087s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem.py" [FAIL] 5.5s 1087s Time: 5.52 1087s Return code: 139 1087s OKs: 0 1087s Standard error: 1087s Segmentation fault (core dumped) 1090s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1090s 139 1090s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1090s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reciprocal_space_asu.py" P312 [FAIL] 4.8s 1090s Time: 4.80 1090s Return code: 139 1090s OKs: 0 1090s Standard error: 1090s Segmentation fault (core dumped) 1092s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1092s 139 1092s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1092s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_triplet_generator.py" P41 [FAIL] 4.9s 1092s Time: 4.86 1092s Return code: 139 1092s OKs: 0 1092s Standard error: 1092s Segmentation fault (core dumped) 1095s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1095s 139 1095s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1095s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_emma.py" P31 [FAIL] 5.3s 1095s Time: 5.28 1095s Return code: 139 1095s OKs: 0 1095s Standard error: 1095s Segmentation fault (core dumped) 1098s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1098s 139 1098s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1098s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_expand_to_p1.py" P31 [FAIL] 5.3s 1098s Time: 5.30 1098s Return code: 139 1098s OKs: 0 1098s Standard error: 1098s Segmentation fault (core dumped) 1100s Standard error: 1100s Segmentation fault (core dumped) 1100s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1100s 139 1100s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1100s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_change_basis.py" P31 [FAIL] 5.0s 1100s Time: 4.97 1100s Return code: 139 1100s OKs: 0 1103s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1103s 139 1103s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1103s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wilson_plot.py" P31 [FAIL] 4.9s 1103s Time: 4.94 1103s Return code: 139 1103s OKs: 0 1103s Standard error: 1103s Segmentation fault (core dumped) 1105s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1105s 139 1105s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1105s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_derivatives.py" P31 [FAIL] 4.9s 1105s Time: 4.89 1105s Return code: 139 1105s OKs: 0 1105s Standard error: 1105s Segmentation fault (core dumped) 1108s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1108s 139 1108s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1108s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_fast_gradients.py" P31 [FAIL] 5.0s 1108s Time: 5.01 1108s Return code: 139 1108s OKs: 0 1108s Standard error: 1108s Segmentation fault (core dumped) 1110s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1110s 139 1110s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1110s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F P31 [FAIL] 5.0s 1110s Time: 4.98 1110s Return code: 139 1110s OKs: 0 1110s Standard error: 1110s Segmentation fault (core dumped) 1110s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1110s 139 1110s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1110s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F_sq P31 [FAIL] 2.4s 1110s Time: 2.42 1110s Return code: 139 1110s OKs: 0 1110s Standard error: 1110s Segmentation fault (core dumped) 1113s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1113s 139 1113s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1113s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_structure_factors.py" P31 [FAIL] 2.7s 1113s Time: 2.68 1113s Return code: 139 1113s OKs: 0 1113s Standard error: 1113s Segmentation fault (core dumped) 1115s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1115s 139 1115s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1115s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_weights_for_symmetry_summation.py" Pmmm [FAIL] 5.0s 1115s Time: 5.02 1115s Return code: 139 1115s OKs: 0 1115s Standard error: 1115s Segmentation fault (core dumped) 1118s Standard error: 1118s Segmentation fault (core dumped) 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/cctbx/maptbx/tst_real_space_refinement_simple.py" [FAIL] 4.9s 1118s Time: 4.91 1118s Return code: 139 1118s OKs: 0 1120s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1120s 139 1120s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1120s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation.py" [FAIL] 4.9s 1120s Time: 4.91 1120s Return code: 139 1120s OKs: 0 1120s Standard error: 1120s Segmentation fault (core dumped) 1123s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1123s 139 1123s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1123s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation_2.py" [FAIL] 4.9s 1123s Time: 4.90 1123s Return code: 139 1123s OKs: 0 1123s Standard error: 1123s Segmentation fault (core dumped) 1126s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1126s 139 1126s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1126s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_loc_res.py" [FAIL] 6.2s 1126s Time: 6.17 1126s Return code: 139 1126s OKs: 0 1126s Standard error: 1126s Segmentation fault (core dumped) 1129s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1129s 139 1129s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1129s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_target_and_gradients.py" [FAIL] 6.2s 1129s Time: 6.15 1129s Return code: 139 1129s OKs: 0 1129s Standard error: 1129s Segmentation fault (core dumped) 1132s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1132s 139 1132s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1132s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_merge_equivalents.py" P31 [FAIL] 5.1s 1132s Time: 5.10 1132s Return code: 139 1132s OKs: 0 1132s Standard error: 1132s Segmentation fault (core dumped) 1134s Standard error: 1134s Segmentation fault (core dumped) 1134s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1134s 139 1134s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1134s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grouped_data.py" P31 [FAIL] 5.2s 1134s Time: 5.20 1134s Return code: 139 1134s OKs: 0 1137s Standard error: 1137s Segmentation fault (core dumped) 1137s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1137s 139 1137s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1137s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_fft_map.py" P31 [FAIL] 5.2s 1137s Time: 5.15 1137s Return code: 139 1137s OKs: 0 1139s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1139s 139 1139s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1139s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sampled_model_density.py" P31 [FAIL] 5.1s 1139s Time: 5.08 1139s Return code: 139 1139s OKs: 0 1139s Standard error: 1139s Segmentation fault (core dumped) 1140s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints.py" [OK] 0.6s 1140s Time: 0.60 1140s Return code: 0 1140s OKs: 1 1140s Standard out: 1140s OK 1142s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1142s 139 1142s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1142s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fast_nv1995.py" F222 [FAIL] 5.2s 1142s Time: 5.19 1142s Return code: 139 1142s OKs: 0 1142s Standard error: 1142s Segmentation fault (core dumped) 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/cctbx/regression/tst_geometry_restraints_lbfgs.py" [FAIL] 4.8s 1144s Time: 4.81 1144s Return code: 139 1144s OKs: 0 1144s Standard error: 1144s Segmentation fault (core dumped) 1145s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grm_pickling.py" [OK] 0.3s 1145s Time: 0.32 1145s Return code: 0 1145s OKs: 0 1145s Standard out: 1145s Can not initialize monomer_library, skipping test. 1147s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1147s 139 1147s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1147s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_2.py" [FAIL] 5.8s 1147s Time: 5.85 1147s Return code: 139 1147s OKs: 0 1147s Standard error: 1147s Segmentation fault (core dumped) 1150s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1150s 139 1150s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1150s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_french_wilson.py" [FAIL] 5.5s 1150s Time: 5.50 1150s Return code: 139 1150s OKs: 0 1150s Standard error: 1150s Segmentation fault (core dumped) 1150s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/tst_cns_epsilon.py" P31 [OK] 0.2s 1150s Time: 0.19 1150s Return code: 0 1150s OKs: 0 1150s Standard out: 1150s Skipping tests: cns not available. 1150s u+s,u,s: 0.15 0.14 0.01 1151s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/tst_cns_hl.py" P31 [OK] 0.2s 1151s Time: 0.19 1151s Return code: 0 1151s OKs: 0 1151s Standard out: 1151s Skipping tests: cns not available. 1151s u+s,u,s: 0.14 0.13 0.01 1151s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/run_shelx76.py" P31 [OK] 0.2s 1151s Time: 0.21 1151s Return code: 0 1151s OKs: 0 1151s Standard out: 1151s shelx76 not available. 1153s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1153s 139 1153s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1153s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/make_cns_input.py" P31 [FAIL] 5.3s 1153s Time: 5.28 1153s Return code: 139 1153s OKs: 0 1153s Standard error: 1153s Segmentation fault (core dumped) 1155s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1155s 139 1155s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1155s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pointgroup_tools.py" [FAIL] 4.4s 1155s Time: 4.36 1155s Return code: 139 1155s OKs: 0 1155s Standard error: 1155s Segmentation fault (core dumped) 1158s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1158s 139 1158s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1158s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/sub_lattice_tools.py" [FAIL] 5.0s 1158s Time: 4.96 1158s Return code: 139 1158s OKs: 0 1158s Standard error: 1158s 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/cctbx/sgtbx/rational_matrices_point_groups.py" [FAIL] 4.9s 1160s Time: 4.94 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/cctbx/sgtbx/cosets.py" [FAIL] 4.9s 1163s Time: 4.85 1163s Return code: 139 1163s OKs: 0 1163s Standard error: 1163s Segmentation fault (core dumped) 1165s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1165s 139 1165s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1165s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_pg_tools.py" [FAIL] 5.0s 1165s Time: 4.99 1165s Return code: 139 1165s OKs: 0 1165s Standard error: 1165s Segmentation fault (core dumped) 1168s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1168s 139 1168s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1168s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_twin_laws.py" [FAIL] 5.1s 1168s Time: 5.07 1168s Return code: 139 1168s OKs: 0 1168s Standard error: 1168s Segmentation fault (core dumped) 1170s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1170s 139 1170s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1170s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_find_best_cell.py" [FAIL] 5.0s 1170s Time: 5.01 1170s Return code: 139 1170s OKs: 0 1170s Standard error: 1170s Segmentation fault (core dumped) 1173s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1173s 139 1173s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1173s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_amplitude_normalisation.py" [FAIL] 5.1s 1173s Time: 5.09 1173s Return code: 139 1173s OKs: 0 1173s Standard error: 1173s 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/cctbx/regression/tst_statistics_graphs.py" [FAIL] 5.3s 1175s Time: 5.34 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/cctbx/regression/tst_web_change_basis.py" [FAIL] 5.7s 1178s Time: 5.75 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/cctbx/sgtbx/direct_space_asu/proto/tst_asu.py" [FAIL] 6.0s 1181s Time: 5.95 1181s Return code: 139 1181s OKs: 0 1181s Standard error: 1181s Segmentation fault (core dumped) 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/cctbx/regression/tst_sgtbx_tidy_pickling.py" [FAIL] 5.6s 1184s Time: 5.61 1184s Return code: 139 1184s OKs: 0 1184s Standard error: 1184s Segmentation fault (core dumped) 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/cctbx/masks/tests/tst_flood_fill.py" [FAIL] 5.2s 1187s Time: 5.23 1187s Return code: 139 1187s OKs: 0 1187s Standard error: 1187s Segmentation fault (core dumped) 1187s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/observations/tst_observations.py" [OK] 0.3s 1187s Time: 0.35 1187s Return code: 0 1187s OKs: 1 1187s Standard out: 1187s OK 1189s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1189s 139 1189s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1189s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_r_free_utils.py" [FAIL] 5.4s 1189s Time: 5.42 1189s Return code: 139 1189s OKs: 0 1189s Standard error: 1189s Segmentation fault (core dumped) 1192s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1192s 139 1192s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1192s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_ccp.py" [FAIL] 5.4s 1192s Time: 5.38 1192s Return code: 139 1192s OKs: 0 1192s Standard error: 1192s Segmentation fault (core dumped) 1195s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1195s 139 1195s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1195s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_mask.py" [FAIL] 5.8s 1195s Time: 5.84 1195s Return code: 139 1195s OKs: 0 1195s Standard error: 1195s Segmentation fault (core dumped) 1198s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1198s 139 1198s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1198s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_map_peak_3d_as_2d.py" [FAIL] 5.8s 1198s Standard error: 1198s Segmentation fault (core dumped) 1198s Time: 5.78 1198s Return code: 139 1198s OKs: 0 1201s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1201s 139 1201s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1201s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_asymmetric_map.py" [FAIL] 5.4s 1201s Time: 5.44 1201s Return code: 139 1201s OKs: 0 1201s Standard error: 1201s Segmentation fault (core dumped) 1204s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1204s 139 1204s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1204s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_peak_volume_estimate.py" [FAIL] 5.4s 1204s Time: 5.38 1204s Return code: 139 1204s OKs: 0 1204s Standard error: 1204s Segmentation fault (core dumped) 1207s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1207s 139 1207s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1207s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_resolution_from_map_and_model.py" [FAIL] 6.2s 1207s Time: 6.18 1207s Return code: 139 1207s OKs: 0 1207s Standard error: 1207s Segmentation fault (core dumped) 1210s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1210s 139 1210s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1210s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_curves.py" [FAIL] 6.8s 1210s Time: 6.85 1210s Return code: 139 1210s OKs: 0 1210s Standard error: 1210s Segmentation fault (core dumped) 1213s Standard error: 1213s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1213s 139 1213s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1213s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_radius_as_central_peak_width.py" [FAIL] 6.2s 1213s Time: 6.24 1213s Return code: 139 1213s OKs: 0 1213s Segmentation fault (core dumped) 1214s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_box.py" [OK] 0.7s 1214s Time: 0.71 1214s Return code: 0 1214s OKs: 0 1214s Standard out: 1214s phenix is not available, skipping test 1214s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_create_models_or_maps.py" [OK] 0.6s 1214s Time: 0.59 1214s Return code: 0 1214s OKs: 1 1214s Standard out: 1214s Skipping exercise(): chem_data directory not available 1214s OK 1216s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1216s 139 1216s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1216s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_get_percentile_cutoffs.py" [FAIL] 5.5s 1216s Time: 5.52 1216s Return code: 139 1216s OKs: 0 1216s Standard error: 1216s Segmentation fault (core dumped) 1219s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1219s 139 1219s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1219s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sphericity.py" [FAIL] 4.2s 1219s Time: 4.20 1219s Return code: 139 1219s OKs: 0 1219s Standard error: 1219s Segmentation fault (core dumped) 1219s libtbx.python "/usr/lib/python3/dist-packages/cctbx/merging/brehm_diederichs.py" [OK] 0.2s 1219s Time: 0.20 1219s Return code: 0 1219s OKs: 1 1219s Standard out: 1219s OK 1219s libtbx.python "/usr/lib/python3/dist-packages/cctbx/multipolar/regression/tst_multipolar.py" [OK] 0.1s 1219s Time: 0.13 1219s Return code: 0 1219s OKs: 3 1219s Standard out: 1219s OK 1219s 0 1219s 1 1219s 2 1219s OK 1219s Skipping exercise(): chem_data directory not available 1219s OK 1221s Standard error: 1221s Segmentation fault (core dumped) 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/cctbx/regression/tst_miller_statistics.py" [FAIL] 5.2s 1221s Time: 5.24 1221s Return code: 139 1221s OKs: 0 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/cctbx/regression/tst_connectivity.py" [FAIL] 4.9s 1224s Time: 4.85 1224s Return code: 139 1224s OKs: 0 1224s Standard error: 1224s Segmentation fault (core dumped) 1226s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1226s 139 1226s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1226s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity_allsym.py" [FAIL] 5.3s 1226s Time: 5.32 1226s Return code: 139 1226s OKs: 0 1226s Standard error: 1226s Segmentation fault (core dumped) 1227s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grm_modifications.py" [OK] 0.7s 1227s Time: 0.67 1227s Return code: 0 1227s OKs: 1 1227s Standard out: 1227s Can not initialize monomer_library, skipping test. 1227s OK 1231s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1231s 1 1231s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1231s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py" [FAIL] 6.9s 1231s Time: 6.92 1231s Return code: 1 1231s OKs: 0 1231s Standard error: 1231s Segmentation fault (core dumped) 1231s Traceback (most recent call last): 1231s File "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py", line 140, in 1231s exercise() 1231s ~~~~~~~~^^ 1231s File "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py", line 126, in exercise 1231s assert not easy_run.call(cmd) 1231s ^^^^^^^^^^^^^^^^^^^^^^ 1231s AssertionError 1233s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wavelength_units.py" [OK] 2.0s 1233s Time: 2.00 1233s Return code: 0 1233s OKs: 1 1233s Standard out: 1233s OK 1233s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1233s 139 1233s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1233s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_prepare_map_for_docking.py" [FAIL] 5.9s 1233s Time: 5.94 1233s Return code: 139 1233s OKs: 0 1233s Standard error: 1233s Segmentation fault (core dumped) 1236s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1236s 139 1236s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1236s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fcalc_fft_stability.py" [EXPECTED UNSTABLE] 3.2s 1236s Time: 3.17 1236s Return code: 139 1236s OKs: 0 1236s Standard error: 1236s Segmentation fault (core dumped) 1236s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_ext.py" [OK] 0.1s 1236s Time: 0.10 1236s Return code: 0 1236s OKs: 1 1236s Standard out: 1236s OK 1236s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_equivalence.py" [OK] 0.1s 1236s Time: 0.10 1236s Return code: 0 1236s OKs: 1 1236s Standard out: 1236s OK 1237s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_read.py" [OK] 0.5s 1237s Time: 0.50 1237s Return code: 0 1237s OKs: 1 1237s Standard out: 1237s OK 1237s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_cout.py" [OK] 0.4s 1237s Time: 0.41 1237s Return code: 0 1237s OKs: 1 1237s Standard out: 1237s OK 1237s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_show_calls.py" [OK] 0.4s 1237s Time: 0.38 1237s Return code: 0 1237s OKs: 1 1237s Standard out: 1237s OK 1238s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1238s 139 1238s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1238s libtbx.python "/usr/lib/python3/dist-packages/cma_es/tst_cma_es.py" [FAIL] 5.0s 1238s Time: 5.03 1238s Return code: 139 1238s OKs: 0 1238s Standard error: 1238s Segmentation fault (core dumped) 1243s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_command_line.py" [OK] 5.8s 1243s Time: 5.82 1243s Return code: 0 1243s OKs: 1 1243s Standard out: 1243s fable.split "/usr/lib/python3/dist-packages/fable/test/valid/subroutine_1.f" 1243s fable.read --each "/usr/lib/python3/dist-packages/fable/test/valid/write_star.f" 1243s fable.read --warnings "/usr/lib/python3/dist-packages/fable/test/valid/equivalence_mixed.f" 1243s fable.show_calls --write-graphviz-dot=tmp.dot --top-procedure=sub "/usr/lib/python3/dist-packages/fable/test/valid/external_arg_layers.f" 1243s fable.show_calls "/usr/lib/python3/dist-packages/fable/test/valid/dependency_cycle.f" 1243s fable.fem_include_search_paths --with-quotes 1243s fable.cout --each "/usr/lib/python3/dist-packages/fable/test/valid/write_star.f" 1243s fable.cout "/usr/lib/python3/dist-packages/fable/test/valid/common_variants.f" 1243s fable.cout "/usr/lib/python3/dist-packages/fable/test/valid/subroutine_3.f" --top-procedure=sub3 --fortran-file-comments 1243s fable.cout --compile "/usr/lib/python3/dist-packages/fable/test/valid/write_star.f" 1243s fable.cout --namespace=test --run "/usr/lib/python3/dist-packages/fable/test/valid/write_star.f" 1243s fable.cout --example 1243s fable.cout /usr/lib/python3/dist-packages/fable/test/valid/sf.f --namespace example --run 1243s fable.cout "/usr/lib/python3/dist-packages/fable/test/valid/dynamic_parameters_1.f" --dynamic-parameter="int root_size=1" 1243s OK 1247s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_cout_compile.py" stop [OK] 3.4s 1247s Time: 3.36 1247s Return code: 0 1247s OKs: 1 1247s Standard out: 1247s 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" 1247s 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" 1247s 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" 1247s OK 1247s usr+sys time: 0.09 seconds 1247s wall clock time: 3.32 seconds 1249s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_separate_files.py" [OK] 10.9s 1249s Time: 10.92 1249s Return code: 0 1249s OKs: 1 1249s Standard out: 1249s 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" 1249s 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" 1249s 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" 1249s 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" 1249s 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" 1249s 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" 1249s 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" 1249s 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" 1249s 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" 1249s 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" 1249s 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" 1249s 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" 1249s 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" 1249s 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" 1249s 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" 1249s 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" 1249s 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" 1249s OK 1249s usr+sys time: 0.19 seconds 1249s wall clock time: 10.90 seconds 1249s libtbx.python "/usr/lib/python3/dist-packages/gltbx/tst_ellipsoids.py" [OK] 0.4s 1249s Time: 0.38 1249s Return code: 0 1249s OKs: 1 1249s Standard out: 1249s OK 1252s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1252s 139 1252s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1252s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mrc_io.py" [FAIL] 2.9s 1252s Time: 2.94 1252s Return code: 139 1252s OKs: 0 1252s Standard error: 1252s Segmentation fault (core dumped) 1252s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_wildcard.py" [OK] 0.1s 1252s Time: 0.07 1252s Return code: 0 1252s OKs: 1 1252s Standard out: 1252s OK 1254s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_io.py" [OK] 7.4s 1254s Time: 7.37 1254s Return code: 0 1254s OKs: 1 1254s Standard out: 1254s OK 1254s usr+sys time: 0.13 seconds 1254s wall clock time: 7.33 seconds 1254s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_parser.py" [OK] 0.1s 1254s Time: 0.06 1254s Return code: 0 1254s OKs: 1 1254s Standard out: 1254s OK 1256s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1256s 139 1256s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1256s libtbx.python "/usr/lib/python3/dist-packages/iotbx/gui_tools/tst.py" [FAIL] 3.5s 1256s Time: 3.49 1256s Return code: 139 1256s OKs: 0 1256s Standard error: 1256s Segmentation fault (core dumped) 1256s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_cif_inputs.py" [OK] 0.3s 1256s Time: 0.33 1256s Return code: 0 1256s OKs: 1 1256s Standard out: 1256s OK 1259s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1259s 139 1259s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1259s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phil.py" [FAIL] 5.0s 1259s Time: 5.01 1259s Return code: 139 1259s OKs: 0 1259s Standard error: 1259s 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/iotbx/regression/tst_data_manager.py" [FAIL] 7.8s 1264s Time: 7.81 1264s Return code: 139 1264s OKs: 0 1264s Standard error: 1264s Segmentation fault (core dumped) 1267s Standard error: 1267s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1267s 139 1267s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1267s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager_wrapping.py" [FAIL] 8.4s 1267s Time: 8.36 1267s Return code: 139 1267s OKs: 0 1267s Segmentation fault (core dumped) 1268s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager.py" [OK] 0.6s 1268s Time: 0.58 1268s Return code: 0 1268s OKs: 1 1268s Standard out: 1268s Skip test_01, chem_data not available 1268s OK 1269s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_2.py" [OK] 0.6s 1269s Time: 0.59 1269s Return code: 0 1269s OKs: 0 1269s Standard out: 1269s chem_data is not available, skipping 1269s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_3.py" [OK] 0.5s 1269s Time: 0.55 1269s Return code: 0 1269s OKs: 1 1269s Standard out: 1269s Skipped: Requires phenix module 1269s OK 1269s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_4.py" [OK] 0.1s 1269s Time: 0.13 1269s Return code: 0 1269s OKs: 1 1269s Standard out: 1269s Skipping tst_map_model_manager_4 tests becuase Phenix is not available. 1269s OK 1270s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_model_sharpening_5.py" [OK] 0.6s 1270s Time: 0.63 1270s Return code: 0 1270s OKs: 1 1270s Standard out: 1270s Skip test_01, chem_data not available 1270s OK 1271s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_model_sharpening_5_cif.py" [OK] 0.8s 1271s Time: 0.76 1271s Return code: 0 1271s OKs: 1 1271s Standard out: 1271s Skip test_01, chem_data not available 1271s OK 1271s Standard error: 1271s 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/iotbx/regression/tst_map_manager.py" [FAIL] 6.8s 1271s Time: 6.85 1271s Return code: 139 1271s OKs: 0 1271s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_call_consistency.py" [OK] 0.7s 1271s Time: 0.65 1271s Return code: 0 1271s OKs: 1 1271s Standard out: 1271s 1271s Expected and actual args in calls for with_bounds 1271s 1271s box.with_bounds.__init__ : 1271s 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'] 1271s 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'] 1271s 1271s box_all_maps_with_bounds_and_shift_origin : 1271s 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'] 1271s 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'] 1271s 1271s extract_all_maps_with_bounds : 1271s Expected :['lower_bounds', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'upper_bounds', 'use_cubic_boxing'] 1271s 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'] 1271s 1271s Expected and actual args in calls for around_model 1271s 1271s box.around_model.__init__ : 1271s 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'] 1271s 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'] 1271s 1271s box_all_maps_around_model_and_shift_origin : 1271s 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'] 1271s 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'] 1271s 1271s extract_all_maps_around_model : 1271s 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'] 1271s 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'] 1271s 1271s Expected and actual args in calls for around_density 1271s 1271s box.around_density.__init__ : 1271s 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'] 1271s 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'] 1271s 1271s box_all_maps_around_density_and_shift_origin : 1271s 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'] 1271s 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'] 1271s 1271s extract_all_maps_around_density : 1271s 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'] 1271s 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'] 1271s 1271s Expected and actual args in calls for around_mask 1271s 1271s box.around_mask.__init__ : 1271s 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'] 1271s 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'] 1271s 1271s box_all_maps_around_mask_and_shift_origin : 1271s 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'] 1271s 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'] 1271s 1271s extract_all_maps_around_mask : 1271s Expected :['box_cushion', 'mask_id', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'use_cubic_boxing'] 1271s 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'] 1271s 1271s Expected and actual args in calls for around_unique 1271s 1271s box.around_unique.__init__ : 1271s 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'] 1271s 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'] 1271s 1271s box_all_maps_around_unique_and_shift_origin : 1271s 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'] 1271s 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'] 1271s 1271s extract_all_maps_around_unique : 1271s 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'] 1271s 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'] 1271s 1271s Expected and actual args in calls for around_atoms 1271s 1271s cctbx.maptbx.mask.create_mask_around_atoms.__init__ : 1271s Expected :['invert_mask', 'map_manager', 'mask_atoms_atom_radius', 'model', 'n_real', 'self', 'wrapping', 'xray_structure'] 1271s Found : ['invert_mask', 'map_manager', 'mask_atoms_atom_radius', 'model', 'n_real', 'self', 'wrapping', 'xray_structure'] 1271s 1271s map_model_manager.create_mask_around_atoms : 1271s Expected :['invert_mask', 'mask_atoms_atom_radius', 'mask_id', 'model', 'self', 'soft_mask', 'soft_mask_radius'] 1271s Found : ['invert_mask', 'mask_atoms_atom_radius', 'mask_id', 'model', 'self', 'soft_mask', 'soft_mask_radius'] 1271s 1271s Expected and actual args in calls for around_edges 1271s 1271s cctbx.maptbx.mask.create_mask_around_edges.__init__ : 1271s Expected :['boundary_radius', 'map_manager', 'self'] 1271s Found : ['boundary_radius', 'map_manager', 'self'] 1271s 1271s map_model_manager.create_mask_around_edges : 1271s Expected :['boundary_radius', 'mask_id', 'self'] 1271s Found : ['boundary_radius', 'boundary_to_smoothing_ratio', 'mask_id', 'self', 'soft_mask_radius'] 1271s 1271s Expected and actual args in calls for around_density 1271s 1271s cctbx.maptbx.mask.create_mask_around_density.__init__ : 1271s Expected :['map_manager', 'molecular_mass', 'resolution', 'self', 'sequence', 'solvent_content'] 1271s Found : ['map_manager', 'molecular_mass', 'resolution', 'self', 'sequence', 'solvent_content'] 1271s 1271s map_model_manager.create_mask_around_density : 1271s Expected :['map_id', 'mask_id', 'resolution', 'self', 'soft_mask', 'soft_mask_radius', 'solvent_content'] 1271s Found : ['map_id', 'mask_id', 'resolution', 'self', 'soft_mask', 'soft_mask_radius', 'solvent_content'] 1271s OK 1272s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_external_sharpening_7.py" [OK] 0.7s 1272s Time: 0.70 1272s Return code: 0 1272s OKs: 1 1272s Standard out: 1272s Skip test_01, chem_data not available 1272s OK 1272s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_half_map_sharpening_6.py" [OK] 0.7s 1272s Time: 0.72 1272s Return code: 0 1272s OKs: 1 1272s Standard out: 1272s Skip test_01, chem_data not available 1272s OK 1272s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_tls_from_map_8.py" [OK] 0.7s 1272s Time: 0.68 1272s Return code: 0 1272s OKs: 1 1272s Standard out: 1272s Skip test_01, chem_data not available 1272s OK 1273s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_cif.py" [OK] 0.7s 1273s Time: 0.66 1273s Return code: 0 1273s OKs: 1 1273s Standard out: 1273s Skip test_01, chem_data not available 1273s OK 1277s Standard error: 1277s Segmentation fault (core dumped) 1277s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1277s 139 1277s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1277s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry.py" [FAIL] 4.7s 1277s Time: 4.72 1277s Return code: 139 1277s OKs: 0 1278s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_local_resolution_10.py" [OK] 0.6s 1278s Time: 0.58 1278s Return code: 0 1278s OKs: 1 1278s Standard out: 1278s Skip test_01, chem_data not available 1278s OK 1281s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1281s 139 1281s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1281s 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] 8.0s 1281s Time: 7.96 1281s Return code: 139 1281s OKs: 0 1281s Standard error: 1281s Segmentation fault (core dumped) 1281s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_patterson.py" [OK] 0.1s 1281s Time: 0.05 1281s Return code: 0 1281s OKs: 1 1281s Standard out: 1281s phenix_regression not available, skipping 1281s OK 1281s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_restraints_merge.py" [OK] 0.2s 1281s Time: 0.24 1281s Return code: 0 1281s OKs: 0 1283s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1283s 139 1283s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1283s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_tools.py" [FAIL] 5.7s 1283s Time: 5.66 1283s Return code: 139 1283s OKs: 0 1283s Standard error: 1283s Segmentation fault (core dumped) 1283s libtbx.python "/usr/lib/python3/dist-packages/iotbx/ranges.py" [OK] 0.0s 1283s Time: 0.02 1283s Return code: 0 1283s OKs: 1 1283s Standard out: 1283s OK 1286s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1286s 139 1286s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1286s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_atom_selections_10k.py" [FAIL] 5.1s 1286s Time: 5.13 1286s Return code: 139 1286s OKs: 0 1286s Standard error: 1286s Segmentation fault (core dumped) 1286s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_poscar.py" [OK] 0.1s 1286s Time: 0.07 1286s Return code: 0 1286s OKs: 1 1286s Standard out: 1286s Skipping POSCAR tests: input files not available 1286s OK 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/iotbx/regression/tst_crystal_symmetry_from_any.py" [FAIL] 5.7s 1289s Time: 5.72 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/iotbx/kriber/tst_strudat.py" [FAIL] 5.4s 1292s Time: 5.41 1292s Return code: 139 1292s OKs: 0 1292s Standard error: 1292s Segmentation fault (core dumped) 1294s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1294s 139 1294s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1294s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_geometry.py" [FAIL] 5.1s 1294s Time: 5.08 1294s Return code: 139 1294s OKs: 0 1294s Standard error: 1294s Segmentation fault (core dumped) 1297s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1297s 139 1297s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1297s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_lex_parse_build.py" [FAIL] 5.6s 1297s Time: 5.62 1297s Return code: 139 1297s OKs: 0 1297s Standard error: 1297s Segmentation fault (core dumped) 1300s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1300s 139 1300s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1300s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model.py" [FAIL] 5.6s 1300s Time: 5.56 1300s Return code: 139 1300s OKs: 0 1300s Standard error: 1300s Segmentation fault (core dumped) 1301s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1301s 1 1301s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1301s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py" [FAIL] 1.8s 1301s Time: 1.76 1301s Return code: 1 1301s OKs: 0 1301s Standard out: 1301s Skipping tst_validation.exercise_smart_load() because of URLError. 1301s Standard error: 1301s Traceback (most recent call last): 1301s File "/usr/lib/python3.13/urllib/request.py", line 1541, in ftp_open 1301s fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout) 1301s File "/usr/lib/python3.13/urllib/request.py", line 1561, in connect_ftp 1301s return ftpwrapper(user, passwd, host, port, dirs, timeout, 1301s persistent=False) 1301s File "/usr/lib/python3.13/urllib/request.py", line 2409, in __init__ 1301s self.init() 1301s ~~~~~~~~~^^ 1301s File "/usr/lib/python3.13/urllib/request.py", line 2418, in init 1301s self.ftp.connect(self.host, self.port, self.timeout) 1301s ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1301s File "/usr/lib/python3.13/ftplib.py", line 158, in connect 1301s self.sock = socket.create_connection((self.host, self.port), self.timeout, 1301s ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1301s source_address=self.source_address) 1301s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1301s File "/usr/lib/python3.13/socket.py", line 864, in create_connection 1301s raise exceptions[0] 1301s File "/usr/lib/python3.13/socket.py", line 849, in create_connection 1301s sock.connect(sa) 1301s ~~~~~~~~~~~~^^^^ 1301s ConnectionRefusedError: [Errno 111] Connection refused 1301s 1301s The above exception was the direct cause of the following exception: 1301s 1301s Traceback (most recent call last): 1301s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 327, in 1301s exercise(sys.argv[1:]) 1301s ~~~~~~~~^^^^^^^^^^^^^^ 1301s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 26, in exercise 1301s exercise_validation() 1301s ~~~~~~~~~~~~~~~~~~~^^ 1301s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 29, in exercise_validation 1301s cd = validation.smart_load_dictionary(name="cif_core.dic") 1301s File "/usr/lib/python3/dist-packages/iotbx/cif/validation.py", line 111, in smart_load_dictionary 1301s url = locate_dictionary(name, registry_location=registry_location) 1301s File "/usr/lib/python3/dist-packages/iotbx/cif/validation.py", line 129, in locate_dictionary 1301s cm = cif.reader(file_object=urlopen(registry_location)).model() 1301s ~~~~~~~^^^^^^^^^^^^^^^^^^^ 1301s File "/usr/lib/python3.13/urllib/request.py", line 189, in urlopen 1301s return opener.open(url, data, timeout) 1301s ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1301s File "/usr/lib/python3.13/urllib/request.py", line 489, in open 1301s response = self._open(req, data) 1301s File "/usr/lib/python3.13/urllib/request.py", line 506, in _open 1301s result = self._call_chain(self.handle_open, protocol, protocol + 1301s '_open', req) 1301s File "/usr/lib/python3.13/urllib/request.py", line 466, in _call_chain 1301s result = func(*args) 1301s File "/usr/lib/python3.13/urllib/request.py", line 1558, in ftp_open 1301s raise URLError(exp) from exp 1301s urllib.error.URLError: 1302s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_parser.py" [OK] 0.2s 1302s Time: 0.24 1302s Return code: 0 1302s OKs: 0 1302s Standard out: 1302s 1 0 0 1302s 1 0 0 1302s 1 0 0 1302s 1 0 0 1302s 1 0 0 1302s 1 0 0 1302s 1 0 0 1302s 1 0 0 1302s 1 0 0 1302s 0 0 0 1302s 0 0 0 1302s 1 0 0 1302s 0 0 0 1302s 0 0 0 1302s 1 0 0 1302s 1 0 0 1302s 1 0 0 1302s 1 0 0 1302s 1 0 0 1302s 1 0 0 1302s 1 0 0 1302s 1 0 0 1302s 1 0 0 1302s 1 0 0 1302s 1 0 0 1302s 1 0 0 1302s 0 0 0 1302s 1 0 0 1302s 1 0 0 1302s 1 0 0 1302s 1 0 0 1302s 1 0 0 1302s 0 0 0 1302s 0 1 0 1302s 0 1 0 1302s 0 0 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 0 1 0 1302s 1 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s 2 0 0 1302s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_citations.py" [OK] 0.3s 1302s Time: 0.29 1302s Return code: 0 1302s OKs: 1 1302s Standard out: 1302s OK 1302s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model_builder.py" [OK] 0.2s 1302s Time: 0.18 1302s Return code: 0 1302s OKs: 0 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/iotbx/cif/tests/tst_restraints.py" [FAIL] 5.1s 1302s Time: 5.11 1302s Return code: 139 1302s OKs: 0 1302s Standard error: 1302s Segmentation fault (core dumped) 1305s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1305s 139 1305s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1305s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_lex_parse_build.py" [FAIL] 3.3s 1305s Time: 3.33 1305s Return code: 139 1305s OKs: 0 1305s Standard error: 1305s Segmentation fault (core dumped) 1308s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1308s 139 1308s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1308s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_hklf.py" [FAIL] 5.8s 1308s Time: 5.78 1308s Return code: 139 1308s OKs: 0 1308s Standard error: 1308s Segmentation fault (core dumped) 1311s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1311s 139 1311s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1311s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_writer.py" [FAIL] 5.1s 1311s Standard error: 1311s Segmentation fault (core dumped) 1311s Time: 5.10 1311s Return code: 139 1311s OKs: 0 1313s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1313s 139 1313s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1313s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_fvar_encoding.py" [FAIL] 4.9s 1313s Time: 4.93 1313s Return code: 139 1313s OKs: 0 1313s Standard error: 1313s Segmentation fault (core dumped) 1313s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif.py" [OK] 0.2s 1313s Time: 0.23 1313s Return code: 0 1313s OKs: 1 1313s Standard out: 1313s OK 1316s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1316s 134 1316s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1316s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_pdb.py" [FAIL] 5.1s 1316s Time: 5.14 1316s Return code: 134 1316s OKs: 0 1316s Standard error: 1316s *** buffer overflow detected ***: terminated 1316s Aborted (core dumped) 1317s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy_2.py" [OK] 1.8s 1317s Time: 1.81 1317s Return code: 0 1317s OKs: 1 1317s Standard out: 1317s OK 1318s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_tls.py" [OK] 0.6s 1318s Time: 0.58 1318s Return code: 0 1318s OKs: 1 1318s Standard out: 1318s Skipping exercise_mmcif_tls(): missing phenix_regression directory. 1318s OK 1318s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/hybrid_36.py" exercise [OK] 0.1s 1318s Time: 0.08 1318s Return code: 0 1318s OKs: 1 1318s Standard out: 1318s OK 1319s "/usr/lib/cctbx/python3.13/iotbx/pdb/hybrid_36_fem" [OK] 0.9s 1319s Time: 0.94 1319s Return code: 0 1319s OKs: 0 1319s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1319s 134 1319s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1319s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy.py" [FAIL] 6.3s 1319s Time: 6.29 1319s Return code: 134 1319s OKs: 0 1319s Standard error: 1319s *** buffer overflow detected ***: terminated 1319s Aborted (core dumped) 1320s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy_atom_sort.py" [OK] 0.3s 1320s Time: 0.28 1320s Return code: 0 1320s OKs: 1 1320s Standard out: 1320s OK 1320s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy_flip_symmetric.py" [OK] 0.2s 1320s Time: 0.23 1320s Return code: 0 1320s OKs: 0 1320s Standard out: 1320s chem_data is missing, skipping test 1320s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_selected_hierarchy_flip.py" [OK] 0.3s 1320s Time: 0.27 1320s Return code: 0 1320s OKs: 0 1323s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1323s 139 1323s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy.py" [FAIL] 3.6s 1323s Time: 3.58 1323s Return code: 139 1323s OKs: 0 1323s Standard error: 1323s Segmentation fault (core dumped) 1326s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1326s 139 1326s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1326s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_ext.py" [FAIL] 5.3s 1326s Time: 5.26 1326s Return code: 139 1326s OKs: 0 1326s Standard error: 1326s Segmentation fault (core dumped) 1326s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_rna_dna_atom_names.py" [OK] 0.2s 1326s Time: 0.24 1326s Return code: 0 1326s OKs: 1 1326s Standard out: 1326s OK 1326s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_name_interpretation.py" [OK] 0.3s 1326s Time: 0.26 1326s Return code: 0 1326s OKs: 1 1326s Standard out: 1326s OK 1326s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_extract_rfactors_resolutions_sigma.py" [OK] 0.3s 1326s Time: 0.26 1326s Return code: 0 1326s OKs: 1 1326s Standard out: 1326s OK 1326s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/modified_aa_names.py" [OK] 0.0s 1326s Time: 0.02 1326s Return code: 0 1326s OKs: 0 1326s Standard out: 1326s 2141 1326s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/modified_rna_dna_names.py" [OK] 0.0s 1326s Time: 0.02 1326s Return code: 0 1326s OKs: 0 1326s Standard out: 1326s 792 1327s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_sheet.py" [OK] 0.2s 1327s Time: 0.24 1327s Return code: 0 1327s OKs: 1 1327s Standard out: 1327s OK 1327s u+s,u,s: 0.17 0.16 0.01 1328s Standard error: 1328s Segmentation fault (core dumped) 1328s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1328s 139 1328s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1328s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection.py" [FAIL] 5.6s 1328s Time: 5.57 1328s Return code: 139 1328s OKs: 0 1328s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation_long.py" [OK] 0.2s 1328s Time: 0.22 1328s Return code: 0 1328s OKs: 1 1328s Standard out: 1328s OK time = 0.012 1329s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/secondary_structure.py" [OK] 0.2s 1329s Time: 0.22 1329s Return code: 0 1329s OKs: 0 1332s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1332s 139 1332s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1332s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation.py" [FAIL] 5.3s 1332s Time: 5.31 1332s Return code: 139 1332s OKs: 0 1332s Standard error: 1332s Segmentation fault (core dumped) 1333s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_secondary_structure.py" [OK] 0.6s 1333s Time: 0.62 1333s Return code: 0 1333s OKs: 5 1333s Standard out: 1333s OK 1333s OK 1333s OK 1333s OK 1333s OK 1335s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1335s 139 1335s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1335s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection_string.py" [FAIL] 6.1s 1335s Standard error: 1335s Segmentation fault (core dumped) 1335s Time: 6.11 1335s Return code: 139 1335s OKs: 0 1336s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_secondary_structure_2.py" [OK] 1.5s 1336s Time: 1.53 1336s Return code: 0 1336s OKs: 2 1336s Standard out: 1336s OK 1336s OK 1337s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/remediation/tst_remediator.py" [OK] 0.7s 1337s Time: 0.67 1337s Return code: 0 1337s OKs: 0 1337s Standard out: 1337s chem_data is not available for remediator tests, skipping 1337s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_to_map_simple.py" [OK] 0.2s 1337s Time: 0.21 1337s Return code: 0 1337s OKs: 0 1337s Standard out: 1337s Usage: iotbx.python pdb_to_map_simple.py [options] pdb_file... 1337s 1337s Options: 1337s -h, --help show this help message and exit 1337s --d_min=FLOAT high-resolution limit for structure-factor calculation 1338s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1338s 139 1338s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1338s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_utils.py" [FAIL] 5.2s 1338s Time: 5.17 1338s Return code: 139 1338s OKs: 0 1338s Standard error: 1338s Segmentation fault (core dumped) 1338s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_tardy_conf_sampling_simple.py" [OK] 0.2s 1338s Time: 0.20 1338s Return code: 0 1338s OKs: 0 1338s Standard out: 1338s Time importing extensions: 0.16 1338s skipping test: phenix_regression not available. 1340s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1340s 134 1340s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1340s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_truncate_to_ala/tst.py" [FAIL] 3.2s 1340s Time: 3.21 1340s Return code: 134 1340s OKs: 0 1340s Standard error: 1340s *** buffer overflow detected ***: terminated 1340s Aborted (core dumped) 1344s Standard error: 1344s Segmentation fault (core dumped) 1344s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1344s 139 1344s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1344s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_examples.py" [FAIL] 6.1s 1344s Time: 6.11 1344s Return code: 139 1344s OKs: 0 1346s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1346s 139 1346s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1346s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/space_group_symbols.py" [FAIL] 5.8s 1346s Time: 5.85 1346s Return code: 139 1346s OKs: 0 1346s Standard error: 1346s Segmentation fault (core dumped) 1349s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1349s 139 1349s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1349s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/tst_cns.py" [FAIL] 4.8s 1349s Time: 4.80 1349s Return code: 139 1349s OKs: 0 1349s Standard error: 1349s Segmentation fault (core dumped) 1351s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1351s 139 1351s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1351s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_merge.py" P31 [FAIL] 5.2s 1351s Time: 5.21 1351s Return code: 139 1351s OKs: 0 1351s Standard error: 1351s Segmentation fault (core dumped) 1354s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1354s 139 1354s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1354s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/no_merge_original_index.py" [FAIL] 5.5s 1354s Time: 5.45 1354s Return code: 139 1354s OKs: 0 1354s Standard error: 1354s Segmentation fault (core dumped) 1357s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1357s 139 1357s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1357s libtbx.python "/usr/lib/python3/dist-packages/iotbx/ccp4_map/tst.py" [FAIL] 5.2s 1357s Time: 5.18 1357s Return code: 139 1357s OKs: 0 1357s Standard error: 1357s Segmentation fault (core dumped) 1360s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1360s 139 1360s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1360s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_ext.py" [FAIL] 5.5s 1360s Time: 5.54 1360s Return code: 139 1360s OKs: 0 1360s Standard error: 1360s Segmentation fault (core dumped) 1363s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1363s 139 1363s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1363s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_extract_from_symmetry_lib.py" [FAIL] 5.8s 1363s Time: 5.84 1363s Return code: 139 1363s OKs: 0 1363s Standard error: 1363s /usr/lib/python3/dist-packages/ccp4io_adaptbx/__init__.py:25: UserWarning: ccp4io_adaptbx: cannot locate syminfo.lib 1363s warnings.warn("ccp4io_adaptbx: cannot locate syminfo.lib") 1363s Segmentation fault (core dumped) 1363s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_miller_dict.py" [OK] 0.2s 1363s Time: 0.24 1363s Return code: 0 1363s OKs: 0 1363s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_unmerged.py" [OK] 0.2s 1363s Time: 0.22 1363s Return code: 0 1363s OKs: 0 1363s Standard out: 1363s Title: . 1363s Space group symbol from file: I23 1363s Space group number from file: 197 1363s Space group from matrices: I 2 3 (No. 197) 1363s Point group symbol from file: PG23 1363s Number of batches: 45 1363s Number of crystals: 2 1363s Number of Miller indices: 13 1363s Resolution range: 39.0022 31.8451 1363s History: 1363s From MTZUTILS 21/11/2017 16:26:11 after history: 1363s From MOSFLM run on 1/ 7/08 1363s From MOSFLM run on 1/ 7/08 1363s Crystal 1: 1363s Name: HKL_base 1363s Project: HKL_base 1363s Id: 1 1363s Unit cell: (78.0043, 78.0043, 78.0043, 90, 90, 90) 1363s Number of datasets: 1 1363s Dataset 1: 1363s Name: HKL_base 1363s Id: 0 1363s Wavelength: 0 1363s Number of columns: 18 1363s label #valid %valid min max type 1363s H 13 100.00% 0.00 1.00 H: index h,k,l 1363s K 13 100.00% 2.00 2.00 H: index h,k,l 1363s L 13 100.00% 0.00 1.00 H: index h,k,l 1363s M_ISYM 13 100.00% 6.00 272.00 Y: M/ISYM, packed partial/reject flag and symmetry number 1363s BATCH 13 100.00% 16.00 43.00 B: BATCH number 1363s I 13 100.00% -19.71 7.39 J: intensity 1363s SIGI 13 100.00% 0.41 3.05 Q: standard deviation 1363s IPR 13 100.00% -10.84 4.99 J: intensity 1363s SIGIPR 13 100.00% 0.41 3.05 Q: standard deviation 1363s FRACTIONCALC 13 100.00% 0.07 1.15 R: real 1363s XDET 13 100.00% 1099.43 1215.80 R: real 1363s YDET 13 100.00% 1110.92 1201.06 R: real 1363s ROT 13 100.00% 15.33 41.55 R: real 1363s WIDTH 13 100.00% 0.37 2.19 R: real 1363s LP 13 100.00% 0.00 0.03 R: real 1363s MPART 13 100.00% 0.00 303.00 I: integer 1363s FLAG 13 100.00% 0.00 40.00 I: integer 1363s BGPKRATIOS 13 100.00% 8.04 10610.05 R: real 1363s Crystal 2: 1363s Name: DEFAULT 1363s Project: AUTOMATIC 1363s Id: 2 1363s Unit cell: (78.0043, 78.0043, 78.0043, 90, 90, 90) 1363s Number of datasets: 1 1363s Dataset 1: 1363s Name: NATIVE_SWEEP1 1363s Id: 1 1363s Wavelength: 0.979 1363s Number of columns: 0 1363s asu: (1, 2, 1) orig: (-1, 1, -2) M/ISYM: 15 1363s asu: (1, 2, 1) orig: (1, -1, 2) M/ISYM: 272 1363s asu: (1, 2, 1) orig: (1, -1, 2) M/ISYM: 272 1363s asu: (1, 2, 1) orig: (-1, 2, 1) M/ISYM: 6 1363s asu: (1, 2, 1) orig: (1, -2, -1) M/ISYM: 261 1363s asu: (1, 2, 1) orig: (-1, 2, -1) M/ISYM: 263 1363s asu: (1, 2, 1) orig: (1, -2, -1) M/ISYM: 261 1363s asu: (1, 2, 1) orig: (-1, 2, -1) M/ISYM: 263 1363s asu: (1, 2, 1) orig: (1, -2, 1) M/ISYM: 264 1363s asu: (1, 2, 1) orig: (1, -2, 1) M/ISYM: 264 1363s asu: (0, 2, 0) orig: (0, 0, -2) M/ISYM: 266 1363s asu: (0, 2, 0) orig: (0, 0, -2) M/ISYM: 266 1363s asu: (0, 2, 0) orig: (0, 0, -2) M/ISYM: 266 1365s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1365s 139 1365s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1365s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_dano.py" [FAIL] 5.2s 1365s Time: 5.17 1365s Return code: 139 1365s OKs: 0 1365s Standard error: 1365s Segmentation fault (core dumped) 1365s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/tst_mtz_free_flipper.py" [OK] 0.3s 1365s Time: 0.29 1365s Return code: 0 1365s OKs: 0 1365s Standard out: 1365s Skipping exercise(): input file not available 1365s u+s,u,s: 0.20 0.17 0.03 1368s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1368s 139 1368s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1368s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst.py" P31 [FAIL] 4.7s 1368s Time: 4.67 1368s Return code: 139 1368s OKs: 0 1368s Standard error: 1368s Segmentation fault (core dumped) 1368s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_adsc.py" [OK] 0.2s 1368s Time: 0.21 1368s Return code: 0 1368s OKs: 1 1368s Standard out: 1368s Skipping exercise_adscread(): input file not available 1368s OK 1368s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_detectors.py" [OK] 0.1s 1368s Time: 0.06 1368s Return code: 0 1368s OKs: 0 1368s Standard out: 1368s bpcx_regression not configured, skipping test 1371s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1371s 139 1371s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1371s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_utils.py" [FAIL] 5.3s 1371s Time: 5.31 1371s Return code: 139 1371s OKs: 0 1371s Standard error: 1371s Segmentation fault (core dumped) 1373s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1373s 139 1373s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1373s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xplor/tst_xplormap.py" [FAIL] 5.2s 1373s Time: 5.23 1373s Return code: 139 1373s OKs: 0 1373s Standard error: 1373s Segmentation fault (core dumped) 1373s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdbx_mmcif_tutorial.py" [OK] 0.1s 1373s Time: 0.06 1373s Return code: 0 1373s OKs: 1 1373s Standard out: 1373s phenix_regression not configured, skipping tst_pdbx_mmcif_tutorial.py 1373s OK 1376s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1376s 139 1376s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1376s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phases.py" P31 [FAIL] 5.4s 1376s Time: 5.43 1376s Return code: 139 1376s OKs: 0 1376s Standard error: 1376s Segmentation fault (core dumped) 1381s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1381s 1 1381s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1381s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py" [FAIL] 7.3s 1381s Time: 7.27 1381s Return code: 1 1381s OKs: 0 1381s Standard error: 1381s Traceback (most recent call last): 1381s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 477, in 1381s exercise(sys.argv[1:]) 1381s ~~~~~~~~^^^^^^^^^^^^^^ 1381s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 22, in exercise 1381s run_and_compare( 1381s ~~~~~~~~~~~~~~~^ 1381s ['iotbx.lattice_symmetry' 1381s ^^^^^^^^^^^^^^^^^^^^^^^^^ 1381s ...<31 lines>... 1381s 1381s 1381s """) 1381s ^^^^ 1381s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 17, in run_and_compare 1381s command=command).raise_if_errors().stdout_lines 1381s ~~~~~~~~~~~~~~~^^ 1381s File "/usr/lib/python3/dist-packages/libtbx/easy_run.py", line 46, in raise_if_errors 1381s raise Error(msg) 1381s RuntimeError: child process stderr output: 1381s command: 'iotbx.lattice_symmetry --unit_cell="12.7923,12.8923,29.4356,102.846,103.846,22.7475"' 1381s Segmentation fault (core dumped) 1381s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_plots.py" [OK] 0.1s 1381s Time: 0.06 1381s Return code: 0 1381s OKs: 1 1381s Standard out: 1381s OK 1381s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_csv_utils.py" [OK] 0.1s 1381s Time: 0.13 1381s Return code: 0 1381s OKs: 1 1381s Standard out: 1381s OK 1382s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1382s 139 1382s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_statistics.py" Fdd2 P31m [FAIL] 5.8s 1382s Time: 5.76 1382s Return code: 139 1382s OKs: 0 1382s Standard error: 1382s Segmentation fault (core dumped) 1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_bioinformatics.py" [OK] 0.1s 1382s Time: 0.09 1382s Return code: 0 1382s OKs: 3 1382s Standard out: 1382s Testing guess_chain_types ... OK 1382s Testing merge_sequences ... OK 1382s testEquality (__main__.test_sequence.testEquality) ... ok 1382s testNonEquality (__main__.test_sequence.testNonEquality) ... ok 1382s testFormat (__main__.test_fasta_sequence.testFormat) ... ok 1382s testStr (__main__.test_fasta_sequence.testStr) ... ok 1382s testFormat (__main__.test_pir_sequence.testFormat) ... ok 1382s testStr (__main__.test_pir_sequence.testStr) ... ok 1382s testConservationCode (__main__.test_midline.testConservationCode) ... ok 1382s testMidline (__main__.test_midline.testMidline) ... ok 1382s test__str__ (__main__.test_alignment.test__str__) ... ok 1382s test_copy (__main__.test_alignment.test_copy) ... ok 1382s test_error (__main__.test_alignment.test_error) ... ok 1382s test_extend (__main__.test_alignment.test_extend) ... ok 1382s test_identity_count (__main__.test_alignment.test_identity_count) ... ok 1382s test_identity_fraction (__main__.test_alignment.test_identity_fraction) ... ok 1382s test_length (__main__.test_alignment.test_length) ... ok 1382s test_multiplicity (__main__.test_alignment.test_multiplicity) ... ok 1382s test__str__ (__main__.test_fasta_alignment.test__str__) ... ok 1382s test_copy (__main__.test_fasta_alignment.test_copy) ... ok 1382s test_error (__main__.test_fasta_alignment.test_error) ... ok 1382s test_format (__main__.test_fasta_alignment.test_format) ... ok 1382s test__str__ (__main__.test_pir_alignment.test__str__) ... ok 1382s test_copy (__main__.test_pir_alignment.test_copy) ... ok 1382s test_error (__main__.test_pir_alignment.test_error) ... ok 1382s test_format (__main__.test_pir_alignment.test_format) ... ok 1382s test__str__ (__main__.test_clustal_alignment.test__str__) ... ok 1382s test_copy (__main__.test_clustal_alignment.test_copy) ... ok 1382s test_format (__main__.test_clustal_alignment.test_format) ... ok 1382s testFasta (__main__.test_sequence_parse.testFasta) ... ok 1382s testPir (__main__.test_sequence_parse.testPir) ... ok 1382s testSequence (__main__.test_sequence_parse.testSequence) ... ok 1382s testTolerantPir (__main__.test_sequence_parse.testTolerantPir) ... ok 1382s test_dbfetch_parse (__main__.test_sequence_parse.test_dbfetch_parse) ... ok 1382s test_filename_selection (__main__.test_sequence_parse.test_filename_selection) ... ok 1382s test_known_formats (__main__.test_sequence_parse.test_known_formats) ... ok 1382s test_ls_parse (__main__.test_sequence_parse.test_ls_parse) ... ok 1382s test_tf_parse (__main__.test_sequence_parse.test_tf_parse) ... ok 1382s testAli (__main__.test_alignment_parse.testAli) ... ok 1382s testClustal (__main__.test_alignment_parse.testClustal) ... ok 1382s testFasta (__main__.test_alignment_parse.testFasta) ... ok 1382s testPir (__main__.test_alignment_parse.testPir) ... ok 1382s test_filename_selection (__main__.test_alignment_parse.test_filename_selection) ... ok 1382s test_known_formats (__main__.test_alignment_parse.test_known_formats) ... ok 1382s test_process_header (__main__.test_hhsearch_parser.test_process_header) ... ok 1382s test_process_hits (__main__.test_hhsearch_parser.test_process_hits) ... ok 1382s test_process_header (__main__.test_hhalign_parser.test_process_header) ... ok 1382s test_process_hits (__main__.test_hhalign_parser.test_process_hits) ... ok 1382s 1382s ---------------------------------------------------------------------- 1382s Ran 46 tests in 0.004s 1382s 1382s OK 1385s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1385s 139 1385s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1385s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_file_reader.py" [FAIL] 3.9s 1385s Time: 3.87 1385s Return code: 139 1385s OKs: 0 1385s Standard error: 1385s Segmentation fault (core dumped) 1390s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1390s 1 1390s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1390s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py" [FAIL] 8.0s 1390s Time: 8.00 1390s Return code: 1 1390s OKs: 0 1390s Standard out: 1390s Starting iotbx.pdb.box_around_molecule 1390s on Sat Mar 22 13:29:02 2025 by ubuntu 1390s =============================================================================== 1390s 1390s Standard error: 1390s *** buffer overflow detected ***: terminated 1390s Aborted (core dumped) 1390s Traceback (most recent call last): 1390s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py", line 138, in 1390s exercise() 1390s ~~~~~~~~^^ 1390s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py", line 48, in exercise 1390s assert not easy_run.call("iotbx.pdb.box_around_molecule %s.pdb" % ( 1390s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1390s prefix)) 1390s ^^^^^^^^ 1390s AssertionError 1390s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_input.py" [OK] 0.3s 1390s Time: 0.26 1390s Return code: 0 1390s OKs: 0 1391s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1391s 134 1391s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1391s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_segids.py" [FAIL] 6.2s 1391s Time: 6.25 1391s Return code: 134 1391s OKs: 0 1391s Standard error: 1391s *** buffer overflow detected ***: terminated 1391s Aborted (core dumped) 1391s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_multimodel.py" [OK] 0.5s 1391s Time: 0.54 1391s Return code: 0 1391s OKs: 0 1391s Standard out: 1391s ['_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'] 1391s ['_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'] 1392s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_add_conformations.py" [OK] 0.2s 1392s Time: 0.24 1392s Return code: 0 1392s OKs: 0 1392s Standard out: 1392s phenix_regression not available, skipping test. 1393s Standard error: 1393s *** buffer overflow detected ***: terminated 1393s Aborted (core dumped) 1393s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1393s 134 1393s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1393s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_forward_compatible_pdb.py" [FAIL] 3.3s 1393s Time: 3.33 1393s Return code: 134 1393s OKs: 0 1394s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reindex.py" [OK] 0.1s 1394s Time: 0.06 1394s Return code: 0 1394s OKs: 1 1394s Standard out: 1394s Skipping 1394s OK 1396s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1396s 139 1396s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1396s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_symmetry.py" [FAIL] 4.1s 1396s Time: 4.13 1396s Return code: 139 1396s OKs: 0 1396s Standard error: 1396s Segmentation fault (core dumped) 1398s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1398s 139 1398s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1398s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_editor.py" [FAIL] 4.8s 1398s Time: 4.78 1398s Return code: 139 1398s OKs: 0 1398s Standard error: 1398s Segmentation fault (core dumped) 1399s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_as_fasta.py" [OK] 0.2s 1399s Time: 0.22 1399s Return code: 0 1399s OKs: 1 1399s Standard out: 1399s OK 1399s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_link_records.py" [OK] 0.2s 1399s Time: 0.23 1399s Return code: 0 1399s OKs: 0 1399s Standard out: 1399s Can not initialize monomer_library, skipping test. 1399s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_merging_statistics.py" [OK] 0.2s 1399s Time: 0.15 1399s Return code: 0 1399s OKs: 1 1399s Standard out: 1399s phenix_regression not configured, skipping. 1399s OK 1402s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1402s 1 1402s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1402s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py" [FAIL] 6.7s 1402s Time: 6.69 1402s Return code: 1 1402s OKs: 0 1402s Standard error: 1402s Traceback (most recent call last): 1402s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py", line 60, in 1402s exercise() 1402s ~~~~~~~~^^ 1402s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py", line 48, in exercise 1402s assert (len(out.stdout_lines) == 2) and (len(out.stderr_lines) == 0) 1402s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1402s AssertionError 1404s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1404s 139 1404s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1404s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_map_coefficients.py" [FAIL] 4.9s 1404s Time: 4.93 1404s Return code: 139 1404s OKs: 0 1404s Standard error: 1404s Segmentation fault (core dumped) 1404s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_xparm.py" [OK] 0.1s 1404s Time: 0.06 1404s Return code: 0 1404s OKs: 3 1404s Standard out: 1404s OK 1404s OK 1404s OK 1404s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_xds_inp.py" [OK] 0.1s 1404s Time: 0.06 1404s Return code: 0 1404s OKs: 1 1404s Standard out: 1404s OK 1409s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1409s 1 1409s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1409s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py" [FAIL] 6.2s 1409s Time: 6.18 1409s Return code: 1 1409s OKs: 0 1409s Standard error: 1409s Segmentation fault (core dumped) 1409s Traceback (most recent call last): 1409s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py", line 815, in 1409s exercise_1() 1409s ~~~~~~~~~~^^ 1409s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py", line 806, in exercise_1 1409s assert not easy_run.call(cmd) 1409s ^^^^^^^^^^^^^^^^^^^^^^ 1409s AssertionError 1409s Standard out: 1409s iotbx.pdb.sort_atoms tst_sort_atoms_1.pdb 1409s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_spots_xds.py" [OK] 0.1s 1409s Time: 0.05 1409s Return code: 0 1409s OKs: 1 1409s Standard out: 1409s OK 1409s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_as_cif.py" [OK] 0.4s 1409s Time: 0.40 1409s Return code: 0 1409s OKs: 1 1409s Standard out: 1409s Can not initialize monomer_library, skipping tst_pdb_as_cif. 1409s OK 1410s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1410s 139 1410s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1410s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_integrate_hkl.py" [FAIL] 6.2s 1410s Time: 6.17 1410s Return code: 139 1410s OKs: 0 1410s Standard error: 1410s Segmentation fault (core dumped) 1412s Standard error: 1412s Segmentation fault (core dumped) 1412s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1412s 139 1412s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1412s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_no_merge_original_index.py" [FAIL] 3.4s 1412s Time: 3.42 1412s Return code: 139 1412s OKs: 0 1415s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1415s 139 1415s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1415s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_export_scalepack_unmerged.py" [FAIL] 5.2s 1415s Time: 5.22 1415s Return code: 139 1415s OKs: 0 1415s Standard error: 1415s Segmentation fault (core dumped) 1416s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_mtrix_biomt_cmdl.py" [OK] 0.2s 1416s Time: 0.21 1416s Return code: 0 1416s OKs: 0 1416s Standard out: 1416s Skipping tests: phenix not found 1416s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_mmcif_biomt_reduction_output.py" [OK] 0.5s 1416s Time: 0.52 1416s Return code: 0 1416s OKs: 0 1416s Standard out: 1416s chem_data is not available, skipping 1418s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1418s 139 1418s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1418s libtbx.python "/usr/lib/python3/dist-packages/iotbx/dsn6/tst.py" P31 [FAIL] 5.3s 1418s Time: 5.32 1418s Return code: 139 1418s OKs: 0 1418s Standard error: 1418s Segmentation fault (core dumped) 1421s Standard error: 1421s Segmentation fault (core dumped) 1421s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1421s 139 1421s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1421s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_ligs.py" [FAIL] 4.4s 1421s Time: 4.42 1421s Return code: 139 1421s OKs: 0 1423s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1423s 139 1423s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1423s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_broken_chain.py" [FAIL] 5.4s 1423s Time: 5.37 1423s Return code: 139 1423s OKs: 0 1423s Standard error: 1423s Segmentation fault (core dumped) 1426s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1426s 139 1426s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1426s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_shortcut_1.py" [FAIL] 5.3s 1426s Time: 5.31 1426s Return code: 139 1426s OKs: 0 1426s Standard error: 1426s Segmentation fault (core dumped) 1429s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1429s 139 1429s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1429s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_groups_preprocessing.py" [FAIL] 6.2s 1429s Time: 6.22 1429s Return code: 139 1429s OKs: 0 1429s Standard error: 1429s Segmentation fault (core dumped) 1432s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1432s 139 1432s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1432s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_input.py" [FAIL] 6.2s 1432s Time: 6.21 1432s Return code: 139 1432s OKs: 0 1432s Standard error: 1432s Segmentation fault (core dumped) 1435s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1435s 139 1435s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1435s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_user_selections.py" [FAIL] 5.3s 1435s Time: 5.33 1435s Return code: 139 1435s OKs: 0 1435s Standard error: 1435s Segmentation fault (core dumped) 1438s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1438s 139 1438s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1438s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs.py" [FAIL] 6.1s 1438s Time: 6.11 1438s Return code: 139 1438s OKs: 0 1438s Standard error: 1438s Segmentation fault (core dumped) 1441s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1441s 139 1441s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1441s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_without_validation.py" [FAIL] 6.1s 1441s Time: 6.08 1441s Return code: 139 1441s OKs: 0 1441s Standard error: 1441s Segmentation fault (core dumped) 1444s Standard error: 1444s Segmentation fault (core dumped) 1444s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1444s 139 1444s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1444s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_read_mtrix_records_from_cif.py" [FAIL] 6.0s 1444s Time: 6.03 1444s Return code: 139 1444s OKs: 0 1447s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1447s 139 1447s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1447s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_show_systematic_absences.py" [FAIL] 6.1s 1447s Time: 6.14 1447s Return code: 139 1447s OKs: 0 1447s Standard error: 1447s Segmentation fault (core dumped) 1447s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_reader.py" [OK] 0.3s 1447s Time: 0.31 1447s Return code: 0 1447s OKs: 1 1447s Standard out: 1447s OK 1449s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1449s 139 1449s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1449s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_miller_sort_asu.py" [FAIL] 5.1s 1449s Standard error: 1449s Segmentation fault (core dumped) 1449s Time: 5.11 1449s Return code: 139 1449s OKs: 0 1449s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_alignment_as_hsearch.py" [OK] 0.1s 1449s Time: 0.07 1449s Return code: 0 1449s OKs: 0 1449s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_ebi_wu_blast_xml.py" [OK] 0.1s 1449s Time: 0.08 1449s Return code: 0 1449s OKs: 0 1450s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_ncbi_blast_xml.py" [OK] 0.1s 1450s Time: 0.11 1450s Return code: 0 1450s OKs: 0 1450s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/pdb_info.py" [OK] 0.8s 1450s Time: 0.76 1450s Return code: 0 1450s OKs: 0 1453s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1453s 134 1453s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1453s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_xray_scale.py" [FAIL] 5.5s 1453s Time: 5.53 1453s Return code: 134 1453s OKs: 0 1453s Standard error: 1453s *** buffer overflow detected ***: terminated 1453s Aborted (core dumped) 1456s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1456s 139 1456s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1456s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_as_pdb_1atom.py" [FAIL] 5.8s 1456s Time: 5.85 1456s Return code: 139 1456s OKs: 0 1456s Standard error: 1456s Segmentation fault (core dumped) 1460s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1460s 139 1460s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1460s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_1.py" [FAIL] 6.8s 1460s Time: 6.82 1460s Return code: 139 1460s OKs: 0 1460s Standard error: 1460s Segmentation fault (core dumped) 1464s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1464s 1 1464s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1464s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py" [FAIL] 8.2s 1464s Standard error: 1464s Traceback (most recent call last): 1464s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py", line 395, in 1464s tst_1() 1464s ~~~~~^^ 1464s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py", line 370, in tst_1 1464s assert os.path.isfile('%s.cif_%s_000.mtz' % (prefix, bn)) 1464s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1464s AssertionError 1464s Time: 8.23 1464s Return code: 1 1464s OKs: 0 1467s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1467s 134 1467s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1467s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_all_chain_ids.py" [FAIL] 6.9s 1467s Time: 6.90 1467s Return code: 134 1467s OKs: 0 1467s Standard error: 1467s *** buffer overflow detected ***: terminated 1467s Aborted (core dumped) 1469s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1469s 139 1469s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1469s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_extract_xtal_data.py" [FAIL] 4.9s 1469s Time: 4.89 1469s Return code: 139 1469s OKs: 0 1469s Standard error: 1469s Segmentation fault (core dumped) 1470s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mtz_as_cif.py" [OK] 0.3s 1470s Time: 0.29 1470s Return code: 0 1470s OKs: 1 1470s Standard out: 1470s Skipping 1akg.mtz test: input file not available 1470s Skipping 1zff.mtz test: input file not available 1470s Skipping l.mtz test: input file not available 1470s Skipping outside_4_exptl_fobs_phases_freeR_flags.mtz test: input file not available 1470s Skipping r1wqzsf.mtz test: input file not available 1470s Skipping ur0013.sf.mtz test: input file not available 1470s Skipping 1aba_test.mtz test: input file not available 1470s OK 1470s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_group_rounding.py" [OK] 0.2s 1470s Time: 0.19 1470s Return code: 0 1470s OKs: 0 1473s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1473s 139 1473s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1473s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cli_parser.py" [FAIL] 6.5s 1473s Time: 6.47 1473s Return code: 139 1473s OKs: 0 1473s Standard error: 1473s Segmentation fault (core dumped) 1473s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_merge_atoms_at_end_to_residues.py" [OK] 0.2s 1473s Time: 0.19 1473s Return code: 0 1473s OKs: 1 1473s Standard out: 1473s [('1', 22), ('3', 17), ('1', 1), ('3', 1)] 1473s [('1', 22), ('3', 18), ('1', 1)] 1473s OK 1474s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_chain_ids_1.py" [OK] 0.9s 1474s Time: 0.86 1474s Return code: 0 1474s OKs: 1 1474s Standard out: 1474s 1474s total number of: 1474s models: 1 1474s chains: 3 1474s alt. conf.: 0 1474s residues: 12 1474s atoms: 174 1474s anisou: 0 1474s number of atom element+charge types: 4 1474s histogram of atom element+charge frequency: 1474s " H " 78 1474s " C " 60 1474s " O " 21 1474s " N " 15 1474s residue name classes: 1474s "common_amino_acid" 12 1474s number of chain ids: 3 1474s histogram of chain id frequency: 1474s "A" 1 1474s "A-2" 1 1474s "A-5" 1 1474s number of alt. conf. ids: 0 1474s number of residue names: 4 1474s histogram of residue name frequency: 1474s "ASN" 3 1474s "PHE" 3 1474s "SER" 3 1474s "THR" 3 1474s Can not initialize monomer_library, skipping test. 1474s OK. Time: 0.348 1475s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_1.py" [OK] 0.5s 1475s Time: 0.53 1475s Return code: 0 1475s OKs: 1 1475s Standard out: 1475s OK. Time: 0.325 1475s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_2.py" [OK] 0.6s 1475s Time: 0.62 1475s Return code: 0 1475s OKs: 1 1475s Standard out: 1475s Can not initialize monomer_library, skipping test. 1475s OK. Time: 0.014 1475s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1475s 134 1475s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1475s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_occupancies_rounding.py" [FAIL] 5.7s 1475s Time: 5.71 1475s Return code: 134 1475s OKs: 0 1475s Standard error: 1475s *** buffer overflow detected ***: terminated 1475s Aborted (core dumped) 1476s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_3.py" [OK] 0.6s 1476s Time: 0.59 1476s Return code: 0 1476s OKs: 1 1476s Standard out: 1476s Can not initialize monomer_library, skipping test. 1476s OK. Time: 0.012 1476s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_copy_select.py" [OK] 0.3s 1476s Time: 0.25 1476s Return code: 0 1476s OKs: 1 1476s Standard out: 1476s There is no info: pdb=" N " 1476s And no parent: None 1476s Info is gone: pdb=" N " 1476s Info is still here: pdb=" N GLY A 1 " 1476s OK. Time: 0.032 1476s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_4.py" [OK] 0.6s 1476s Time: 0.61 1476s Return code: 0 1476s OKs: 1 1476s Standard out: 1476s Can not initialize monomer_library, skipping test. 1476s OK. Time: 0.013 1476s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_id_str.py" [OK] 0.2s 1476s Time: 0.20 1476s Return code: 0 1476s OKs: 0 1476s Standard out: 1476s u+s,u,s: 0.15 0.14 0.01 1476s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_altlocs.py" [OK] 0.2s 1476s Time: 0.22 1476s Return code: 0 1476s OKs: 1 1476s Standard out: 1476s OK 1479s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1479s 139 1479s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1479s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_debug_write.py" [FAIL] 2.3s 1479s Time: 2.34 1479s Return code: 139 1479s OKs: 0 1479s Standard error: 1479s Segmentation fault (core dumped) 1482s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1482s 139 1482s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1482s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_reordered_chains.py" [EXPECTED FAIL] 2.9s 1482s Time: 2.94 1482s Return code: 139 1482s OKs: 0 1482s Standard error: 1482s Segmentation fault (core dumped) 1485s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1485s 134 1485s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1485s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_to_from_hierarchy.py" [EXPECTED FAIL] 3.4s 1485s Time: 3.43 1485s Return code: 134 1485s OKs: 0 1485s Standard error: 1485s *** buffer overflow detected ***: terminated 1485s Aborted (core dumped) 1485s libtbx.python "/usr/lib/python3/dist-packages/libtbx/metric_prefixes.py" [OK] 0.0s 1485s Time: 0.02 1485s Return code: 0 1485s OKs: 1 1485s Standard out: 1485s OK 1489s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_utils.py" [OK] 4.2s 1489s Time: 4.20 1489s Return code: 0 1489s OKs: 0 1489s Standard out: 1489s Skipping exercise_retrieve_unless_exists 1489s ### USER = ubuntu 1489s ### PID = 10469 1489s multiprocessing problem: None 1489s base36_timestamp(): 00m8k8yn96 now 1489s base36_timestamp(): zzydazd000 year 115855 CE 1489s get_svn_revision(): None 1489s get_build_tag(): None 1489s u+s,u,s: 0.07 0.06 0.01 1490s libtbx.python "/usr/lib/python3/dist-packages/libtbx/test_utils/__init__.py" [OK] 0.5s 1490s Time: 0.51 1490s Return code: 0 1490s OKs: 1 1490s Standard out: 1490s OK 1490s libtbx.python "/usr/lib/python3/dist-packages/libtbx/queuing_system_utils/pbs_utils.py" [OK] 0.0s 1490s Time: 0.02 1490s Return code: 0 1490s OKs: 1 1490s Standard out: 1490s *** MY_PBS_ARRAY_SIZE = None 1490s *** MY_PBS_ARRAYID_OFFSET = None 1490s *** PBS_ARRAYID = None 1490s *** OMPI_MCA_ns_nds_num_procs = None 1490s *** OMPI_MCA_ns_nds_vpid = None 1490s n,i: 1 0 1490s OK 1490s libtbx.python "/usr/lib/python3/dist-packages/libtbx/queuing_system_utils/sge_utils.py" [OK] 0.0s 1490s Time: 0.02 1490s Return code: 0 1490s OKs: 1 1490s Standard out: 1490s *** JOB_ID = None 1490s *** SGE_ARCH = None 1490s *** SGE_TASK_FIRST = None 1490s *** SGE_TASK_LAST = None 1490s *** SGE_TASK_ID = None 1490s OK 1490s libtbx.python "/usr/lib/python3/dist-packages/libtbx/introspection.py" [OK] 0.0s 1490s Time: 0.04 1490s Return code: 0 1490s OKs: 1 1490s Standard out: 1490s number of processors: 2 1490s Virtual memory size: 21,397,504 1490s Resident set size: 12,537,856 1490s Stack size: 139,264 1490s Virtual memory size: 21,520,384 exact max: 29,523,968 1490s Resident set size: 13,221,888 approx. max: 21,164,032 1490s Stack size: 139,264 approx. max: 139,264 1490s Memory total: 4,190,969,856 1490s Memory free: 84,955,136 1490s OK 1512s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_thread_utils.py" [OK] 21.7s 1512s Time: 21.73 1512s Return code: 0 1512s OKs: 1 1512s Standard out: 1512s OK 1513s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp.py" [OK] 1.9s 1513s Time: 1.91 1513s Return code: 0 1513s OKs: 1 1513s Standard out: 1513s multiprocessing pool size: 2 1513s wall clock time: 0.00 seconds 1513s OK 1514s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp_state.py" [OK] 0.6s 1514s Time: 0.56 1514s Return code: 0 1514s OKs: 3 1514s Standard out: 1514s Running threading test with 1 processes, 1 threads, 3 tasks 1514s (0x3ffaebb6ba0-11688) object in state -init- 1514s (0x3ffaebb6ba0-11688) changing state from -init- to UEZ2EJ 1514s (0x3ffaebb6ba0-11688) changing state from UEZ2EJ to F19R97 1514s (0x3ffaebb6ba0-11688) changing state from F19R97 to D9OCF6 1514s (0x3ffaebb6ba0-11688) object in state D9OCF6 1514s OK 1514s Running threading test with 2 processes, 1 threads, 3 tasks 1514s (0x3ffaea7e210-11688) object in state -init- 1514s (0x3ffaea7e210-11688) changing state from -init- to SYSX4R 1514s (0x3ffaea7e210-11688) changing state from SYSX4R to UG6P82 1514s (0x3ffaea7e210-11688) changing state from UG6P82 to SKBR3Z 1514s (0x3ffaea7e210-11688) object in state SKBR3Z 1514s OK 1514s Running multiprocessing test with 1 processes, 1 threads, 3 tasks 1514s (0x3ffaea7e210-11688) object in state -init- 1514s (0x3ffaea7e210-11688) changing state from -init- to 2UMQ4A 1514s (0x3ffaea7e210-11688) changing state from 2UMQ4A to 9PYPQK 1514s (0x3ffaea7e210-11688) changing state from 9PYPQK to 1AUTJL 1514s (0x3ffaea7e210-11688) object in state 1AUTJL 1514s OK 1514s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_pickle.py" [OK] 0.0s 1514s Time: 0.04 1514s Return code: 0 1514s OKs: 1 1514s Standard out: 1514s test.dat 1514s dump: 0.00 s 1514s load buffered: 0.00 s 1514s load direct: 0.00 s 1514s test.dat.gz 1514s dump: 0.00 s 1514s load buffered: 0.00 s 1514s load direct: 0.00 s 1514s dumps/loads 1514s dump: 0.00 s 1514s load buffered: 0.00 s 1514s OK 1514s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_fully_buffered_timeout.py" [OK] 0.1s 1514s Time: 0.06 1514s Return code: 0 1514s OKs: 0 1514s Standard out: 1514s Skipping test: probe not configured 1518s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_fetch.py" [OK] 41.8s 1518s Time: 41.84 1518s Return code: 0 1518s OKs: 1 1518s Standard out: 1518s data_r1yjpsf 1518s # 1518s loop_ 1518s _audit.revision_id 1518s _audit.creation_date 1518s _audit.update_record 1518s 1_0 2005-06-14 'Initial release' 1518s 1_1 2013-05-08 'Status correction and format standardization' 1518s # 1518s _cell.entry_id 1yjp 1518s _cell.length_a 21.937 1518s _cell.length_b 4.866 1518s _cell.length_c 23.477 1518s _cell.angle_alpha 90.000 1518s _cell.angle_beta 107.080 1518s _cell.angle_gamma 90.000 1518s # 1518s _diffrn_radiation_wavelength.id 1 1518s _diffrn_radiation_wavelength.wavelength 0.97500 1518s # 1518s _entry.id 1yjp 1518s # 1518s _exptl_crystal.id 1 1518s # 1518s _reflns_scale.group_code 1 1518s # 1518s _symmetry.entry_id 1yjp 1518s _symmetry.space_group_name_H-M 'P 1 21 1' 1518s # 1518s # 1518s loop_ 1518s _refln.crystal_id 1518s _refln.wavelength_id 1518s _refln.scale_group_code 1518s _refln.index_h 1518s _refln.index_k 1518s _refln.index_l 1518s _refln.status 1518s _refln.F_meas_au 1518s _refln.F_meas_sigma_au 1518s 1 1 1 -12 0 2 o 3.49 2.34 1518s 1 1 1 -12 0 3 o 3.31 2.43 1518s 1 1 1 -12 0 4 o 7.32 4.25 1518s 1 1 1 -12 0 5 o 8.88 5.39 1518s 1 1 1 -11 0 1 o 9.46 4.13 1518s 1 1 1 -11 0 2 o 4.91 3.21 1518s 1 1 1 -11 0 3 o 6.37 3.70 1518s 1 1 1 -11 0 4 o 8.50 4.91 1518s 1 1 1 -11 0 5 o 17.44 8.06 1518s 1 1 1 -11 0 6 o 5.89 3.64 1518s 1 1 1 -11 0 8 o 6.39 3.90 1518s 1 1 1 -11 1 2 o 5.69 2.18 1518s 1 1 1 -11 1 3 o 6.53 2.53 1518s 1 1 1 -11 1 5 o 7.26 3.20 1518s 1 1 1 -11 1 6 o 11.05 3.47 1518s 1 1 1 -10 0 2 o 6.32 3.74 1518s 1 1 1 -10 0 3 o 9.36 4.67 1518s 1 1 1 -10 0 5 o 7.20 4.12 1518s 1 1 1 -10 0 6 o 4.88 3.25 1518s 1 1 1 -10 0 7 o 11.84 5.41 1518s 1 1 1 -10 0 8 o 14.49 6.53 1518s 1 1 1 -10 0 9 o 6.21 3.91 1518s 1 1 1 -10 0 10 o 5.55 3.37 1518s 1 1 1 -10 1 1 o 4.58 1.49 1518s 1 1 1 -10 1 3 o 12.40 3.65 1518s 1 1 1 -10 1 4 o 9.07 2.47 1518s 1 1 1 -10 1 5 o 17.23 6.02 1518s 1 1 1 -10 1 6 o 4.60 2.10 1518s 1 1 1 -10 1 7 o 6.34 2.43 1518s 1 1 1 -10 1 8 o 9.04 2.92 1518s 1 1 1 -9 0 2 o 8.10 3.98 1518s 1 1 1 -9 0 3 o 14.22 5.11 1518s 1 1 1 -9 0 5 o 6.01 3.78 1518s 1 1 1 -9 0 6 o 10.48 4.68 1518s 1 1 1 -9 0 7 o 8.79 4.52 1518s 1 1 1 -9 0 8 o 6.15 3.63 1518s 1 1 1 -9 0 9 o 10.27 4.16 1518s 1 1 1 -9 0 10 o 4.38 3.04 1518s 1 1 1 -9 0 11 o 7.27 4.16 1518s 1 1 1 -9 1 3 o 10.75 2.38 1518s 1 1 1 -9 1 4 o 11.86 1.95 1518s 1 1 1 -9 1 5 o 10.95 3.27 1518s 1 1 1 -9 1 6 o 13.31 2.59 1518s 1 1 1 -9 1 7 o 8.06 2.92 1518s 1 1 1 -9 1 8 o 14.75 2.87 1518s 1 1 1 -9 1 9 o 9.04 2.82 1518s 1 1 1 -8 0 2 f 15.88 3.97 1518s 1 1 1 -8 0 3 o 26.78 5.79 1518s 1 1 1 -8 0 5 o 32.83 7.52 1518s 1 1 1 -8 0 7 o 12.74 3.54 1518s 1 1 1 -8 0 8 o 29.46 9.29 1518s 1 1 1 -8 0 9 f 22.09 3.59 1518s 1 1 1 -8 0 10 o 18.81 5.24 1518s 1 1 1 -8 0 11 o 12.76 7.11 1518s 1 1 1 -8 1 1 o 6.26 2.08 1518s 1 1 1 -8 1 2 o 6.97 2.14 1518s 1 1 1 -8 1 4 o 19.24 4.18 1518s 1 1 1 -8 1 5 o 15.46 2.43 1518s 1 1 1 -8 1 6 o 16.87 2.78 1518s 1 1 1 -8 1 7 o 15.66 2.34 1518s 1 1 1 -8 1 8 o 7.07 2.43 1518s 1 1 1 -8 1 9 o 8.81 2.80 1518s 1 1 1 -8 1 10 o 8.61 3.09 1518s 1 1 1 -8 2 1 o 4.39 1.52 1518s 1 1 1 -8 2 2 o 4.20 1.87 1518s 1 1 1 -8 2 3 o 6.14 1.87 1518s 1 1 1 -8 2 4 o 9.38 2.80 1518s 1 1 1 -7 0 3 o 23.46 3.83 1518s 1 1 1 -7 0 4 o 37.35 7.40 1518s 1 1 1 -7 0 6 o 7.44 3.60 1518s 1 1 1 -7 0 7 o 43.94 5.36 1518s 1 1 1 -7 0 8 o 18.96 2.98 1518s 1 1 1 -7 0 9 o 4.95 3.22 1518s 1 1 1 -7 0 10 o 31.73 4.61 1518s 1 1 1 -7 0 11 o 6.31 3.82 1518s 1 1 1 -7 0 12 o 5.05 3.33 1518s 1 1 1 -7 1 1 o 8.89 1.60 1518s 1 1 1 -7 1 2 o 13.70 1.71 1518s 1 1 1 -7 1 3 o 21.03 2.45 1518s 1 1 1 -7 1 4 f 7.57 2.36 1518s 1 1 1 -7 1 5 o 11.31 3.34 1518s 1 1 1 -7 1 6 o 19.93 3.06 1518s 1 1 1 -7 1 7 o 22.86 3.28 1518s 1 1 1 -7 1 8 o 10.32 2.58 1518s 1 1 1 -7 1 9 f 5.13 2.34 1518s 1 1 1 -7 1 10 o 9.91 3.03 1518s 1 1 1 -7 1 11 o 5.61 2.33 1518s 1 1 1 -7 2 1 o 12.28 3.86 1518s 1 1 1 -7 2 2 o 11.29 3.50 1518s 1 1 1 -7 2 3 f 7.22 2.40 1518s 1 1 1 -7 2 4 o 11.13 2.74 1518s 1 1 1 -7 2 5 o 7.86 2.92 1518s 1 1 1 -7 2 6 o 5.23 2.15 1518s 1 1 1 -6 0 2 o 35.03 5.13 1518s 1 1 1 -6 0 3 o 15.64 3.61 1518s 1 1 1 -6 0 4 o 12.60 4.22 1518s 1 1 1 -6 0 5 o 21.36 2.47 1518s 1 1 1 -6 0 6 o 31.19 3.17 1518s 1 1 1 -6 0 7 o 33.66 3.99 1518s 1 1 1 -6 0 8 o 13.70 4.22 1518s 1 1 1 -6 0 9 o 10.99 4.16 1518s 1 1 1 -6 0 10 o 24.56 3.98 1518s 1 1 1 -6 0 11 o 4.41 3.08 1518s 1 1 1 -6 0 12 o 4.07 2.83 1518s 1 1 1 -6 1 1 o 10.24 1.40 1518s 1 1 1 -6 1 2 o 20.59 2.28 1518s 1 1 1 -6 1 3 o 32.14 3.57 1518s 1 1 1 -6 1 4 f 11.60 2.18 1518s 1 1 1 -6 1 5 o 22.15 2.66 1518s 1 1 1 -6 1 6 o 7.68 2.64 1518s 1 1 1 -6 1 7 o 6.39 2.58 1518s 1 1 1 -6 1 8 o 6.60 2.60 1518s 1 1 1 -6 1 9 o 8.21 2.82 1518s 1 1 1 -6 1 10 o 13.25 3.07 1518s 1 1 1 -6 1 11 o 10.62 3.80 1518s 1 1 1 -6 2 1 o 13.78 2.98 1518s 1 1 1 -6 2 2 o 5.95 2.11 1518s 1 1 1 -6 2 3 o 8.96 3.00 1518s 1 1 1 -6 2 4 o 4.88 2.17 1518s 1 1 1 -6 2 5 o 7.35 2.58 1518s 1 1 1 -6 2 6 o 6.93 2.91 1518s 1 1 1 -6 2 7 o 8.14 2.74 1518s 1 1 1 -5 0 2 o 44.04 6.46 1518s 1 1 1 -5 0 3 o 15.30 3.69 1518s 1 1 1 -5 0 4 o 16.95 2.51 1518s 1 1 1 -5 0 5 o 14.82 4.54 1518s 1 1 1 -5 0 6 o 29.73 3.15 1518s 1 1 1 -5 0 7 f 55.71 13.43 1518s 1 1 1 -5 0 8 o 15.06 3.67 1518s 1 1 1 -5 0 9 o 8.76 4.15 1518s 1 1 1 -5 0 10 o 4.69 3.13 1518s 1 1 1 -5 0 11 o 16.56 5.19 1518s 1 1 1 -5 0 12 o 5.59 3.77 1518s 1 1 1 -5 1 1 o 26.70 2.49 1518s 1 1 1 -5 1 2 o 38.67 3.63 1518s 1 1 1 -5 1 3 o 20.45 2.09 1518s 1 1 1 -5 1 4 o 6.46 2.54 1518s 1 1 1 -5 1 5 o 20.55 2.58 1518s 1 1 1 -5 1 6 o 28.68 2.67 1518s 1 1 1 -5 1 7 o 5.68 2.48 1518s 1 1 1 -5 1 8 o 6.99 2.70 1518s 1 1 1 -5 1 9 o 20.74 2.59 1518s 1 1 1 -5 1 10 o 14.70 3.00 1518s 1 1 1 -5 1 11 o 8.62 2.89 1518s 1 1 1 -5 2 1 o 6.26 2.16 1518s 1 1 1 -5 2 2 o 7.93 2.10 1518s 1 1 1 -5 2 3 o 19.90 4.18 1518s 1 1 1 -5 2 4 o 4.98 2.02 1518s 1 1 1 -5 2 5 o 16.85 3.60 1518s 1 1 1 -5 2 7 o 8.15 2.74 1518s 1 1 1 -5 2 8 o 8.89 2.75 1518s 1 1 1 -4 0 2 o 4.55 2.74 1518s 1 1 1 -4 0 3 o 23.50 2.52 1518s 1 1 1 -4 0 4 o 19.15 3.81 1518s 1 1 1 -4 0 7 o 20.06 2.98 1518s 1 1 1 -4 0 8 o 28.85 3.55 1518s 1 1 1 -4 0 9 o 5.36 3.45 1518s 1 1 1 -4 0 10 o 25.68 3.87 1518s 1 1 1 -4 0 11 o 23.28 3.81 1518s 1 1 1 -4 0 12 o 11.39 4.82 1518s 1 1 1 -4 0 13 o 7.07 3.96 1518s 1 1 1 -4 1 1 o 31.99 4.35 1518s 1 1 1 -4 1 2 o 18.48 1.94 1518s 1 1 1 -4 1 3 f 18.93 2.01 1518s 1 1 1 -4 1 4 o 38.05 3.65 1518s 1 1 1 -4 1 5 o 36.34 3.49 1518s 1 1 1 -4 1 6 o 18.08 3.24 1518s 1 1 1 -4 1 7 o 20.11 2.29 1518s 1 1 1 -4 1 8 o 11.25 2.61 1518s 1 1 1 -4 1 9 o 27.09 3.02 1518s 1 1 1 -4 1 10 o 17.78 3.55 1518s 1 1 1 -4 1 11 o 10.45 3.55 1518s 1 1 1 -4 1 12 o 7.42 2.61 1518s 1 1 1 -4 2 1 o 7.72 2.01 1518s 1 1 1 -4 2 2 o 30.88 3.36 1518s 1 1 1 -4 2 3 o 19.14 2.65 1518s 1 1 1 -4 2 4 o 4.44 2.00 1518s 1 1 1 -4 2 5 f 26.44 8.10 1518s 1 1 1 -4 2 6 o 10.83 3.21 1518s 1 1 1 -4 2 7 o 6.03 2.73 1518s 1 1 1 -4 2 8 o 12.78 2.87 1518s 1 1 1 -3 0 2 o 3.40 2.13 1518s 1 1 1 -3 0 3 o 5.40 2.78 1518s 1 1 1 -3 0 4 o 11.52 2.39 1518s 1 1 1 -3 0 5 o 55.13 5.36 1518s 1 1 1 -3 0 6 f 31.55 3.22 1518s 1 1 1 -3 0 7 o 6.95 4.11 1518s 1 1 1 -3 0 8 o 6.00 3.79 1518s 1 1 1 -3 0 9 o 23.03 3.41 1518s 1 1 1 -3 0 10 o 4.79 3.36 1518s 1 1 1 -3 0 11 o 10.46 5.21 1518s 1 1 1 -3 0 12 o 11.53 6.07 1518s 1 1 1 -3 0 13 o 3.22 2.15 1518s 1 1 1 -3 1 1 o 53.95 5.22 1518s 1 1 1 -3 1 2 o 21.50 3.03 1518s 1 1 1 -3 1 3 o 42.88 4.08 1518s 1 1 1 -3 1 4 o 42.70 6.13 1518s 1 1 1 -3 1 5 o 41.12 3.18 1518s 1 1 1 -3 1 6 o 17.31 2.67 1518s 1 1 1 -3 1 7 o 35.59 4.21 1518s 1 1 1 -3 1 8 o 18.53 2.36 1518s 1 1 1 -3 1 9 o 11.55 2.71 1518s 1 1 1 -3 1 10 o 11.41 2.79 1518s 1 1 1 -3 1 11 o 6.92 2.69 1518s 1 1 1 -3 1 12 o 7.03 2.45 1518s 1 1 1 -3 2 1 o 18.65 2.01 1518s 1 1 1 -3 2 2 o 16.33 1.93 1518s 1 1 1 -3 2 3 o 32.88 5.01 1518s 1 1 1 -3 2 4 o 9.99 2.93 1518s 1 1 1 -3 2 5 o 20.62 2.93 1518s 1 1 1 -3 2 6 o 9.18 3.06 1518s 1 1 1 -3 2 7 o 6.90 2.83 1518s 1 1 1 -3 2 8 o 5.26 2.23 1518s 1 1 1 -2 0 1 o 37.92 5.29 1518s 1 1 1 -2 0 2 o 25.98 3.53 1518s 1 1 1 -2 0 3 o 20.20 2.27 1518s 1 1 1 -2 0 4 o 43.74 4.27 1518s 1 1 1 -2 0 5 o 32.34 3.28 1518s 1 1 1 -2 0 6 o 61.28 6.06 1518s 1 1 1 -2 0 7 o 39.92 3.91 1518s 1 1 1 -2 0 8 o 5.73 3.51 1518s 1 1 1 -2 0 9 o 34.44 8.22 1518s 1 1 1 -2 0 10 o 5.00 3.24 1518s 1 1 1 -2 0 11 o 5.95 3.63 1518s 1 1 1 -2 0 12 o 7.57 4.58 1518s 1 1 1 -2 1 1 o 5.64 1.74 1518s 1 1 1 -2 1 2 o 27.80 2.66 1518s 1 1 1 -2 1 3 f 58.08 5.70 1518s 1 1 1 -2 1 4 o 17.13 2.16 1518s 1 1 1 -2 1 5 o 17.82 1.84 1518s 1 1 1 -2 1 6 o 38.29 4.36 1518s 1 1 1 -2 1 7 o 21.32 2.41 1518s 1 1 1 -2 1 8 o 14.24 2.30 1518s 1 1 1 -2 1 9 o 23.48 2.71 1518s 1 1 1 -2 1 10 f 12.02 2.17 1518s 1 1 1 -2 1 11 o 15.91 5.89 1518s 1 1 1 -2 1 12 o 7.00 2.53 1518s 1 1 1 -2 2 1 o 15.73 2.27 1518s 1 1 1 -2 2 2 o 24.74 2.59 1518s 1 1 1 -2 2 3 o 16.53 2.59 1518s 1 1 1 -2 2 4 o 6.46 2.78 1518s 1 1 1 -2 2 5 o 13.27 4.40 1518s 1 1 1 -2 2 6 o 5.58 2.29 1518s 1 1 1 -2 2 7 o 6.76 2.38 1518s 1 1 1 -2 2 8 o 5.29 2.14 1518s 1 1 1 -1 0 1 o 28.12 3.79 1518s 1 1 1 -1 0 2 o 21.59 2.21 1518s 1 1 1 -1 0 3 o 33.14 3.24 1518s 1 1 1 -1 0 4 o 43.39 4.18 1518s 1 1 1 -1 0 5 f 46.52 4.56 1518s 1 1 1 -1 0 6 o 76.28 14.50 1518s 1 1 1 -1 0 7 o 5.12 3.18 1518s 1 1 1 -1 0 9 o 37.08 8.90 1518s 1 1 1 -1 0 10 o 6.65 3.72 1518s 1 1 1 -1 0 11 o 6.86 4.45 1518s 1 1 1 -1 0 12 o 4.18 2.86 1518s 1 1 1 -1 1 1 o 36.99 3.46 1518s 1 1 1 -1 1 2 o 40.11 3.76 1518s 1 1 1 -1 1 3 o 15.12 3.05 1518s 1 1 1 -1 1 4 o 11.44 2.42 1518s 1 1 1 -1 1 5 f 7.66 2.37 1518s 1 1 1 -1 1 6 o 37.21 3.40 1518s 1 1 1 -1 1 7 o 13.99 2.19 1518s 1 1 1 -1 1 8 o 23.42 2.40 1518s 1 1 1 -1 1 9 o 12.59 2.48 1518s 1 1 1 -1 1 10 o 14.84 2.83 1518s 1 1 1 -1 1 11 o 13.90 3.02 1518s 1 1 1 -1 2 1 o 7.71 2.59 1518s 1 1 1 -1 2 2 o 5.95 2.09 1518s 1 1 1 -1 2 3 o 25.96 3.59 1518s 1 1 1 -1 2 4 o 16.53 2.52 1518s 1 1 1 -1 2 5 o 12.51 2.97 1518s 1 1 1 -1 2 6 o 12.40 3.34 1518s 1 1 1 -1 2 7 o 5.97 2.01 1518s 1 1 1 -1 2 8 o 8.24 2.40 1518s 1 1 1 0 0 1 o 40.04 3.82 1518s 1 1 1 0 0 2 o 58.22 5.69 1518s 1 1 1 0 0 3 o 47.47 4.60 1518s 1 1 1 0 0 4 o 7.98 2.75 1518s 1 1 1 0 0 5 o 50.74 7.60 1518s 1 1 1 0 0 6 o 14.87 1.94 1518s 1 1 1 0 0 7 o 3.62 2.41 1518s 1 1 1 0 0 8 o 36.19 7.98 1518s 1 1 1 0 0 9 o 10.11 5.01 1518s 1 1 1 0 0 10 o 18.08 3.24 1518s 1 1 1 0 0 11 o 12.35 4.26 1518s 1 1 1 0 0 12 o 9.41 4.38 1518s 1 1 1 0 1 1 o 92.10 11.26 1518s 1 1 1 0 1 2 o 47.48 4.50 1518s 1 1 1 0 1 3 o 22.08 2.22 1518s 1 1 1 0 1 4 o 8.62 2.51 1518s 1 1 1 0 1 5 o 24.16 1.98 1518s 1 1 1 0 1 6 o 16.72 1.95 1518s 1 1 1 0 1 7 o 5.50 2.46 1518s 1 1 1 0 1 8 o 21.06 2.19 1518s 1 1 1 0 1 9 o 5.99 2.45 1518s 1 1 1 0 1 10 o 8.62 3.03 1518s 1 1 1 0 1 11 o 9.15 3.06 1518s 1 1 1 0 2 0 o 27.82 5.58 1518s 1 1 1 0 2 1 o 29.68 4.10 1518s 1 1 1 0 2 2 o 37.82 4.30 1518s 1 1 1 0 2 3 o 14.42 1.91 1518s 1 1 1 0 2 4 o 13.55 2.70 1518s 1 1 1 0 2 5 o 8.67 3.07 1518s 1 1 1 0 2 6 o 22.77 5.53 1518s 1 1 1 0 2 7 o 5.74 2.12 1518s 1 1 1 0 2 8 o 9.78 2.64 1518s 1 1 1 1 0 1 o 10.19 1.09 1518s 1 1 1 1 0 2 o 20.07 1.88 1518s 1 1 1 1 0 3 o 28.76 2.81 1518s 1 1 1 1 0 4 o 3.16 2.18 1518s 1 1 1 1 0 5 o 35.75 3.54 1518s 1 1 1 1 0 6 f 52.32 5.12 1518s 1 1 1 1 0 7 o 37.09 5.54 1518s 1 1 1 1 0 8 o 6.52 3.32 1518s 1 1 1 1 0 9 o 3.67 2.45 1518s 1 1 1 1 0 10 o 6.03 3.17 1518s 1 1 1 1 0 11 o 3.13 2.20 1518s 1 1 1 1 0 12 o 4.06 2.74 1518s 1 1 1 1 1 0 o 34.97 2.64 1518s 1 1 1 1 1 1 o 15.45 1.46 1518s 1 1 1 1 1 2 o 27.96 2.66 1518s 1 1 1 1 1 3 o 55.14 5.35 1518s 1 1 1 1 1 4 o 14.46 1.65 1518s 1 1 1 1 1 5 o 7.23 2.19 1518s 1 1 1 1 1 6 o 10.31 2.54 1518s 1 1 1 1 1 7 o 11.70 2.22 1518s 1 1 1 1 1 8 o 11.24 2.14 1518s 1 1 1 1 1 9 o 7.60 2.88 1518s 1 1 1 1 1 10 o 8.83 2.34 1518s 1 1 1 1 1 11 o 12.55 3.17 1518s 1 1 1 1 2 0 o 24.36 5.60 1518s 1 1 1 1 2 1 o 13.12 2.09 1518s 1 1 1 1 2 2 o 10.37 2.52 1518s 1 1 1 1 2 3 o 14.39 1.98 1518s 1 1 1 1 2 4 o 26.67 8.23 1518s 1 1 1 1 2 5 o 22.53 5.20 1518s 1 1 1 1 2 6 o 13.94 2.61 1518s 1 1 1 1 2 7 o 7.45 2.38 1518s 1 1 1 1 2 8 o 4.51 2.05 1518s 1 1 1 2 0 1 o 13.06 1.30 1518s 1 1 1 2 0 2 o 10.37 1.36 1518s 1 1 1 2 0 3 o 20.89 2.04 1518s 1 1 1 2 0 4 o 45.12 4.31 1518s 1 1 1 2 0 5 o 15.37 1.91 1518s 1 1 1 2 0 6 o 28.38 2.79 1518s 1 1 1 2 0 7 o 16.02 2.31 1518s 1 1 1 2 0 8 o 3.40 2.35 1518s 1 1 1 2 0 9 o 4.23 2.72 1518s 1 1 1 2 0 10 o 3.89 2.43 1518s 1 1 1 2 0 11 o 10.26 3.01 1518s 1 1 1 2 1 0 o 34.61 2.64 1518s 1 1 1 2 1 1 o 53.93 5.22 1518s 1 1 1 2 1 2 o 20.62 2.08 1518s 1 1 1 2 1 3 o 44.45 3.37 1518s 1 1 1 2 1 4 o 24.41 2.00 1518s 1 1 1 2 1 5 o 40.33 4.58 1518s 1 1 1 2 1 6 o 41.76 5.03 1518s 1 1 1 2 1 7 o 28.20 3.43 1518s 1 1 1 2 1 8 o 33.56 3.76 1518s 1 1 1 2 1 9 o 4.41 1.97 1518s 1 1 1 2 1 10 o 15.24 3.10 1518s 1 1 1 2 2 0 o 25.09 3.38 1518s 1 1 1 2 2 1 o 9.96 2.30 1518s 1 1 1 2 2 2 o 15.79 2.28 1518s 1 1 1 2 2 3 f 23.73 2.57 1518s 1 1 1 2 2 4 o 31.55 3.47 1518s 1 1 1 2 2 5 o 22.42 5.53 1518s 1 1 1 2 2 6 o 21.84 3.98 1518s 1 1 1 2 2 7 o 11.92 3.24 1518s 1 1 1 3 0 1 o 20.22 2.60 1518s 1 1 1 3 0 2 o 15.58 1.67 1518s 1 1 1 3 0 3 o 43.75 4.24 1518s 1 1 1 3 0 4 o 53.24 5.13 1518s 1 1 1 3 0 5 o 9.04 2.60 1518s 1 1 1 3 0 6 o 16.05 2.16 1518s 1 1 1 3 0 7 o 10.18 3.61 1518s 1 1 1 3 0 8 f 21.57 2.93 1518s 1 1 1 3 0 9 o 5.10 2.75 1518s 1 1 1 3 0 10 o 9.06 4.48 1518s 1 1 1 3 0 11 o 7.20 4.29 1518s 1 1 1 3 1 0 o 6.01 1.35 1518s 1 1 1 3 1 1 o 38.17 5.32 1518s 1 1 1 3 1 2 o 88.61 10.65 1518s 1 1 1 3 1 3 o 46.76 4.49 1518s 1 1 1 3 1 4 o 21.38 1.98 1518s 1 1 1 3 1 5 o 10.82 1.68 1518s 1 1 1 3 1 6 o 9.92 1.96 1518s 1 1 1 3 1 7 o 13.79 1.74 1518s 1 1 1 3 1 8 o 18.26 2.25 1518s 1 1 1 3 1 9 o 10.74 2.36 1518s 1 1 1 3 1 10 o 4.53 1.95 1518s 1 1 1 3 2 0 o 36.54 6.90 1518s 1 1 1 3 2 1 o 7.87 2.79 1518s 1 1 1 3 2 2 o 18.30 2.61 1518s 1 1 1 3 2 3 o 17.39 2.45 1518s 1 1 1 3 2 4 o 17.18 2.74 1518s 1 1 1 3 2 5 o 13.02 2.60 1518s 1 1 1 3 2 6 o 4.72 1.98 1518s 1 1 1 4 0 1 o 3.64 2.08 1518s 1 1 1 4 0 2 o 63.80 6.24 1518s 1 1 1 4 0 3 o 19.19 1.93 1518s 1 1 1 4 0 4 o 63.44 6.28 1518s 1 1 1 4 0 5 o 30.78 6.03 1518s 1 1 1 4 0 6 o 9.03 2.53 1518s 1 1 1 4 0 7 o 18.16 2.40 1518s 1 1 1 4 0 8 o 8.94 3.14 1518s 1 1 1 4 0 9 o 6.87 3.36 1518s 1 1 1 4 0 10 o 9.58 4.40 1518s 1 1 1 4 1 0 o 24.37 2.38 1518s 1 1 1 4 1 1 o 49.48 4.80 1518s 1 1 1 4 1 2 o 10.45 1.03 1518s 1 1 1 4 1 3 o 15.01 1.64 1518s 1 1 1 4 1 4 o 4.52 1.88 1518s 1 1 1 4 1 5 f 35.40 3.27 1518s 1 1 1 4 1 6 o 8.15 2.10 1518s 1 1 1 4 1 7 o 9.72 1.59 1518s 1 1 1 4 1 8 o 5.93 1.88 1518s 1 1 1 4 1 9 o 13.31 3.66 1518s 1 1 1 4 2 0 o 12.03 2.31 1518s 1 1 1 4 2 1 o 13.76 1.98 1518s 1 1 1 4 2 2 o 10.87 2.55 1518s 1 1 1 4 2 3 o 7.78 2.40 1518s 1 1 1 4 2 4 o 19.45 4.53 1518s 1 1 1 4 2 5 o 11.32 4.24 1518s 1 1 1 4 2 6 o 7.29 3.50 1518s 1 1 1 5 0 1 o 67.42 11.14 1518s 1 1 1 5 0 2 o 13.50 3.13 1518s 1 1 1 5 0 3 o 22.37 2.21 1518s 1 1 1 5 0 4 o 56.42 6.72 1518s 1 1 1 5 0 5 o 25.46 3.07 1518s 1 1 1 5 0 6 o 38.61 4.82 1518s 1 1 1 5 0 7 o 14.33 2.65 1518s 1 1 1 5 0 8 f 4.56 2.78 1518s 1 1 1 5 0 9 o 8.50 3.26 1518s 1 1 1 5 1 0 o 21.65 2.85 1518s 1 1 1 5 1 1 o 12.29 1.67 1518s 1 1 1 5 1 2 o 11.21 3.27 1518s 1 1 1 5 1 3 o 9.29 2.49 1518s 1 1 1 5 1 4 o 12.76 2.42 1518s 1 1 1 5 1 5 o 4.61 0.86 1518s 1 1 1 5 1 6 o 21.81 2.38 1518s 1 1 1 5 1 7 o 11.05 2.11 1518s 1 1 1 5 1 8 o 4.27 1.64 1518s 1 1 1 5 2 0 o 17.82 3.76 1518s 1 1 1 5 2 1 o 13.94 3.96 1518s 1 1 1 5 2 2 o 14.67 2.97 1518s 1 1 1 5 2 3 o 12.27 4.35 1518s 1 1 1 5 2 4 o 12.90 2.88 1518s 1 1 1 5 2 5 o 8.21 2.77 1518s 1 1 1 6 0 1 o 4.02 2.51 1518s 1 1 1 6 0 2 o 14.11 3.04 1518s 1 1 1 6 0 4 o 44.86 5.41 1518s 1 1 1 6 0 5 f 22.85 4.74 1518s 1 1 1 6 0 6 o 41.69 6.63 1518s 1 1 1 6 0 7 o 7.42 2.96 1518s 1 1 1 6 0 8 o 13.47 5.61 1518s 1 1 1 6 1 0 o 25.42 2.26 1518s 1 1 1 6 1 1 o 9.87 3.01 1518s 1 1 1 6 1 2 o 28.37 5.85 1518s 1 1 1 6 1 3 o 16.66 3.91 1518s 1 1 1 6 1 4 o 23.02 5.62 1518s 1 1 1 6 1 6 o 26.51 4.88 1518s 1 1 1 6 1 7 o 3.67 1.58 1518s 1 1 1 6 2 0 o 8.22 2.50 1518s 1 1 1 6 2 2 o 9.67 2.35 1518s 1 1 1 6 2 3 o 3.73 1.60 1518s 1 1 1 7 0 1 o 10.99 3.37 1518s 1 1 1 7 0 2 o 17.23 3.99 1518s 1 1 1 7 0 3 o 5.15 2.69 1518s 1 1 1 7 0 4 o 5.19 3.01 1518s 1 1 1 7 0 5 o 23.76 3.00 1518s 1 1 1 7 0 6 o 5.48 3.05 1518s 1 1 1 7 0 7 o 6.05 3.12 1518s 1 1 1 7 0 8 o 7.94 3.69 1518s 1 1 1 7 1 0 o 33.08 3.93 1518s 1 1 1 7 1 1 o 8.43 3.00 1518s 1 1 1 7 1 2 o 10.12 3.61 1518s 1 1 1 7 1 3 o 14.66 3.85 1518s 1 1 1 7 1 4 o 9.43 3.13 1518s 1 1 1 7 1 6 o 14.64 4.20 1518s 1 1 1 7 2 0 o 14.80 3.92 1518s 1 1 1 7 2 1 o 6.02 2.00 1518s 1 1 1 8 0 2 o 29.07 8.06 1518s 1 1 1 8 0 3 o 5.29 2.84 1518s 1 1 1 8 0 4 o 22.81 5.95 1518s 1 1 1 8 0 5 o 4.11 2.70 1518s 1 1 1 8 1 0 o 7.24 1.50 1518s 1 1 1 8 1 1 o 8.85 3.06 1518s 1 1 1 8 1 2 o 6.83 3.09 1518s 1 1 1 8 1 3 o 18.14 5.99 1518s 1 1 1 9 0 1 o 13.49 3.22 1518s 1 1 1 9 0 2 o 11.72 3.95 1518s 1 1 1 10 0 2 o 7.39 3.73 1518s 1 1 1 10 1 0 o 16.08 6.44 1518s #END OF REFLECTIONS 1518s 1518s Starting iotbx.fetch_pdb 1518s on Sat Mar 22 13:30:40 2025 by ubuntu 1518s =============================================================================== 1518s 1518s Processing files: 1518s ------------------------------------------------------------------------------- 1518s 1518s No files found 1518s 1518s Processing PHIL parameters: 1518s ------------------------------------------------------------------------------- 1518s 1518s Adding command-line PHIL: 1518s ------------------------- 1518s action=all 1518s 1518s Final processed PHIL parameters: 1518s ------------------------------------------------------------------------------- 1518s fetch { 1518s pdb_ids = "6yvd" 1518s action = model data sequence half_maps *all 1518s } 1518s 1518s 1518s Starting job 1518s =============================================================================== 1518s Validating inputs: 1518s 1518s Model in PDB format saved to /tmp/autopkgtest.R528VC/autopkgtest_tmp/python3.13/6yvd.pdb 1518s Model in mmCIF format saved to /tmp/autopkgtest.R528VC/autopkgtest_tmp/python3.13/6yvd.cif 1518s Couldn't download sf for 6yvd at https://files.rcsb.org/download/6yvd-sf.cif.gz. 1518s Cryo-EM map saved to /tmp/autopkgtest.R528VC/autopkgtest_tmp/python3.13/emd_10944.map.gz 1518s Cryo-EM half map 1 saved to /tmp/autopkgtest.R528VC/autopkgtest_tmp/python3.13/emd_10944_half_map_1.map.gz 1518s Cryo-EM half map 2 saved to /tmp/autopkgtest.R528VC/autopkgtest_tmp/python3.13/emd_10944_half_map_2.map.gz 1518s Sequence saved to /tmp/autopkgtest.R528VC/autopkgtest_tmp/python3.13/6yvd.fa 1518s 1518s =============================================================================== 1518s Job complete 1518s Total CPU time: 0.39 seconds 1518s Starting iotbx.fetch_pdb 1518s on Sat Mar 22 13:30:52 2025 by ubuntu 1518s =============================================================================== 1518s 1518s Processing files: 1518s ------------------------------------------------------------------------------- 1518s 1518s No files found 1518s 1518s Processing PHIL parameters: 1518s ------------------------------------------------------------------------------- 1518s 1518s Adding command-line PHIL: 1518s ------------------------- 1518s action=model 1518s 1518s Final processed PHIL parameters: 1518s ------------------------------------------------------------------------------- 1518s fetch { 1518s pdb_ids = "6yvd" 1518s } 1518s 1518s 1518s Starting job 1518s =============================================================================== 1518s Validating inputs: 1518s 1518s Model in PDB format saved to /tmp/autopkgtest.R528VC/autopkgtest_tmp/python3.13/6yvd.pdb 1518s Model in mmCIF format saved to /tmp/autopkgtest.R528VC/autopkgtest_tmp/python3.13/6yvd.cif 1518s 1518s =============================================================================== 1518s Job complete 1518s Total CPU time: 0.34 seconds 1518s Starting iotbx.fetch_pdb 1518s on Sat Mar 22 13:30:54 2025 by ubuntu 1518s =============================================================================== 1518s 1518s Processing files: 1518s ------------------------------------------------------------------------------- 1518s 1518s No files found 1518s 1518s Processing PHIL parameters: 1518s ------------------------------------------------------------------------------- 1518s 1518s Adding command-line PHIL: 1518s ------------------------- 1518s action=model 1518s 1518s Final processed PHIL parameters: 1518s ------------------------------------------------------------------------------- 1518s fetch { 1518s pdb_ids = "6yvd" 1518s } 1518s 1518s 1518s Starting job 1518s =============================================================================== 1518s Validating inputs: 1518s 1518s Model in PDB format saved to /tmp/autopkgtest.R528VC/autopkgtest_tmp/python3.13/6yvd.pdb 1518s Model in mmCIF format saved to /tmp/autopkgtest.R528VC/autopkgtest_tmp/python3.13/6yvd.cif 1518s 1518s =============================================================================== 1518s Job complete 1518s Total CPU time: 0.33 seconds 1518s Starting iotbx.fetch_pdb 1518s on Sat Mar 22 13:30:56 2025 by ubuntu 1518s =============================================================================== 1518s 1518s Processing files: 1518s ------------------------------------------------------------------------------- 1518s 1518s No files found 1518s 1518s Processing PHIL parameters: 1518s ------------------------------------------------------------------------------- 1518s 1518s Adding command-line PHIL: 1518s ------------------------- 1518s action=data 1518s 1518s Final processed PHIL parameters: 1518s ------------------------------------------------------------------------------- 1518s fetch { 1518s pdb_ids = "6yvd" 1518s action = model *data sequence half_maps all 1518s } 1518s 1518s 1518s Starting job 1518s =============================================================================== 1518s Validating inputs: 1518s 1518s Couldn't download sf for 6yvd at https://files.rcsb.org/download/6yvd-sf.cif.gz. 1518s Cryo-EM map saved to /tmp/autopkgtest.R528VC/autopkgtest_tmp/python3.13/emd_10944.map.gz 1518s 1518s =============================================================================== 1518s Job complete 1518s Total CPU time: 0.33 seconds 1518s Starting iotbx.fetch_pdb 1518s on Sat Mar 22 13:31:01 2025 by ubuntu 1518s =============================================================================== 1518s 1518s Processing files: 1518s ------------------------------------------------------------------------------- 1518s 1518s No files found 1518s 1518s Processing PHIL parameters: 1518s ------------------------------------------------------------------------------- 1518s 1518s Adding command-line PHIL: 1518s ------------------------- 1518s action=half_maps 1518s 1518s Final processed PHIL parameters: 1518s ------------------------------------------------------------------------------- 1518s fetch { 1518s pdb_ids = "6yvd" 1518s action = model data sequence *half_maps all 1518s } 1518s 1518s 1518s Starting job 1518s =============================================================================== 1518s Validating inputs: 1518s 1518s Cryo-EM half map 1 saved to /tmp/autopkgtest.R528VC/autopkgtest_tmp/python3.13/emd_10944_half_map_1.map.gz 1518s Cryo-EM half map 2 saved to /tmp/autopkgtest.R528VC/autopkgtest_tmp/python3.13/emd_10944_half_map_2.map.gz 1518s 1518s =============================================================================== 1518s Job complete 1518s Total CPU time: 0.35 seconds 1518s Starting iotbx.fetch_pdb 1518s on Sat Mar 22 13:31:05 2025 by ubuntu 1518s =============================================================================== 1518s 1518s Processing files: 1518s ------------------------------------------------------------------------------- 1518s 1518s No files found 1518s 1518s Processing PHIL parameters: 1518s ------------------------------------------------------------------------------- 1518s 1518s Adding command-line PHIL: 1518s ------------------------- 1518s action=sequence 1518s 1518s Final processed PHIL parameters: 1518s ------------------------------------------------------------------------------- 1518s fetch { 1518s pdb_ids = "6yvd" 1518s action = model data *sequence half_maps all 1518s } 1518s 1518s 1518s Starting job 1518s =============================================================================== 1518s Validating inputs: 1518s 1518s Sequence saved to /tmp/autopkgtest.R528VC/autopkgtest_tmp/python3.13/6yvd.fa 1518s 1518s =============================================================================== 1518s Job complete 1518s Total CPU time: 0.32 seconds 1518s Starting iotbx.fetch_pdb 1518s on Sat Mar 22 13:31:06 2025 by ubuntu 1518s =============================================================================== 1518s 1518s Processing files: 1518s ------------------------------------------------------------------------------- 1518s 1518s No files found 1518s 1518s Processing PHIL parameters: 1518s ------------------------------------------------------------------------------- 1518s 1518s Adding command-line PHIL: 1518s ------------------------- 1518s action=all 1518s 1518s Final processed PHIL parameters: 1518s ------------------------------------------------------------------------------- 1518s fetch { 1518s pdb_ids = "6yvd" 1518s action = model data sequence half_maps *all 1518s } 1518s 1518s 1518s Starting job 1518s =============================================================================== 1518s Validating inputs: 1518s 1518s Model in PDB format saved to /tmp/autopkgtest.R528VC/autopkgtest_tmp/python3.13/6yvd.pdb 1518s Model in mmCIF format saved to /tmp/autopkgtest.R528VC/autopkgtest_tmp/python3.13/6yvd.cif 1518s Couldn't download sf for 6yvd at https://files.rcsb.org/download/6yvd-sf.cif.gz. 1518s Cryo-EM map saved to /tmp/autopkgtest.R528VC/autopkgtest_tmp/python3.13/emd_10944.map.gz 1518s Cryo-EM half map 1 saved to /tmp/autopkgtest.R528VC/autopkgtest_tmp/python3.13/emd_10944_half_map_1.map.gz 1518s Cryo-EM half map 2 saved to /tmp/autopkgtest.R528VC/autopkgtest_tmp/python3.13/emd_10944_half_map_2.map.gz 1518s Sequence saved to /tmp/autopkgtest.R528VC/autopkgtest_tmp/python3.13/6yvd.fa 1518s 1518s =============================================================================== 1518s Job complete 1518s Total CPU time: 0.39 seconds 1518s OK 1518s u+s,u,s: 0.25 0.23 0.02 1520s libtbx.python "/usr/lib/python3/dist-packages/libtbx/easy_run.py" [OK] 1.5s 1520s Time: 1.47 1520s Return code: 0 1520s OKs: 1 1520s Standard out: 1520s OK 1520s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_containers.py" [OK] 0.0s 1520s Time: 0.02 1520s Return code: 0 1520s OKs: 1 1520s Standard out: 1520s OK 1520s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_path.py" [OK] 0.0s 1520s Time: 0.04 1520s Return code: 0 1520s OKs: 1 1520s Standard out: 1520s OK 1520s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_math_utils.py" [OK] 0.2s 1520s Time: 0.23 1520s Return code: 0 1520s OKs: 1 1520s Standard out: 1520s OK 1520s libtbx.python "/usr/lib/python3/dist-packages/libtbx/assert_utils.py" [OK] 0.1s 1520s Time: 0.11 1520s Return code: 0 1520s OKs: 1 1520s Standard out: 1520s OK 1520s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_str_utils.py" [OK] 0.2s 1520s Time: 0.22 1520s Return code: 0 1520s OKs: 1 1520s Standard out: 1520s OK 1520s libtbx.python "/usr/lib/python3/dist-packages/libtbx/table_utils.py" [OK] 0.0s 1520s Time: 0.03 1520s Return code: 0 1520s OKs: 1 1520s Standard out: 1520s OK 1520s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_scheduling.py" [OK] 6.3s 1520s Time: 6.30 1520s Return code: 0 1520s OKs: 0 1520s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_tokenizer.py" [OK] 0.0s 1520s Time: 0.04 1520s Return code: 0 1520s OKs: 1 1520s Standard out: 1520s OK 1521s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst.py" [OK] 0.2s 1521s Time: 0.18 1521s Return code: 0 1521s OKs: 1 1521s Standard out: 1521s OK 1521s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_experimental.py" [OK] 0.0s 1521s Time: 0.04 1521s Return code: 0 1521s OKs: 1 1521s Standard out: 1521s OK 1521s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_interface.py" [OK] 0.1s 1521s Time: 0.07 1521s Return code: 0 1521s OKs: 1 1521s Standard out: 1521s phenix module not available: skipping advanced tests 1521s phaser module not available: skipping advanced tests 1521s OK 1521s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_object_oriented_patterns.py" [OK] 0.1s 1521s Time: 0.06 1521s Return code: 0 1521s OKs: 0 1521s libtbx.python "/usr/lib/python3/dist-packages/libtbx/find_reference_cycles.py" [OK] 0.0s 1521s Time: 0.03 1521s Return code: 0 1521s OKs: 1 1521s Standard out: 1521s OK 1521s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_binary_search.py" [OK] 0.0s 1521s Time: 0.02 1521s Return code: 0 1521s OKs: 1 1521s Standard out: 1521s OK 1521s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_topological_sort.py" [OK] 0.0s 1521s Time: 0.02 1521s Return code: 0 1521s OKs: 1 1521s Standard out: 1521s OK 1521s libtbx.python "/usr/lib/python3/dist-packages/libtbx/clusterTests.py" [OK] 0.1s 1521s Time: 0.13 1521s Return code: 0 1521s OKs: 1 1521s Standard out: 1521s ---------------------------------------------------------------------- 1521s Ran 13 tests in 0.088s 1521s 1521s OK 1521s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_citations.py" [OK] 0.1s 1521s Time: 0.14 1521s Return code: 0 1521s OKs: 1 1521s Standard out: 1521s OK 1521s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_python_code_parsing.py" [OK] 0.0s 1521s Time: 0.03 1521s Return code: 0 1521s OKs: 1 1521s Standard out: 1521s OK 1521s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_representation.py" [OK] 0.0s 1521s Time: 0.02 1521s Return code: 0 1521s OKs: 0 1521s Standard out: 1521s 99999999999999950039963891867 1521s 99999999999999963917751699682 1521s 99999999999999977795539507496 1521s 99999999999999991673327315311 1521s 100000000000000005551115123125 1521s 100000000000000019428902930940 1521s 100000000000000033306690738754 1521s 100000000000000047184478546569 1521s 100000000000000061062266354383 1521s 100000000000000074940054162198 1521s 100000000000000088817841970012 1521s 100000000000000102695629777826 1521s 100000000000000116573417585641 1521s 100000000000000130451205393455 1521s 100000000000000144328993201270 1521s 100000000000000158206781009084 1521s 100000000000000172084568816899 1521s 100000000000000185962356624713 1521s 100000000000000199840144432528 1521s 100000000000000213717932240342 1521s 100000000000000227595720048157 1521s 100000000000000241473507855971 1521s 100000000000000255351295663786 1521s 100000000000000269229083471600 1521s 100000000000000283106871279414 1521s 100000000000000296984659087229 1521s 100000000000000310862446895043 1521s 100000000000000324740234702858 1521s 100000000000000338618022510672 1521s 100000000000000352495810318487 1521s BEst 450359962737049.6 1521s 900719925474099.2 1521s 55.32192809488736 1521s 56.32192809488736 1521s True 1521s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_find_unused_imports.py" [OK] 0.0s 1521s Time: 0.02 1521s Return code: 0 1521s OKs: 1 1521s Standard out: 1521s OK 1521s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_program_template.py" [OK] 0.2s 1521s Time: 0.22 1521s Return code: 0 1521s OKs: 0 1522s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_version.py" [OK] 0.0s 1522s Time: 0.05 1522s Return code: 0 1522s OKs: 0 1522s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp_multicore.py" [OK] 0.3s 1522s Time: 0.27 1522s Return code: 0 1522s OKs: 0 1522s Standard out: 1522s [1] 1 1522s [2] 2 1522s [3] 6 1522s [4] 24 1522s [5] 120 1522s [6] 720 1522s [7] 5040 1522s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_dlite.py" [OK] 2.0s 1522s Time: 2.05 1522s Return code: 0 1522s OKs: 1 1522s Standard out: 1522s OK 1524s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1524s 1 1524s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1524s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_xmlrpc_utils.py" [EXPECTED FAIL] 1.3s 1524s Time: 1.34 1524s Return code: 1 1524s OKs: 0 1524s Standard error: 1524s Traceback (most recent call last): 1524s File "/usr/lib/python3/dist-packages/libtbx/tst_xmlrpc_utils.py", line 42, in 1524s exercise() 1524s ~~~~~~~~^^ 1524s File "/usr/lib/python3/dist-packages/libtbx/tst_xmlrpc_utils.py", line 15, in exercise 1524s server = xmlrpc_utils.external_program_server(command=full_cmd, 1524s program_id="TEST", 1524s timeout=None, 1524s cache_requests=True, 1524s log=log) 1524s TypeError: external_program_server.__init__() got an unexpected keyword argument 'command' 1526s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1526s 139 1526s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1526s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_smoothing.py" [FAIL] 2.4s 1526s Time: 2.37 1526s Return code: 139 1526s OKs: 0 1526s Standard error: 1526s Segmentation fault (core dumped) 1528s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_runtime_utils.py" [OK] 5.9s 1528s Time: 5.93 1528s Return code: 0 1528s OKs: 1 1528s Standard out: 1528s OK 1528s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1528s 139 1528s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1528s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_genetic_algorithm_with_mp.py" [FAIL] 2.4s 1528s Time: 2.42 1528s Return code: 139 1528s OKs: 0 1528s Standard error: 1528s Segmentation fault (core dumped) 1528s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_1" [OK] 0.0s 1528s Time: 0.00 1528s Return code: 0 1528s OKs: 1 1528s Standard out: 1528s Total OK: 511 1528s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_2" [OK] 0.0s 1528s Time: 0.00 1528s Return code: 0 1528s OKs: 1 1528s Standard out: 1528s Total OK: 268 1528s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_3" [OK] 0.0s 1528s Time: 0.00 1528s Return code: 0 1528s OKs: 1 1528s Standard out: 1528s Total OK: 164 1528s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_4" [OK] 0.0s 1528s Time: 0.00 1528s Return code: 0 1528s OKs: 1 1528s Standard out: 1528s Total OK: 1420 1528s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_5" [OK] 0.0s 1528s Time: 0.00 1528s Return code: 0 1528s OKs: 1 1528s Standard out: 1528s Total OK: 23 1528s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_vec3" [OK] 0.0s 1528s Time: 0.00 1528s Return code: 0 1528s OKs: 1 1528s Standard out: 1528s Total OK: 83 1528s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_unsigned_float_arithmetic" [OK] 0.0s 1528s Time: 0.00 1528s Return code: 0 1528s OKs: 1 1528s Standard out: 1528s OK 1528s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_mat3" [OK] 0.0s 1528s Time: 0.00 1528s Return code: 0 1528s OKs: 1 1528s Standard out: 1528s Total OK: 129 1528s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_sym_mat3" [OK] 0.0s 1528s Time: 0.00 1528s Return code: 0 1528s OKs: 1 1528s Standard out: 1528s Total OK: 91 1528s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_ref_matrix_facet" [OK] 0.0s 1528s Time: 0.00 1528s Return code: 0 1528s OKs: 1 1528s Standard out: 1528s OK 1528s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_accessors" [OK] 0.0s 1528s Time: 0.00 1528s Return code: 0 1528s OKs: 1 1528s Standard out: 1528s Total OK: 1730 1528s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_optional_copy" [OK] 0.0s 1528s Time: 0.00 1528s Return code: 0 1528s OKs: 1 1528s Standard out: 1528s OK 1528s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_rectangular_full_packed" [OK] 0.0s 1528s Time: 0.00 1528s Return code: 0 1528s OKs: 0 1528s Standard out: 1528s Test of accessor for rectangular full packed format skipped 1529s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex_argument_passing.py" [OK] 0.1s 1529s Time: 0.10 1529s Return code: 0 1529s OKs: 1 1529s Standard out: 1529s OK 1529s "/usr/lib/cctbx/python3.13/scitbx/serialization/tst_base_256" [OK] 0.3s 1529s Time: 0.30 1529s Return code: 0 1529s OKs: 1 1529s Standard out: 1529s OK 1531s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1531s 139 1531s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1531s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_basic.py" [FAIL] 2.9s 1531s Time: 2.92 1531s Return code: 139 1531s OKs: 1 1531s Standard out: 1531s 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' 1531s Size of an empty container. 1531s Some of those containers store a pointer to a raw storage: 1531s the 'cumulative' entry refers to the total memory footprint 1531s whereas the other entry does not include the raw storage. 1531s 1531s int : 4 1531s af::ref : 32 1531s scitbx::auto_array : 8 1531s boost::shared_array : 16 1531s boost::ptr_vector : 24 1531s std::vector : 24 1531s af::shared : 16 1531s af::shared [cumulative] : 64 1531s std::valarray : 16 1531s af::versa : 24 1531s af::versa > : 280 1531s af::versa > [cumulative] : 328 1531s 1531s double : 8 1531s af::ref : 32 1531s scitbx::auto_array : 8 1531s boost::shared_array : 16 1531s boost::ptr_vector : 24 1531s std::vector : 24 1531s af::shared : 16 1531s af::shared [cumulative] : 64 1531s std::valarray : 16 1531s af::versa : 24 1531s af::versa > : 280 1531s af::versa > [cumulative] : 328 1531s 1531s OK 1531s Standard error: 1531s Segmentation fault (core dumped) 1533s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1533s 139 1533s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1533s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_minimum_covering_ellipsoid.py" [FAIL] 4.0s 1533s Time: 4.03 1533s Return code: 139 1533s OKs: 0 1533s Standard error: 1533s Segmentation fault (core dumped) 1535s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1535s 139 1535s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1535s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian_fit_1d_analytical.py" [FAIL] 4.6s 1535s Time: 4.64 1535s Return code: 139 1535s OKs: 0 1535s Standard error: 1535s Segmentation fault (core dumped) 1535s "/usr/lib/cctbx/python3.13/scitbx/math/tests/tst" [OK] 0.0s 1535s Time: 0.00 1535s Return code: 0 1535s OKs: 2 1535s Standard out: 1535s copysign(3.f, +0.f) = 3 instead of 0.f as per C99 1535s copysign(3.f, -0.f) = -3 instead of -0.f as per C99 1535s linear interpolation test OK 1535s OK 1535s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_givens" [OK] 0.0s 1535s Time: 0.01 1535s Return code: 0 1535s OKs: 1 1535s Standard out: 1535s OK 1535s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_householder" [OK] 0.0s 1535s Time: 0.00 1535s Return code: 0 1535s OKs: 1 1535s Standard out: 1535s OK 1535s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_svd" [OK] 0.0s 1535s Time: 0.01 1535s Return code: 0 1535s OKs: 1 1535s Standard out: 1535s OK 1535s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_cholesky" [OK] 0.1s 1535s Time: 0.13 1535s Return code: 0 1535s OKs: 1 1535s Standard out: 1535s Exercising sizes up to 100 1535s Hilbert 1535s Condition 1 1535s Condition 2 1535s Condition 3 1535s Condition 4 1535s OK 1535s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/tests/tst_row_echelon.py" [OK] 0.1s 1535s Time: 0.06 1535s Return code: 0 1535s OKs: 1 1535s Standard out: 1535s OK 1536s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/tests/tst_householder.py" [OK] 0.1s 1536s Time: 0.12 1536s Return code: 0 1536s OKs: 1 1536s Standard out: 1536s OK 1536s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_matrix.py" [OK] 0.1s 1536s Time: 0.12 1536s Return code: 0 1536s OKs: 1 1536s Standard out: 1536s OK 1538s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1538s 139 1538s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1538s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_cubic_equation.py" [FAIL] 4.7s 1538s Time: 4.70 1538s Return code: 139 1538s OKs: 0 1538s Standard error: 1538s Segmentation fault (core dumped) 1540s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1540s 139 1540s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1540s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_cholesky.py" [FAIL] 4.1s 1540s Time: 4.06 1540s Return code: 139 1540s OKs: 0 1540s Standard error: 1540s Segmentation fault (core dumped) 1542s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1542s 139 1542s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1542s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_svd.py" [FAIL] 4.5s 1542s Time: 4.47 1542s Return code: 139 1542s OKs: 0 1542s Standard error: 1542s Segmentation fault (core dumped) 1544s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1544s 139 1544s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1544s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_eigensystem.py" [FAIL] 4.5s 1544s Time: 4.49 1544s Return code: 139 1544s OKs: 0 1544s Standard error: 1544s Segmentation fault (core dumped) 1546s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1546s 139 1546s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1546s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_svd.py" [FAIL] 4.5s 1546s Time: 4.47 1546s Return code: 139 1546s OKs: 0 1546s Standard error: 1546s Segmentation fault (core dumped) 1547s libtbx.python "/usr/lib/python3/dist-packages/scitbx/error/tst_error.py" [OK] 0.1s 1547s Time: 0.06 1547s Return code: 0 1547s OKs: 1 1547s Standard out: 1547s OK 1547s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_map.py" [OK] 0.1s 1547s Time: 0.06 1547s Return code: 0 1547s OKs: 1 1547s Standard out: 1547s OK 1547s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_set.py" [OK] 0.0s 1547s Time: 0.05 1547s Return code: 0 1547s OKs: 1 1547s Standard out: 1547s OK 1547s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_vector.py" [OK] 0.1s 1547s Time: 0.07 1547s Return code: 0 1547s OKs: 1 1547s Standard out: 1547s OK 1549s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1549s 139 1549s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1549s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_dsyev.py" [FAIL] 4.5s 1549s Time: 4.50 1549s Return code: 139 1549s OKs: 0 1549s Standard error: 1549s Segmentation fault (core dumped) 1551s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1551s 139 1551s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1551s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/regression_test.py" [FAIL] 4.3s 1551s Time: 4.33 1551s Return code: 139 1551s OKs: 0 1551s Standard error: 1551s Segmentation fault (core dumped) 1554s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1554s 139 1554s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1554s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex.py" [FAIL] 5.1s 1554s Time: 5.08 1554s Return code: 139 1554s OKs: 0 1554s Standard error: 1554s Segmentation fault (core dumped) 1556s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1556s 139 1556s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1556s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_numpy_bridge.py" [FAIL] 5.0s 1556s Time: 5.04 1556s Return code: 139 1556s OKs: 0 1556s Standard error: 1556s Segmentation fault (core dumped) 1558s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1558s 139 1558s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1558s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_smart_selection.py" [FAIL] 4.5s 1558s Time: 4.51 1558s Return code: 139 1558s OKs: 0 1558s Standard error: 1558s Segmentation fault (core dumped) 1561s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1561s 139 1561s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1561s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_shared.py" [FAIL] 4.6s 1561s Time: 4.59 1561s Return code: 139 1561s OKs: 0 1561s Standard error: 1561s Segmentation fault (core dumped) 1564s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_cost_of_m_handle_in_af_shared.py" [OK] 3.2s 1564s Time: 3.23 1564s Return code: 0 1564s OKs: 1 1564s Standard out: 1564s Loop over af::shared: 1564s data_size=1000, n_repeats=30000 1564s size+begin inside loop: 0.23 s 1564s begin outside loop: 0.16 s 1564s size+begin outside loop: 0.12 s 1564s 1564s data_size=10000, n_repeats=3000 1564s size+begin inside loop: 0.19 s 1564s begin outside loop: 0.16 s 1564s size+begin outside loop: 0.12 s 1564s 1564s data_size=100000, n_repeats=300 1564s size+begin inside loop: 0.27 s 1564s begin outside loop: 0.18 s 1564s size+begin outside loop: 0.15 s 1564s 1564s data_size=1000000, n_repeats=30 1564s size+begin inside loop: 0.21 s 1564s begin outside loop: 0.14 s 1564s size+begin outside loop: 0.12 s 1564s 1564s data_size=10000000, n_repeats=3 1564s size+begin inside loop: 0.30 s 1564s begin outside loop: 0.25 s 1564s size+begin outside loop: 0.25 s 1564s 1564s OK 1564s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_cubicle_neighbors.py" [OK] 0.2s 1564s Time: 0.16 1564s Return code: 0 1564s OKs: 1 1564s Standard out: 1564s OK 1564s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_r3_utils.py" [OK] 0.2s 1564s Time: 0.15 1564s Return code: 0 1564s OKs: 1 1564s Standard out: 1564s OK 1565s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_regular_grid_on_unit_sphere.py" [OK] 0.5s 1565s Time: 0.49 1565s Return code: 0 1565s OKs: 0 1568s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1568s 139 1568s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1568s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/__init__.py" [FAIL] 2.8s 1568s Time: 2.85 1568s Return code: 139 1568s OKs: 0 1568s Standard error: 1568s Segmentation fault (core dumped) 1570s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1570s 139 1570s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1570s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_random_transform.py" [FAIL] 2.6s 1570s Time: 2.60 1570s Return code: 139 1570s OKs: 0 1570s Standard error: 1570s Segmentation fault (core dumped) 1570s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_graph.py" [OK] 0.0s 1570s Time: 0.05 1570s Return code: 0 1570s OKs: 1 1570s Standard out: 1570s OK 1570s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_robust.py" [OK] 0.1s 1570s Time: 0.12 1570s Return code: 0 1570s OKs: 1 1570s Standard out: 1570s OK 1573s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1573s 139 1573s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1573s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/superpose.py" [FAIL] 2.4s 1573s Time: 2.37 1573s Return code: 139 1573s OKs: 0 1573s Standard error: 1573s Segmentation fault (core dumped) 1575s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_integer_offsets_vs_pointers.py" [OK] 16.4s 1575s Time: 16.38 1575s Return code: 0 1575s OKs: 1 1575s Standard out: 1575s data_size = 1000 n_repeats = 30000 1575s use_pointers = False 1575s use_iterators = 0 time = 0.51 s overhead = 0.00 s (d[p[i]] -1.36424e-08) 1575s use_iterators = 1 time = 0.24 s overhead = 0.00 s (d[*p++] -1.36424e-08) 1575s use_pointers = True 1575s use_iterators = 0 time = 0.22 s overhead = 0.00 s (*dp[i] -1.36424e-08) 1575s use_iterators = 1 time = 0.75 s overhead = 0.00 s (**dpi++ -1.36424e-08) 1575s use_iterators = 2 time = 0.09 s overhead = 0.00 s (**dpp++ -1.36424e-08) 1575s data_size = 10000 n_repeats = 3000 1575s use_pointers = False 1575s use_iterators = 0 time = 0.50 s overhead = 0.00 s (d[p[i]] -1.09145e-08) 1575s use_iterators = 1 time = 0.31 s overhead = 0.00 s (d[*p++] -1.09145e-08) 1575s use_pointers = True 1575s use_iterators = 0 time = 0.26 s overhead = 0.00 s (*dp[i] -1.09145e-08) 1575s use_iterators = 1 time = 0.65 s overhead = 0.00 s (**dpi++ -1.09145e-08) 1575s use_iterators = 2 time = 0.08 s overhead = 0.00 s (**dpp++ -1.09145e-08) 1575s data_size = 100000 n_repeats = 300 1575s use_pointers = False 1575s use_iterators = 0 time = 0.48 s overhead = 0.00 s (d[p[i]] 1.65892e-07) 1575s use_iterators = 1 time = 0.26 s overhead = 0.00 s (d[*p++] 1.65892e-07) 1575s use_pointers = True 1575s use_iterators = 0 time = 0.26 s overhead = 0.00 s (*dp[i] 1.65892e-07) 1575s use_iterators = 1 time = 0.67 s overhead = 0.00 s (**dpi++ 1.65892e-07) 1575s use_iterators = 2 time = 0.09 s overhead = 0.00 s (**dpp++ 1.65892e-07) 1575s data_size = 1000000 n_repeats = 30 1575s use_pointers = False 1575s use_iterators = 0 time = 0.53 s overhead = 0.02 s (d[p[i]] 7.05435e-07) 1575s use_iterators = 1 time = 0.32 s overhead = 0.02 s (d[*p++] 7.05435e-07) 1575s use_pointers = True 1575s use_iterators = 0 time = 0.26 s overhead = 0.02 s (*dp[i] 7.05435e-07) 1575s use_iterators = 1 time = 0.99 s overhead = 0.02 s (**dpi++ 7.05435e-07) 1575s use_iterators = 2 time = 0.16 s overhead = 0.02 s (**dpp++ 7.05435e-07) 1575s data_size = 10000000 n_repeats = 3 1575s use_pointers = False 1575s use_iterators = 0 time = 1.40 s overhead = 0.19 s (d[p[i]] -8.62847e-07) 1575s use_iterators = 1 time = 0.55 s overhead = 0.19 s (d[*p++] -8.62847e-07) 1575s use_pointers = True 1575s use_iterators = 0 time = 0.57 s overhead = 0.19 s (*dp[i] -8.62847e-07) 1575s use_iterators = 1 time = 3.01 s overhead = 0.18 s (**dpi++ -8.62847e-07) 1575s use_iterators = 2 time = 0.40 s overhead = 0.20 s (**dpp++ -8.62847e-07) 1575s OK 1575s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1575s 139 1575s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1575s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/spe.py" [FAIL] 2.4s 1575s Time: 2.43 1575s Return code: 139 1575s OKs: 0 1575s Standard error: 1575s Segmentation fault (core dumped) 1579s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1579s 139 1579s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1579s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/incremental_SO3_sampling.py" [FAIL] 4.2s 1579s Time: 4.24 1579s Return code: 139 1579s OKs: 0 1579s Standard error: 1579s Segmentation fault (core dumped) 1581s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1581s 139 1581s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1581s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_curve_fitting.py" [FAIL] 6.3s 1581s Time: 6.33 1581s Return code: 139 1581s OKs: 0 1581s Standard error: 1581s Segmentation fault (core dumped) 1582s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_similarity_indices.py" [OK] 0.1s 1582s Time: 0.14 1582s Return code: 0 1582s OKs: 1 1582s Standard out: 1582s OK 1584s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1584s 139 1584s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1584s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_weighted_correlation.py" [FAIL] 4.6s 1584s Time: 4.59 1584s Return code: 139 1584s OKs: 0 1584s Standard error: 1584s Segmentation fault (core dumped) 1584s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_fit_quadratic_function.py" [OK] 0.2s 1584s Time: 0.17 1584s Return code: 0 1584s OKs: 1 1584s Standard out: 1584s OK 1584s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gcd.py" [OK] 0.6s 1584s Time: 0.59 1584s Return code: 0 1584s OKs: 1 1584s Standard out: 1584s compare_with_boost_rational_gcd(gcd_int_simple) 1584s compare_with_boost_rational_gcd(gcd_long_simple) 1584s compare_with_boost_rational_gcd(gcd_long_binary) 1584s gcd_int_boost 999 w=0.05 u+s=0.05 1584s gcd_int_simple 999 w=0.03 u+s=0.04 1584s gcd_long_boost 999 w=0.05 u+s=0.05 1584s gcd_long_simple 999 w=0.03 u+s=0.03 1584s gcd_unsigned_long_binary 999 w=0.11 u+s=0.11 1584s gcd_long_binary 999 w=0.11 u+s=0.10 1584s OK 1586s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1586s 139 1586s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1586s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_exp_functions.py" [FAIL] 4.4s 1586s Time: 4.38 1586s Return code: 139 1586s OKs: 0 1586s Standard error: 1586s Segmentation fault (core dumped) 1589s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1589s 139 1589s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1589s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_math.py" [FAIL] 4.2s 1589s Time: 4.24 1589s Return code: 139 1589s OKs: 0 1589s Standard error: 1589s Segmentation fault (core dumped) 1589s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_r3_rotation.py" [OK] 3.2s 1589s Time: 3.16 1589s Return code: 0 1589s OKs: 0 1589s Standard out: 1589s times unit quaternion <-> matrix 1589s py: 0.03 0.02 s 1589s c++: 0.04 0.05 s 1589s ratio: 0.67 0.42 1589s u+s,u,s: 3.00 2.98 0.02 1589s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_line_search.py" [OK] 0.1s 1589s Time: 0.14 1589s Return code: 0 1589s OKs: 1 1589s Standard out: 1589s OK 1591s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1591s 139 1591s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1591s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_resample.py" [FAIL] 2.4s 1591s Time: 2.38 1591s Return code: 139 1591s OKs: 0 1591s Standard error: 1591s Segmentation fault (core dumped) 1593s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1593s 139 1593s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1593s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian.py" [FAIL] 4.0s 1593s Time: 4.04 1593s Return code: 139 1593s OKs: 0 1593s Standard error: 1593s Segmentation fault (core dumped) 1593s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_bessel.py" [OK] 0.1s 1593s Time: 0.13 1593s Return code: 0 1593s OKs: 0 1596s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1596s 139 1596s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1596s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_quadrature.py" [FAIL] 4.7s 1596s Time: 4.65 1596s Return code: 139 1596s OKs: 0 1596s Standard error: 1596s Segmentation fault (core dumped) 1596s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_euler_angles.py" [OK] 0.7s 1596s Time: 0.71 1596s Return code: 0 1596s OKs: 0 1596s Standard out: 1596s u+s,u,s: 0.64 0.63 0.01 1597s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_superpose.py" [OK] 0.2s 1597s Time: 0.22 1597s Return code: 0 1597s OKs: 1 1597s Standard out: 1597s OK 1597s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_uniform_rotation_matrix.py" [OK] 0.1s 1597s Time: 0.15 1597s Return code: 0 1597s OKs: 1 1597s Standard out: 1597s OK 1598s Standard error: 1598s Segmentation fault (core dumped) 1598s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1598s 139 1598s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1598s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_halton.py" [FAIL] 4.4s 1598s Time: 4.36 1598s Return code: 139 1598s OKs: 0 1598s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike_mom.py" [OK] 0.1s 1598s Time: 0.14 1598s Return code: 0 1598s OKs: 1 1598s Standard out: 1598s OK 1598s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/sieve_of_eratosthenes.py" [OK] 0.0s 1598s Time: 0.02 1598s Return code: 0 1598s OKs: 1 1598s Standard out: 1598s OK 1598s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/besselk.py" [OK] 0.0s 1598s Time: 0.03 1598s Return code: 0 1598s OKs: 1 1598s Standard out: 1598s OK 1601s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1601s 139 1601s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1601s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/scale_curves.py" [FAIL] 2.5s 1601s Time: 2.48 1601s Return code: 139 1601s OKs: 0 1601s Standard error: 1601s Segmentation fault (core dumped) 1603s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1603s 139 1603s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1603s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_fit_peak.py" [FAIL] 2.6s 1603s Time: 2.57 1603s Return code: 139 1603s OKs: 0 1603s Standard error: 1603s Segmentation fault (core dumped) 1605s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1605s 139 1605s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1605s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_clustering.py" [FAIL] 2.3s 1605s Time: 2.25 1605s Return code: 139 1605s OKs: 0 1605s Standard error: 1605s Segmentation fault (core dumped) 1606s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_orthonormal_basis.py" [OK] 0.2s 1606s Time: 0.19 1606s Return code: 0 1606s OKs: 1 1606s Standard out: 1606s OK 1606s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_g_function.py" [OK] 0.2s 1606s Time: 0.15 1606s Return code: 0 1606s OKs: 0 1606s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_angle_derivative.py" [OK] 0.1s 1606s Time: 0.15 1606s Return code: 0 1606s OKs: 1 1606s Standard out: 1606s OK 1608s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1608s 139 1608s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1608s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike.py" [FAIL] 11.5s 1608s Time: 11.46 1608s Return code: 139 1608s OKs: 0 1608s Standard error: 1608s Segmentation fault (core dumped) 1610s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1610s 139 1610s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1610s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_periodogram.py" [FAIL] 4.6s 1610s Time: 4.59 1610s Return code: 139 1610s OKs: 0 1610s Standard error: 1610s Segmentation fault (core dumped) 1611s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_tetrahedron.py" [OK] 0.2s 1611s Time: 0.16 1611s Return code: 0 1611s OKs: 1 1611s Standard out: 1611s OK 1611s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_undirected_graph.py" [OK] 0.1s 1611s Time: 0.14 1611s Return code: 0 1611s OKs: 0 1611s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_so3_lie_algebra.py" [OK] 0.1s 1611s Time: 0.13 1611s Return code: 0 1611s OKs: 0 1611s libtbx.python "/usr/lib/python3/dist-packages/scitbx/minpack/tst.py" [OK] 0.1s 1611s Time: 0.15 1611s Return code: 0 1611s OKs: 1 1611s Standard out: 1611s OK 1611s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_ext.py" [OK] 0.1s 1611s Time: 0.14 1611s Return code: 0 1611s OKs: 1 1611s Standard out: 1611s OK 1613s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1613s 139 1613s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1613s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_error_propagation_matrix_inverse.py" [FAIL] 4.6s 1613s Time: 4.65 1613s Return code: 139 1613s OKs: 0 1613s Standard error: 1613s Segmentation fault (core dumped) 1615s Standard error: 1615s Segmentation fault (core dumped) 1615s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1615s 139 1615s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1615s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_curvatures.py" [FAIL] 4.0s 1615s Time: 3.95 1615s Return code: 139 1615s OKs: 0 1615s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_func_free_line_search.py" [OK] 0.2s 1615s Time: 0.19 1615s Return code: 0 1615s OKs: 1 1615s Standard out: 1615s The answer is: [2, -5, 500] 1615s The start value is: [-100, 203, 999] 1615s scitbx.lbfgs: use gradient_only line search: True 1615s scitbx.lbfgs: use gradient_only line search: False 1615s OK 1615s "/usr/lib/cctbx/python3.13/scitbx/lbfgs/tst_lbfgs" [OK] 0.0s 1615s Time: 0.01 1615s Return code: 0 1615s OKs: 0 1615s Standard out: 1615s n: 100 1615s m: 5 1615s xtol: 1e-16 1615s f: 254.065 gnorm: 325.365 1615s 1 2 0.000607303 1615s f: 207.819 gnorm: 54.5204 1615s 2 3 1 1615s f: 206.329 gnorm: 12.6873 1615s 3 4 1 1615s f: 206.158 gnorm: 12.9705 1615s 4 5 1 1615s f: 204.568 gnorm: 36.0649 1615s 5 6 1 1615s f: 201.009 gnorm: 69.9702 1615s 6 7 1 1615s f: 132.076 gnorm: 99.1014 1615s 7 11 2.30835 1615s f: 131.557 gnorm: 80.1033 1615s 8 13 0.152436 1615s f: 120.196 gnorm: 66.244 1615s 9 15 5 1615s f: 105.948 gnorm: 116.627 1615s 10 16 1 1615s f: 87.4002 gnorm: 17.1325 1615s 11 17 1 1615s f: 72.7773 gnorm: 32.6968 1615s 12 18 1 1615s f: 67.7306 gnorm: 49.5851 1615s 13 20 0.213662 1615s f: 60.0913 gnorm: 52.8678 1615s 14 21 1 1615s f: 45.9493 gnorm: 28.0796 1615s 15 22 1 1615s f: 37.3669 gnorm: 39.3487 1615s 16 23 1 1615s f: 23.0492 gnorm: 14.5867 1615s 17 24 1 1615s f: 19.8468 gnorm: 17.9762 1615s 18 26 0.156708 1615s f: 17.6677 gnorm: 48.6045 1615s 19 27 1 1615s f: 13.9465 gnorm: 22.2498 1615s 20 28 1 1615s f: 9.11604 gnorm: 28.0105 1615s 21 29 1 1615s f: 5.82159 gnorm: 10.2151 1615s 22 30 1 1615s f: 4.75971 gnorm: 28.511 1615s 23 32 0.436181 1615s f: 2.35807 gnorm: 22.65 1615s 24 33 1 1615s f: 1.55734 gnorm: 15.4752 1615s 25 34 1 1615s f: 0.810498 gnorm: 2.3865 1615s 26 36 0.404632 1615s f: 0.508703 gnorm: 9.94499 1615s 27 38 0.247512 1615s f: 0.363447 gnorm: 15.2129 1615s 28 39 1 1615s f: 0.167247 gnorm: 9.7728 1615s 29 40 1 1615s f: 0.0372373 gnorm: 1.32586 1615s 30 41 1 1615s f: 0.0098316 gnorm: 4.14194 1615s 31 42 1 1615s f: 0.000471098 gnorm: 0.567595 1615s 32 43 1 1615s f: 3.2788e-06 gnorm: 0.027547 1615s 33 44 1 1615s f: 2.34044e-08 gnorm: 0.00607363 1615s 34 45 1 1615s f: 2.09469e-13 gnorm: 1.31535e-05 1615s 35 46 1 1618s Standard error: 1618s Segmentation fault (core dumped) 1618s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1618s 139 1618s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1618s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgsb/boost_python/tst_lbfgsb.py" [FAIL] 2.8s 1618s Time: 2.81 1618s Return code: 139 1618s OKs: 0 1621s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1621s 139 1621s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1621s libtbx.python "/usr/lib/python3/dist-packages/scitbx/fftpack/boost_python/tst_fftpack.py" [FAIL] 2.5s 1621s Time: 2.48 1621s Return code: 139 1621s OKs: 0 1621s Standard error: 1621s Segmentation fault (core dumped) 1622s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" [OK] 9.4s 1622s Time: 9.41 1622s Return code: 0 1622s OKs: 1 1622s Standard out: 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 5 -1 0 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 5 -1 0 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 5 -1 0 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 4 -1 1 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 4 -1 1 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 4 -1 1 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 5 -1 2 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 5 -1 2 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 5 -1 2 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 5 -1 3 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 5 -1 3 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 5 -1 3 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 6 0 0 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 6 0 0 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 6 0 0 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 6 0 1 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 6 0 1 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 6 0 1 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 4 0 2 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 4 0 2 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 4 0 2 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 2 0 3 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 2 0 3 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 2 0 3 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 6 1 0 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 6 1 0 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 6 1 0 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 4 1 1 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 4 1 1 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 4 1 1 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 7 1 2 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 7 1 2 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 7 1 2 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 7 1 3 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 7 1 3 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 7 1 3 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 5 2 0 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 5 2 0 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 5 2 0 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 4 2 1 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 4 2 1 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 4 2 1 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 4 2 2 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 4 2 2 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 4 2 2 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 6 2 3 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 6 2 3 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 6 2 3 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 5 3 0 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 5 3 0 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 5 3 0 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 2 3 1 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 2 3 1 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 2 3 1 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 2 3 2 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 2 3 2 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 2 3 2 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 7 3 3 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 7 3 3 1622s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 7 3 3 1622s usr+sys time: 0.28 seconds 1622s wall clock time: 9.19 seconds 1622s OK 1622s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_array_loops.py" [OK] 0.1s 1622s Time: 0.11 1622s Return code: 0 1622s OKs: 1 1622s Standard out: 1622s 10.0 1622s 11.0 1622s 12.0 1622s 1622s 10.0 1622s 11.0 1622s 12.0 1622s 1622s 0 10.0 1622s 1 11.0 1622s 2 12.0 1622s 1622s 100.0 1622s 110.0 1622s 120.0 1622s 1622s 200.0 1622s 210.0 1622s 220.0 1622s 1622s OK 1622s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/principal_axes_of_inertia.py" [OK] 0.1s 1622s Time: 0.13 1622s Return code: 0 1622s OKs: 0 1622s Standard out: 1622s (7.796692307692308, 1.365076923076923, 8.357692307692307) 1622s (38.140037692307715, 97.02526753846156, 79.0222196923077, -19.808558307692305, 35.14258523076924, 7.6620366923076935) 1622s [104.22746487361265, 97.26642591377534, 12.693634135689015] 1622s [-0.43905397167468396, 0.8222124337102901, -0.36221309171382476, 0.3037216796237081, 0.5152398514117881, 0.8014243799908461, 0.8455677094610694, 0.24185658843488295, -0.4759418445014057] 1623s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_recipe.py" [OK] 0.1s 1623s Time: 0.12 1623s Return code: 0 1623s OKs: 1 1623s Standard out: 1623s refinery 1623s compute_functional_and_gradients 1623s callback_after_step 1623s OK 1623s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1623s 139 1623s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1623s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_grid.py" [FAIL] 2.2s 1623s Time: 2.16 1623s Return code: 139 1623s OKs: 0 1623s Standard error: 1623s Segmentation fault (core dumped) 1625s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1625s 139 1625s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1625s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_linear_least_squares_fit.py" [FAIL] 2.2s 1625s Time: 2.18 1625s Return code: 139 1625s OKs: 0 1625s Standard error: 1625s Segmentation fault (core dumped) 1627s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1627s 139 1627s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1627s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/chebyshev_lsq_example.py" [FAIL] 4.0s 1627s Time: 4.03 1627s Return code: 139 1627s OKs: 0 1627s Standard error: 1627s Segmentation fault (core dumped) 1627s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/rigid_body_refinement_core.py" [OK] 0.1s 1627s Time: 0.11 1627s Return code: 0 1627s OKs: 1 1627s Standard out: 1627s an ea: [0.0, 0.0, 0.0] 1627s fd ea: [2.9856131013692537e-15, 8.482502921596884e-16, 3.956636706594845e-15] 1627s an lt: [-0.0, -0.0, -0.0] 1627s fd lt: [0.0, 0.0, 0.0] 1627s 1627s an ea: [1.4293798315070272, -4.7699199336056015, -3.2848275925325994] 1627s fd ea: [1.4293798322739804, -4.769919932368083, -3.284827593041939] 1627s an lt: [-2.6395370381698946, 3.8546779254822816, -3.7648774634679576] 1627s fd lt: [-2.6395370364973303, 3.8546779261849906, -3.764877463563465] 1627s 1627s an ea: [-4.386454471339835, 2.1848899436111178, 5.0802158076235635] 1627s fd ea: [-4.386454468985335, 2.184889945411328, 5.080215810693289] 1627s an lt: [-4.688132824683539, -10.874759921610867, -1.9393316543209416] 1627s fd lt: [-4.688132825947378, -10.874759922785415, -1.939331655265164] 1627s 1627s an ea: [-5.097458993694191, 2.0225151159319297, 4.479103261227751] 1627s fd ea: [-5.097458993574833, 2.0225151207142744, 4.479103258958617] 1627s an lt: [-2.8154365578392593, -5.157085781215166, -17.014046644874668] 1627s fd lt: [-2.8154365576682494, -5.157085780638226, -17.014046648000658] 1627s 1627s OK 1629s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1629s 139 1629s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1629s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/immoptibox_ports.py" [FAIL] 4.3s 1629s Time: 4.27 1629s Return code: 139 1629s OKs: 0 1629s Standard error: 1629s Segmentation fault (core dumped) 1631s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1631s 139 1631s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1631s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/integrating_a_weighted_sinc_function.py" [FAIL] 4.2s 1631s Time: 4.17 1631s Return code: 139 1631s OKs: 0 1631s Standard error: 1631s Segmentation fault (core dumped) 1631s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_utils.py" [OK] 0.0s 1631s Time: 0.02 1631s Return code: 0 1631s OKs: 1 1631s Standard out: 1631s OK 1631s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/rigidity.py" [OK] 0.0s 1631s Time: 0.02 1631s Return code: 0 1631s OKs: 0 1631s Standard out: 1631s double banana 3D dof (method=integer): 7 1631s double banana 3D dof (method=float): 7 1631s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_rigidity.py" [OK] 0.2s 1631s Time: 0.21 1631s Return code: 0 1631s OKs: 0 1631s Standard out: 1631s repeat_log = {0: 85} 1631s u+s,u,s: 0.18 0.18 0.00 1632s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/rigidity_matrix_symbolic.py" [OK] 0.2s 1632s Time: 0.19 1632s Return code: 0 1632s OKs: 0 1632s Standard out: 1632s u+s,u,s: 0.16 0.16 0.00 1633s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1633s 139 1633s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1633s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/minimizer_comparisons.py" [FAIL] 4.2s 1633s Time: 4.17 1633s Return code: 139 1633s OKs: 0 1633s Standard error: 1633s Segmentation fault (core dumped) 1633s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree_find_paths.py" [OK] 2.0s 1633s Time: 1.98 1633s Return code: 0 1633s OKs: 1 1633s Standard out: 1633s OK 1634s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/test_cases_tardy_pdb.py" [OK] 0.0s 1634s Time: 0.05 1634s Return code: 0 1634s OKs: 0 1636s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1636s 139 1636s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1636s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree.py" [FAIL] 2.6s 1636s Time: 2.60 1636s Return code: 139 1636s OKs: 0 1636s Standard error: 1636s Segmentation fault (core dumped) 1638s Standard error: 1638s Segmentation fault (core dumped) 1638s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1638s 139 1638s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1638s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_basic.py" [FAIL] 4.4s 1638s Time: 4.44 1638s Return code: 139 1638s OKs: 0 1640s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1640s 139 1640s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1640s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_tardy.py" [FAIL] 4.4s 1640s Time: 4.38 1640s Return code: 139 1640s OKs: 0 1640s Standard error: 1640s Segmentation fault (core dumped) 1642s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1642s 139 1642s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1642s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_energy_plots.py" [FAIL] 4.4s 1642s Time: 4.45 1642s Return code: 139 1642s OKs: 0 1642s Standard error: 1642s Segmentation fault (core dumped) 1642s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/free_motion_reference_impl.py" [OK] 0.0s 1642s Time: 0.03 1642s Return code: 0 1642s OKs: 1 1642s Standard out: 1642s e_kin tot ang lin: 0.04066059413038476 0.012310594130384761 0.02835 1642s e_pot: 0.6403087877704161 1642s e_tot: 0.6809693819008009 1642s ang acc 3D: (0.4499405243671747, -0.22736369685250066, -0.6859763000328927) 1642s lin acc 3D: (0.2108121283092794, 0.3044814367238479, -0.7824311428947446) 1642s 1642s e_kin tot ang lin: 0.043334386720177365 0.012335145793951681 0.030999240926225684 1642s e_pot: 0.6375204431681878 1642s e_tot: 0.6808548298883652 1642s ang acc 3D: (0.4491523283824315, -0.2233952828755118, -0.688364609039924) 1642s lin acc 3D: (0.2063305410676703, 0.3022012812609254, -0.7827791077048256) 1642s 1642s e_kin tot ang lin: 0.04624491637806352 0.012390841212545118 0.0338540751655184 1642s e_pot: 0.6344966498401754 1642s e_tot: 0.6807415662182389 1642s ang acc 3D: (0.4482905223840879, -0.2193464063160701, -0.6906197519803725) 1642s lin acc 3D: (0.20168867739512958, 0.299808900299363, -0.7830079270607541) 1642s 1642s e_kin tot ang lin: 0.049389854602061224 0.01247763222642335 0.036912222375637876 1642s e_pot: 0.6312398275384674 1642s e_tot: 0.6806296821405287 1642s ang acc 3D: (0.44735466644443667, -0.21521902126722914, -0.692740958483326) 1642s lin acc 3D: (0.19688964121862268, 0.29730414639378616, -0.7831155604559972) 1642s 1642s e_kin tot ang lin: 0.05276668787891577 0.012595448079626585 0.04017123979928919 1642s e_pot: 0.6277525800757479 1642s e_tot: 0.6805192679546637 1642s ang acc 3D: (0.4463443200247767, -0.2110151239756078, -0.694727476553102) 1642s lin acc 3D: (0.1919366941490876, 0.29468687861617315, -0.783099948460292) 1642s 1642s e_kin tot ang lin: 0.05637271969939971 0.012744195480724368 0.043628524218675344 1642s e_pot: 0.6240376932449352 1642s e_tot: 0.6804104129443349 1642s ang acc 3D: (0.4452590426839754, -0.2067367517215091, -0.6965785731789051) 1642s lin acc 3D: (0.18683325327725137, 0.29195696483157874, -0.7829590159403469) 1642s 1642s e_kin tot ang lin: 0.060205072713709167 0.012923758676161239 0.04728131403754793 1642s e_pot: 0.6200981325993219 1642s e_tot: 0.680303205313031 1642s ang acc 3D: (0.44409839480429714, -0.20238598167333133, -0.6982935349568492) 1642s lin acc 3D: (0.18158288880693388, 0.2891142841060344, -0.7826906753299725) 1642s 1642s e_kin tot ang lin: 0.06426069102522652 0.013133999536143382 0.051126691489083144 1642s e_pot: 0.6159370410950341 1642s e_tot: 0.6801977321202606 1642s ang acc 3D: (0.4428619383337592, -0.1979649297164907, -0.6998716687235316) 1642s lin acc 3D: (0.17618932152521946, 0.2861587292410898, -0.7822928299444691) 1642s 1642s e_kin tot ang lin: 0.06853634262082685 0.013374757653013635 0.05516158496781321 1642s e_pot: 0.6115577365976127 1642s e_tot: 0.6800940792184396 1642s ang acc 3D: (0.4415492375442347, -0.1934757492571058, -0.7013123022002559) 1642s lin acc 3D: (0.17065642010895676, 0.2830902094290727, -0.7817633773339945) 1642s 1642s e_kin tot ang lin: 0.07302862193581516 0.013645850452066947 0.059382771483748216 1642s e_pot: 0.6069637092547071 1642s e_tot: 0.6799923311905223 1642s ang acc 3D: (0.44015985980451133, -0.18892063000069204, -0.702614784647033) 1642s lin acc 3D: (0.16498819826718966, 0.2799086530227533, -0.7811002126706817) 1642s 1642s OK 1645s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1645s 139 1645s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1645s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/tst.py" [FAIL] 4.4s 1645s Time: 4.41 1645s Return code: 139 1645s OKs: 0 1645s Standard error: 1645s Segmentation fault (core dumped) 1647s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1647s 139 1647s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1647s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_featherstone.py" [FAIL] 4.4s 1647s Time: 4.39 1647s Return code: 139 1647s OKs: 0 1647s Standard error: 1647s Segmentation fault (core dumped) 1649s Standard error: 1649s Segmentation fault (core dumped) 1649s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1649s 139 1649s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1649s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion.py" [FAIL] 4.4s 1649s Time: 4.37 1649s Return code: 139 1649s OKs: 0 1651s Standard error: 1651s Segmentation fault (core dumped) 1651s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1651s 139 1651s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1651s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion_hard.py" [FAIL] 4.3s 1651s Time: 4.33 1651s Return code: 139 1651s OKs: 0 1653s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1653s 139 1653s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1653s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_joint_lib.py" [FAIL] 4.4s 1653s Time: 4.41 1653s Return code: 139 1653s OKs: 0 1653s Standard error: 1653s Segmentation fault (core dumped) 1654s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_spherical_refinement.py" [OK] 0.3s 1654s Time: 0.26 1654s Return code: 0 1654s OKs: 1 1654s Standard out: 1654s OK 1654s usr+sys time: 0.22 seconds 1654s wall clock time: 0.22 seconds 1656s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1656s 139 1656s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1656s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_singular.py" [FAIL] 4.4s 1656s Time: 4.35 1656s Return code: 139 1656s OKs: 0 1656s Standard error: 1656s Segmentation fault (core dumped) 1658s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1658s 139 1658s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1658s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_molecules.py" [FAIL] 4.0s 1658s Time: 4.05 1658s Return code: 139 1658s OKs: 0 1658s Standard error: 1658s Segmentation fault (core dumped) 1660s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1660s 139 1660s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1660s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_sparse.py" [FAIL] 4.3s 1660s Standard error: 1660s Segmentation fault (core dumped) 1660s Time: 4.30 1660s Return code: 139 1660s OKs: 0 1663s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1663s 139 1663s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1663s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_lu_factorization.py" [FAIL] 4.2s 1663s Time: 4.21 1663s Return code: 139 1663s OKs: 0 1663s Standard error: 1663s Segmentation fault (core dumped) 1664s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1664s 139 1664s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1664s libtbx.python "/usr/lib/python3/dist-packages/scitbx/iso_surface/tst_iso_surface.py" [FAIL] 4.2s 1664s Standard error: 1664s Segmentation fault (core dumped) 1664s Time: 4.20 1664s Return code: 139 1664s OKs: 0 1666s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1666s 139 1666s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1666s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/simplex.py" [FAIL] 4.2s 1666s Time: 4.21 1666s Return code: 139 1666s OKs: 0 1666s Standard error: 1666s Segmentation fault (core dumped) 1666s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/golden_section_search.py" [OK] 0.0s 1666s Time: 0.02 1666s Return code: 0 1666s OKs: 0 1668s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1668s 139 1668s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1668s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/differential_evolution.py" [FAIL] 4.0s 1668s Time: 4.02 1668s Return code: 139 1668s OKs: 0 1668s Standard error: 1668s Segmentation fault (core dumped) 1670s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1670s 139 1670s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1670s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/direct_search_simulated_annealing.py" [FAIL] 3.9s 1670s Time: 3.91 1670s Return code: 139 1670s OKs: 0 1670s Standard error: 1670s Segmentation fault (core dumped) 1673s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1673s 139 1673s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1673s libtbx.python "/usr/lib/python3/dist-packages/scitbx/random/tests/tst_random.py" [FAIL] 4.5s 1673s Time: 4.52 1673s Return code: 139 1673s OKs: 0 1673s Standard error: 1673s Segmentation fault (core dumped) 1673s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/test_problems.py" [OK] 0.1s 1673s Time: 0.12 1673s Return code: 0 1673s OKs: 0 1674s libtbx.python "/usr/lib/python3/dist-packages/scitbx/glmtbx/tests/tst.py" [OK] 1.5s 1674s Time: 1.55 1674s Return code: 0 1674s OKs: 2 1674s Standard out: 1674s OK 1674s OK 1675s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1675s 139 1675s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1675s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/tst_normal_equations.py" [FAIL] 4.6s 1675s Time: 4.65 1675s Return code: 139 1675s OKs: 0 1675s Standard error: 1675s Segmentation fault (core dumped) 1677s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1677s 139 1677s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1677s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_basic.py" [FAIL] 2.4s 1677s Time: 2.45 1677s Return code: 139 1677s OKs: 0 1677s Standard error: 1677s Segmentation fault (core dumped) 1679s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1679s 139 1679s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1679s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_booth.py" [FAIL] 4.0s 1679s Time: 3.97 1679s Return code: 139 1679s OKs: 0 1679s Standard error: 1679s Segmentation fault (core dumped) 1679s libtbx.python "/usr/lib/python3/dist-packages/scitbx/suffixtree/test/tst_single.py" [OK] 0.1s 1679s Time: 0.06 1679s Return code: 0 1679s OKs: 0 1681s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1681s 139 1681s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1681s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_twisted.py" [FAIL] 4.0s 1681s Time: 4.02 1681s Return code: 139 1681s OKs: 0 1681s Standard error: 1681s Segmentation fault (core dumped) 1683s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1683s 139 1683s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1683s libtbx.python "/usr/lib/python3/dist-packages/smtbx/absolute_structure/tests/tst_absolute_structure.py" --fix_random_seeds [FAIL] 4.6s 1683s Time: 4.56 1683s Return code: 139 1683s OKs: 0 1683s Standard error: 1683s Segmentation fault (core dumped) 1686s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1686s 139 1686s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1686s libtbx.python "/usr/lib/python3/dist-packages/smtbx/ab_initio/tests/tst_ab_initio_ext.py" [FAIL] 5.0s 1686s Time: 4.95 1686s Return code: 139 1686s OKs: 0 1686s Standard error: 1686s Segmentation fault (core dumped) 1688s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1688s 139 1688s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1688s 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] 4.8s 1688s Time: 4.82 1688s Return code: 139 1688s OKs: 0 1688s Standard error: 1688s Segmentation fault (core dumped) 1691s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1691s 139 1691s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1691s libtbx.python "/usr/lib/python3/dist-packages/smtbx/masks/tests/tst_masks.py" [FAIL] 5.1s 1691s Time: 5.06 1691s Return code: 139 1691s OKs: 0 1691s Standard error: 1691s Segmentation fault (core dumped) 1693s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1693s 139 1693s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1693s libtbx.python "/usr/lib/python3/dist-packages/smtbx/structure_factors/direct/tests/tst_standard_xray.py" [FAIL] 5.2s 1693s Time: 5.16 1693s Return code: 139 1693s OKs: 0 1693s Standard error: 1693s Segmentation fault (core dumped) 1696s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1696s 139 1696s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1696s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_weighting_schemes.py" --fix_random_seeds [FAIL] 5.0s 1696s Time: 5.03 1696s Return code: 139 1696s OKs: 0 1696s Standard error: 1696s Segmentation fault (core dumped) 1696s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_reparametrisation" [OK] 0.0s 1696s Time: 0.00 1696s Return code: 0 1696s OKs: 1 1696s Standard out: 1696s sizeof(parameter) = 32 1696s OK 1698s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1698s 139 1698s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1698s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_lbfgs.py" [FAIL] 5.1s 1698s Time: 5.14 1698s Return code: 139 1698s OKs: 0 1698s Standard error: 1698s Segmentation fault (core dumped) 1698s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens" [OK] 0.0s 1698s Time: 0.00 1698s Return code: 0 1698s OKs: 1 1698s Standard out: 1698s OK 1701s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1701s 139 1701s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1701s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_occupancies.py" [FAIL] 5.4s 1701s Time: 5.39 1701s Return code: 139 1701s OKs: 0 1701s Standard error: 1701s Segmentation fault (core dumped) 1701s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_special_position" [OK] 0.0s 1701s Time: 0.00 1701s Return code: 0 1701s OKs: 1 1701s Standard out: 1701s OK 1704s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1704s 139 1704s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1704s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_same_group.py" [FAIL] 5.3s 1704s Time: 5.27 1704s Return code: 139 1704s OKs: 0 1704s Standard error: 1704s Segmentation fault (core dumped) 1706s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1706s 139 1706s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1706s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_reparametrisation.py" [FAIL] 5.1s 1706s Time: 5.05 1706s Return code: 139 1706s OKs: 0 1706s Standard error: 1706s Segmentation fault (core dumped) 1709s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1709s 139 1709s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1709s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=naive [FAIL] 5.2s 1709s Time: 5.20 1709s Return code: 139 1709s OKs: 0 1709s Standard error: 1709s Segmentation fault (core dumped) 1712s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1712s 139 1712s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1712s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_disorder.py" [FAIL] 5.3s 1712s Time: 5.28 1712s Return code: 139 1712s OKs: 0 1712s Standard error: 1712s Segmentation fault (core dumped) 1712s Standard error: 1712s Segmentation fault (core dumped) 1712s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1712s 139 1712s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1712s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=levenberg-marquardt [FAIL] 2.7s 1712s Time: 2.66 1712s Return code: 139 1712s OKs: 0 1714s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1714s 139 1714s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1714s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_direction.py" [FAIL] 2.8s 1714s Time: 2.77 1714s Return code: 139 1714s OKs: 0 1714s Standard error: 1714s Segmentation fault (core dumped) 1717s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1717s 139 1717s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1717s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_rigid.py" [FAIL] 5.3s 1717s Time: 5.30 1717s Return code: 139 1717s OKs: 0 1717s Standard error: 1717s Segmentation fault (core dumped) 1719s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1719s 139 1719s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1719s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_adp_restraints.py" [FAIL] 5.0s 1719s Time: 5.04 1719s Return code: 139 1719s OKs: 0 1719s Standard error: 1719s Segmentation fault (core dumped) 1722s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1722s 139 1722s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1722s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_manager.py" [FAIL] 5.0s 1722s Time: 5.03 1722s Return code: 139 1722s OKs: 0 1722s Standard error: 1722s Segmentation fault (core dumped) 1724s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1724s 139 1724s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1724s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_restraints.py" --verbose --scatterers=5 --resolution=0.2 [FAIL] 5.1s 1724s Time: 5.06 1724s Return code: 139 1724s OKs: 0 1724s Standard error: 1724s Segmentation fault (core dumped) 1727s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1727s 139 1727s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1727s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_refine.py" [FAIL] 5.4s 1727s Time: 5.37 1727s Return code: 139 1727s OKs: 0 1727s Standard error: 1727s Segmentation fault (core dumped) 1731s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1731s 1 1731s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1731s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py" [FAIL] 6.8s 1731s Time: 6.81 1731s Return code: 1 1731s OKs: 0 1731s Standard out: 1731s 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 1731s Standard error: 1731s Traceback (most recent call last): 1731s File "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py", line 37, in 1731s run() 1731s ~~~^^ 1731s File "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py", line 27, in run 1731s run_buf.raise_if_errors() 1731s ~~~~~~~~~~~~~~~~~~~~~~~^^ 1731s File "/usr/lib/python3/dist-packages/libtbx/easy_run.py", line 46, in raise_if_errors 1731s raise Error(msg) 1731s RuntimeError: child process stderr output: 1731s 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' 1731s Segmentation fault (core dumped) 1733s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1733s 139 1733s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1733s libtbx.python "/usr/lib/python3/dist-packages/smtbx/tests/tst_utils.py" [FAIL] 5.3s 1733s Time: 5.26 1733s Return code: 139 1733s OKs: 0 1733s Standard error: 1733s Segmentation fault (core dumped) 1735s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1735s 139 1735s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1735s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_least_squares.py" [EXPECTED UNSTABLE] 3.9s 1735s Time: 3.92 1735s Return code: 139 1735s OKs: 0 1735s Standard error: 1735s Segmentation fault (core dumped) 1735s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_predict.py" [OK] 0.2s 1735s Time: 0.16 1735s Return code: 0 1735s OKs: 1 1735s Standard out: 1735s OK 1735s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_ewald_sphere.py" [OK] 0.1s 1735s Time: 0.14 1735s Return code: 0 1735s OKs: 1 1735s Standard out: 1735s OK 1736s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_partial_derivatives.py" [OK] 0.1s 1736s Time: 0.13 1736s Return code: 0 1736s OKs: 1 1736s Standard out: 1736s OK 1737s Standard error: 1737s Segmentation fault (core dumped) 1737s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1737s 139 1737s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1737s libtbx.python "/usr/lib/python3/dist-packages/rstbx/dps_core/tst_iotbx_converter.py" [FAIL] 4.9s 1737s Time: 4.89 1737s Return code: 139 1737s OKs: 0 1740s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1740s 139 1740s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1740s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/fastbragg/tst_bragg_minimal.py" [FAIL] 4.4s 1740s Time: 4.41 1740s Return code: 139 1740s OKs: 0 1740s Standard error: 1740s Segmentation fault (core dumped) 1742s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1743s 139 1743s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1743s libtbx.python "/usr/lib/python3/dist-packages/rstbx/sublattice_support/tst_sublattice.py" [FAIL] 4.8s 1743s Time: 4.83 1743s Return code: 139 1743s OKs: 0 1743s Standard error: 1743s Segmentation fault (core dumped) 1743s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/core_toolbox/boost_python/tst_small_image.py" [OK] 0.4s 1743s Time: 0.39 1743s Return code: 0 1743s OKs: 1 1743s Standard out: 1743s OK 1743s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/diffraction/geometry.py" [OK] 0.1s 1743s Time: 0.12 1743s Return code: 0 1743s OKs: 1 1743s Standard out: 1743s OK 1743s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/math_support/sphere_formulae.py" [OK] 0.0s 1743s Time: 0.02 1743s Return code: 0 1743s OKs: 1 1743s Standard out: 1743s OK 1744s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1744s 139 1744s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1744s libtbx.python -c "from rstbx.run_tests import run; run()" [FAIL] 3.7s 1744s Time: 3.68 1744s Return code: 139 1744s OKs: 0 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s ================================================================================ 1744s 1744s Tests finished. Elapsed time: 810.65s 1744s 1744s Distribution of test runtimes: 1744s 0.0s - 4.2s: 300 1744s 4.2s - 8.4s: 240 1744s 8.4s - 12.6s: 3 1744s 12.6s - 16.7s: 1 1744s 16.7s - 20.9s: 0 1744s 20.9s - 25.1s: 1 1744s 25.1s - 29.3s: 0 1744s 29.3s - 33.5s: 0 1744s 33.5s - 37.7s: 0 1744s 37.7s - 41.8s: 1 1744s 1744s 1744s Warning: the following are 5 longest jobs: 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_fetch.py": 41.8s 1744s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_thread_utils.py": 21.7s 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_integer_offsets_vs_pointers.py": 16.4s 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike.py": 11.5s 1744s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_separate_files.py": 10.9s 1744s Please try to reduce overall runtime - consider splitting up these tests. 1744s 1744s 1744s Error: the following jobs returned non-zero exit codes or suspicious stderr output: 1744s 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sf_low_res_accuracy.py" [FAIL] 3.3s 1744s Time: 3.26 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_double_step_filtration.py" [FAIL] 4.3s 1744s Time: 4.31 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_is_periodic.py" [FAIL] 5.8s 1744s Time: 5.77 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_reindexing.py" [FAIL] 5.6s 1744s Time: 5.59 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_data_manipulation.py" [FAIL] 5.0s 1744s Time: 4.99 1744s Return code: 139 1744s OKs: 0 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_bfgs.py" [FAIL] 5.0s 1744s Time: 4.98 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_dev.py" P31 [FAIL] 5.0s 1744s Time: 5.02 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry/tests/tst_geometry.py" [FAIL] 5.5s 1744s Time: 5.53 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/covariance/tests/tst_covariance.py" [FAIL] 5.4s 1744s Time: 5.40 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_goodness_of_symmetry.py" [FAIL] 5.4s 1744s Time: 5.43 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_from_map.py" P312 [FAIL] 5.6s 1744s Time: 5.63 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_xray.py" [FAIL] 5.2s 1744s Time: 5.21 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray.py" I41/acd [FAIL] 5.8s 1744s Time: 5.83 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_r1.py" [FAIL] 5.5s 1744s Time: 5.47 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_shelxl_wght_ls.py" [FAIL] 5.3s 1744s Time: 5.30 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_f_model.py" [FAIL] 5.3s 1744s Time: 5.33 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/array_family/boost_python/tst_flex.py" [FAIL] 5.4s 1744s Time: 5.40 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_uctbx.py" [FAIL] 5.2s 1744s Time: 5.17 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_crystal_orientation.py" [FAIL] 4.8s 1744s Time: 4.83 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_sgtbx.py" [FAIL] 5.1s 1744s Time: 5.11 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_ext.py" [FAIL] 5.5s 1744s Time: 5.49 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_distance_based_connectivity.py" [FAIL] 5.1s 1744s Time: 5.15 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_super_cell.py" [FAIL] 5.9s 1744s Time: 5.94 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adptbx/boost_python/tst_adptbx.py" [FAIL] 6.4s 1744s Time: 6.43 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/boost_python/tst_miller.py" [FAIL] 5.4s 1744s Time: 5.37 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_xray_scattering.py" [FAIL] 4.8s 1744s Time: 4.76 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_formula.py" [FAIL] 4.0s 1744s Time: 3.96 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_attenuation_coefficient.py" [FAIL] 4.4s 1744s Time: 4.37 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/boost_python/tst_maptbx.py" [FAIL] 5.2s 1744s Time: 5.19 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_bcr.py" [FAIL] 6.4s 1744s Time: 6.41 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_loft.py" [FAIL] 6.0s 1744s Time: 5.99 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/dmtbx/boost_python/tst_dmtbx.py" [FAIL] 4.8s 1744s Time: 4.82 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/translation_search/boost_python/tst_translation_search.py" [FAIL] 4.6s 1744s Time: 4.60 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_ext.py" [FAIL] 5.1s 1744s Time: 5.08 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_angle_derivs.py" [FAIL] 3.8s 1744s Time: 3.83 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adp_restraints/tst_ext.py" [FAIL] 4.9s 1744s Time: 4.90 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_krivy_gruber.py" --Quick [FAIL] 5.2s 1744s Time: 5.17 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx.py" [FAIL] 4.9s 1744s Time: 4.91 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_space_group_type_tidy_cb_op_t.py" [FAIL] 4.6s 1744s Time: 4.57 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_denominators.py" P31 [FAIL] 4.6s 1744s Time: 4.56 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_subgroups.py" [FAIL] 4.7s 1744s Time: 4.71 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_lattice_symmetry.py" [FAIL] 4.8s 1744s Time: 4.82 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints.py" P3 [FAIL] 4.9s 1744s Time: 4.91 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints_cartesian.py" [FAIL] 4.9s 1744s Time: 4.94 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reflection_statistics.py" [FAIL] 4.6s 1744s Time: 4.58 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_harker.py" [FAIL] 4.9s 1744s Time: 4.92 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_special_op_simplifier.py" [FAIL] 4.9s 1744s Time: 4.89 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_twin_target.py" [FAIL] 5.1s 1744s Time: 5.08 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/symbol_confidence.py" [FAIL] 4.8s 1744s Time: 4.83 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/bravais_types.py" [FAIL] 4.4s 1744s Time: 4.44 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_lookup_utils.py" [FAIL] 4.7s 1744s Time: 4.73 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal.py" I41/acd [FAIL] 5.2s 1744s Time: 5.18 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_direct_space_asu.py" I41/acd [FAIL] 5.1s 1744s Time: 5.15 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pair_asu_table.py" [FAIL] 5.2s 1744s Time: 5.24 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_asu_clusters.py" [FAIL] 5.1s 1744s Time: 5.11 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_close_packing.py" R-3mr [FAIL] 4.8s 1744s Time: 4.83 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fourier_transform_real_part_at_x.py" P31 [FAIL] 5.1s 1744s Time: 5.12 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller.py" P31 [FAIL] 5.2s 1744s Time: 5.23 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem.py" [FAIL] 5.5s 1744s Time: 5.52 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reciprocal_space_asu.py" P312 [FAIL] 4.8s 1744s Time: 4.80 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_triplet_generator.py" P41 [FAIL] 4.9s 1744s Time: 4.86 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_emma.py" P31 [FAIL] 5.3s 1744s Time: 5.28 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_expand_to_p1.py" P31 [FAIL] 5.3s 1744s Time: 5.30 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_change_basis.py" P31 [FAIL] 5.0s 1744s Time: 4.97 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wilson_plot.py" P31 [FAIL] 4.9s 1744s Time: 4.94 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_derivatives.py" P31 [FAIL] 4.9s 1744s Time: 4.89 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_fast_gradients.py" P31 [FAIL] 5.0s 1744s Time: 5.01 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F P31 [FAIL] 5.0s 1744s Time: 4.98 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F_sq P31 [FAIL] 2.4s 1744s Time: 2.42 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_structure_factors.py" P31 [FAIL] 2.7s 1744s Time: 2.68 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_weights_for_symmetry_summation.py" Pmmm [FAIL] 5.0s 1744s Time: 5.02 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_real_space_refinement_simple.py" [FAIL] 4.9s 1744s Time: 4.91 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation.py" [FAIL] 4.9s 1744s Time: 4.91 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation_2.py" [FAIL] 4.9s 1744s Time: 4.90 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_loc_res.py" [FAIL] 6.2s 1744s Time: 6.17 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_target_and_gradients.py" [FAIL] 6.2s 1744s Time: 6.15 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_merge_equivalents.py" P31 [FAIL] 5.1s 1744s Time: 5.10 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grouped_data.py" P31 [FAIL] 5.2s 1744s Time: 5.20 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_fft_map.py" P31 [FAIL] 5.2s 1744s Time: 5.15 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sampled_model_density.py" P31 [FAIL] 5.1s 1744s Time: 5.08 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fast_nv1995.py" F222 [FAIL] 5.2s 1744s Time: 5.19 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_lbfgs.py" [FAIL] 4.8s 1744s Time: 4.81 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_2.py" [FAIL] 5.8s 1744s Time: 5.85 1744s Return code: 139 1744s OKs: 0 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_french_wilson.py" [FAIL] 5.5s 1744s Time: 5.50 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/make_cns_input.py" P31 [FAIL] 5.3s 1744s Time: 5.28 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pointgroup_tools.py" [FAIL] 4.4s 1744s Time: 4.36 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/sub_lattice_tools.py" [FAIL] 5.0s 1744s Time: 4.96 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/rational_matrices_point_groups.py" [FAIL] 4.9s 1744s Time: 4.94 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/cosets.py" [FAIL] 4.9s 1744s Time: 4.85 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_pg_tools.py" [FAIL] 5.0s 1744s Time: 4.99 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_twin_laws.py" [FAIL] 5.1s 1744s Time: 5.07 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_find_best_cell.py" [FAIL] 5.0s 1744s Time: 5.01 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_amplitude_normalisation.py" [FAIL] 5.1s 1744s Time: 5.09 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_statistics_graphs.py" [FAIL] 5.3s 1744s Time: 5.34 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_web_change_basis.py" [FAIL] 5.7s 1744s Time: 5.75 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/direct_space_asu/proto/tst_asu.py" [FAIL] 6.0s 1744s Time: 5.95 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_tidy_pickling.py" [FAIL] 5.6s 1744s Time: 5.61 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/masks/tests/tst_flood_fill.py" [FAIL] 5.2s 1744s Time: 5.23 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_r_free_utils.py" [FAIL] 5.4s 1744s Time: 5.42 1744s Return code: 139 1744s OKs: 0 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Traceback (most recent call last): 1744s File "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py", line 140, in 1744s exercise() 1744s ~~~~~~~~^^ 1744s File "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py", line 126, in exercise 1744s assert not easy_run.call(cmd) 1744s ^^^^^^^^^^^^^^^^^^^^^^ 1744s AssertionError 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Traceback (most recent call last): 1744s File "/usr/lib/python3.13/urllib/request.py", line 1541, in ftp_open 1744s fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout) 1744s File "/usr/lib/python3.13/urllib/request.py", line 1561, in connect_ftp 1744s return ftpwrapper(user, passwd, host, port, dirs, timeout, 1744s persistent=False) 1744s File "/usr/lib/python3.13/urllib/request.py", line 2409, in __init__ 1744s self.init() 1744s ~~~~~~~~~^^ 1744s File "/usr/lib/python3.13/urllib/request.py", line 2418, in init 1744s self.ftp.connect(self.host, self.port, self.timeout) 1744s ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1744s File "/usr/lib/python3.13/ftplib.py", line 158, in connect 1744s self.sock = socket.create_connection((self.host, self.port), self.timeout, 1744s ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1744s source_address=self.source_address) 1744s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1744s File "/usr/lib/python3.13/socket.py", line 864, in create_connection 1744s raise exceptions[0] 1744s File "/usr/lib/python3.13/socket.py", line 849, in create_connection 1744s sock.connect(sa) 1744s ~~~~~~~~~~~~^^^^ 1744s ConnectionRefusedError: [Errno 111] Connection refused 1744s 1744s The above exception was the direct cause of the following exception: 1744s 1744s Traceback (most recent call last): 1744s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 327, in 1744s exercise(sys.argv[1:]) 1744s ~~~~~~~~^^^^^^^^^^^^^^ 1744s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 26, in exercise 1744s exercise_validation() 1744s ~~~~~~~~~~~~~~~~~~~^^ 1744s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 29, in exercise_validation 1744s cd = validation.smart_load_dictionary(name="cif_core.dic") 1744s File "/usr/lib/python3/dist-packages/iotbx/cif/validation.py", line 111, in smart_load_dictionary 1744s url = locate_dictionary(name, registry_location=registry_location) 1744s File "/usr/lib/python3/dist-packages/iotbx/cif/validation.py", line 129, in locate_dictionary 1744s cm = cif.reader(file_object=urlopen(registry_location)).model() 1744s ~~~~~~~^^^^^^^^^^^^^^^^^^^ 1744s File "/usr/lib/python3.13/urllib/request.py", line 189, in urlopen 1744s return opener.open(url, data, timeout) 1744s ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1744s File "/usr/lib/python3.13/urllib/request.py", line 489, in open 1744s response = self._open(req, data) 1744s File "/usr/lib/python3.13/urllib/request.py", line 506, in _open 1744s result = self._call_chain(self.handle_open, protocol, protocol + 1744s '_open', req) 1744s File "/usr/lib/python3.13/urllib/request.py", line 466, in _call_chain 1744s result = func(*args) 1744s File "/usr/lib/python3.13/urllib/request.py", line 1558, in ftp_open 1744s raise URLError(exp) from exp 1744s urllib.error.URLError: 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_ccp.py" [FAIL] 5.4s 1744s Time: 5.38 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_mask.py" [FAIL] 5.8s 1744s Time: 5.84 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_map_peak_3d_as_2d.py" [FAIL] 5.8s 1744s Time: 5.78 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_asymmetric_map.py" [FAIL] 5.4s 1744s Time: 5.44 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_peak_volume_estimate.py" [FAIL] 5.4s 1744s Time: 5.38 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_resolution_from_map_and_model.py" [FAIL] 6.2s 1744s Time: 6.18 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_curves.py" [FAIL] 6.8s 1744s Time: 6.85 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_radius_as_central_peak_width.py" [FAIL] 6.2s 1744s Time: 6.24 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_get_percentile_cutoffs.py" [FAIL] 5.5s 1744s Time: 5.52 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sphericity.py" [FAIL] 4.2s 1744s Time: 4.20 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_statistics.py" [FAIL] 5.2s 1744s Time: 5.24 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity.py" [FAIL] 4.9s 1744s Time: 4.85 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity_allsym.py" [FAIL] 5.3s 1744s Time: 5.32 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py" [FAIL] 6.9s 1744s Time: 6.92 1744s Return code: 1 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_prepare_map_for_docking.py" [FAIL] 5.9s 1744s Time: 5.94 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/cma_es/tst_cma_es.py" [FAIL] 5.0s 1744s Time: 5.03 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mrc_io.py" [FAIL] 2.9s 1744s Time: 2.94 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/gui_tools/tst.py" [FAIL] 3.5s 1744s Time: 3.49 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phil.py" [FAIL] 5.0s 1744s Time: 5.01 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_manager.py" [FAIL] 7.8s 1744s Time: 7.81 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager_wrapping.py" [FAIL] 8.4s 1744s Time: 8.36 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager.py" [FAIL] 6.8s 1744s Time: 6.85 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry.py" [FAIL] 4.7s 1744s Time: 4.72 1744s Return code: 139 1744s OKs: 0 1744s 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] 8.0s 1744s Time: 7.96 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_tools.py" [FAIL] 5.7s 1744s Time: 5.66 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_atom_selections_10k.py" [FAIL] 5.1s 1744s Time: 5.13 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_crystal_symmetry_from_any.py" [FAIL] 5.7s 1744s Time: 5.72 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/kriber/tst_strudat.py" [FAIL] 5.4s 1744s Time: 5.41 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_geometry.py" [FAIL] 5.1s 1744s Time: 5.08 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_lex_parse_build.py" [FAIL] 5.6s 1744s Time: 5.62 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model.py" [FAIL] 5.6s 1744s Time: 5.56 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py" [FAIL] 1.8s 1744s Time: 1.76 1744s Return code: 1 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_restraints.py" [FAIL] 5.1s 1744s Time: 5.11 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_lex_parse_build.py" [FAIL] 3.3s 1744s Time: 3.33 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_hklf.py" [FAIL] 5.8s 1744s Time: 5.78 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_writer.py" [FAIL] 5.1s 1744s Time: 5.10 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_fvar_encoding.py" [FAIL] 4.9s 1744s Time: 4.93 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_pdb.py" [FAIL] 5.1s 1744s Time: 5.14 1744s Return code: 134 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy.py" [FAIL] 6.3s 1744s Time: 6.29 1744s Return code: 134 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy.py" [FAIL] 3.6s 1744s Time: 3.58 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_ext.py" [FAIL] 5.3s 1744s Time: 5.26 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection.py" [FAIL] 5.6s 1744s Time: 5.57 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation.py" [FAIL] 5.3s 1744s Time: 5.31 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection_string.py" [FAIL] 6.1s 1744s Time: 6.11 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_utils.py" [FAIL] 5.2s 1744s Time: 5.17 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_truncate_to_ala/tst.py" [FAIL] 3.2s 1744s Time: 3.21 1744s Return code: 134 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_examples.py" [FAIL] 6.1s 1744s Time: 6.11 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/space_group_symbols.py" [FAIL] 5.8s 1744s Time: 5.85 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/tst_cns.py" [FAIL] 4.8s 1744s Time: 4.80 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_merge.py" P31 [FAIL] 5.2s 1744s Time: 5.21 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/no_merge_original_index.py" [FAIL] 5.5s 1744s Time: 5.45 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/ccp4_map/tst.py" [FAIL] 5.2s 1744s Time: 5.18 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_ext.py" [FAIL] 5.5s 1744s Time: 5.54 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_extract_from_symmetry_lib.py" [FAIL] 5.8s 1744s Time: 5.84 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_dano.py" [FAIL] 5.2s 1744s Time: 5.17 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst.py" P31 [FAIL] 4.7s 1744s Time: 4.67 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_utils.py" [FAIL] 5.3s 1744s Time: 5.31 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xplor/tst_xplormap.py" [FAIL] 5.2s 1744s Time: 5.23 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phases.py" P31 [FAIL] 5.4s 1744s Time: 5.43 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py" [FAIL] 7.3s 1744s Time: 7.27 1744s Return code: 1 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_statistics.py" Fdd2 P31m [FAIL] 5.8s 1744s Time: 5.76 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_file_reader.py" [FAIL] 3.9s 1744s Time: 3.87 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py" [FAIL] 8.0s 1744s Time: 8.00 1744s Return code: 1 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_segids.py" [FAIL] 6.2s 1744s Time: 6.25 1744s Return code: 134 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_forward_compatible_pdb.py" [FAIL] 3.3s 1744s Time: 3.33 1744s Return code: 134 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_symmetry.py" [FAIL] 4.1s 1744s Time: 4.13 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_editor.py" [FAIL] 4.8s 1744s Time: 4.78 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py" [FAIL] 6.7s 1744s Time: 6.69 1744s Return code: 1 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_map_coefficients.py" [FAIL] 4.9s 1744s Time: 4.93 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py" [FAIL] 6.2s 1744s Time: 6.18 1744s Return code: 1 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_integrate_hkl.py" [FAIL] 6.2s 1744s Time: 6.17 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_no_merge_original_index.py" [FAIL] 3.4s 1744s Time: 3.42 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_export_scalepack_unmerged.py" [FAIL] 5.2s 1744s Time: 5.22 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/dsn6/tst.py" P31 [FAIL] 5.3s 1744s Time: 5.32 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_ligs.py" [FAIL] 4.4s 1744s Time: 4.42 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_broken_chain.py" [FAIL] 5.4s 1744s Time: 5.37 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_shortcut_1.py" [FAIL] 5.3s 1744s Time: 5.31 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_groups_preprocessing.py" [FAIL] 6.2s 1744s Time: 6.22 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_input.py" [FAIL] 6.2s 1744s Time: 6.21 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_user_selections.py" [FAIL] 5.3s 1744s Time: 5.33 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs.py" [FAIL] 6.1s 1744s Time: 6.11 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_without_validation.py" [FAIL] 6.1s 1744s Time: 6.08 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_read_mtrix_records_from_cif.py" [FAIL] 6.0s 1744s Time: 6.03 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_show_systematic_absences.py" [FAIL] 6.1s 1744s Time: 6.14 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_miller_sort_asu.py" [FAIL] 5.1s 1744s Time: 5.11 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_xray_scale.py" [FAIL] 5.5s 1744s Time: 5.53 1744s Return code: 134 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_as_pdb_1atom.py" [FAIL] 5.8s 1744s Time: 5.85 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_1.py" [FAIL] 6.8s 1744s Time: 6.82 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py" [FAIL] 8.2s 1744s Time: 8.23 1744s Return code: 1 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_all_chain_ids.py" [FAIL] 6.9s 1744s Time: 6.90 1744s Return code: 134 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_extract_xtal_data.py" [FAIL] 4.9s 1744s Time: 4.89 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cli_parser.py" [FAIL] 6.5s 1744s Time: 6.47 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_occupancies_rounding.py" [FAIL] 5.7s 1744s Time: 5.71 1744s Return code: 134 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_debug_write.py" [FAIL] 2.3s 1744s Time: 2.34 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_smoothing.py" [FAIL] 2.4s 1744s Time: 2.37 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_genetic_algorithm_with_mp.py" [FAIL] 2.4s 1744s Time: 2.42 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_basic.py" [FAIL] 2.9s 1744s Time: 2.92 1744s Return code: 139 1744s OKs: 1 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_minimum_covering_ellipsoid.py" [FAIL] 4.0s 1744s Time: 4.03 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian_fit_1d_analytical.py" [FAIL] 4.6s 1744s Time: 4.64 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_cubic_equation.py" [FAIL] 4.7s 1744s Time: 4.70 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_cholesky.py" [FAIL] 4.1s 1744s Time: 4.06 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_svd.py" [FAIL] 4.5s 1744s Time: 4.47 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_eigensystem.py" [FAIL] 4.5s 1744s Time: 4.49 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_svd.py" [FAIL] 4.5s 1744s Time: 4.47 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_dsyev.py" [FAIL] 4.5s 1744s Time: 4.50 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/regression_test.py" [FAIL] 4.3s 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s *** buffer overflow detected ***: terminated 1744s Aborted (core dumped) 1744s Standard error: 1744s *** buffer overflow detected ***: terminated 1744s Aborted (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s *** buffer overflow detected ***: terminated 1744s Aborted (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s /usr/lib/python3/dist-packages/ccp4io_adaptbx/__init__.py:25: UserWarning: ccp4io_adaptbx: cannot locate syminfo.lib 1744s warnings.warn("ccp4io_adaptbx: cannot locate syminfo.lib") 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Traceback (most recent call last): 1744s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 477, in 1744s exercise(sys.argv[1:]) 1744s ~~~~~~~~^^^^^^^^^^^^^^ 1744s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 22, in exercise 1744s run_and_compare( 1744s ~~~~~~~~~~~~~~~^ 1744s ['iotbx.lattice_symmetry' 1744s ^^^^^^^^^^^^^^^^^^^^^^^^^ 1744s ...<31 lines>... 1744s 1744s 1744s """) 1744s ^^^^ 1744s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 17, in run_and_compare 1744s command=command).raise_if_errors().stdout_lines 1744s ~~~~~~~~~~~~~~~^^ 1744s File "/usr/lib/python3/dist-packages/libtbx/easy_run.py", line 46, in raise_if_errors 1744s raise Error(msg) 1744s RuntimeError: child process stderr output: 1744s command: 'iotbx.lattice_symmetry --unit_cell="12.7923,12.8923,29.4356,102.846,103.846,22.7475"' 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s *** buffer overflow detected ***: terminated 1744s Aborted (core dumped) 1744s Traceback (most recent call last): 1744s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py", line 138, in 1744s exercise() 1744s ~~~~~~~~^^ 1744s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py", line 48, in exercise 1744s assert not easy_run.call("iotbx.pdb.box_around_molecule %s.pdb" % ( 1744s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1744s prefix)) 1744s ^^^^^^^^ 1744s AssertionError 1744s Standard error: 1744s *** buffer overflow detected ***: terminated 1744s Aborted (core dumped) 1744s Standard error: 1744s *** buffer overflow detected ***: terminated 1744s Aborted (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Traceback (most recent call last): 1744s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py", line 60, in 1744s exercise() 1744s ~~~~~~~~^^ 1744s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py", line 48, in exercise 1744s assert (len(out.stdout_lines) == 2) and (len(out.stderr_lines) == 0) 1744s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1744s AssertionError 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Traceback (most recent call last): 1744s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py", line 815, in 1744s exercise_1() 1744s ~~~~~~~~~~^^ 1744s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py", line 806, in exercise_1 1744s assert not easy_run.call(cmd) 1744s ^^^^^^^^^^^^^^^^^^^^^^ 1744s AssertionError 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s *** buffer overflow detected ***: terminated 1744s Aborted (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Traceback (most recent call last): 1744s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py", line 395, in 1744s tst_1() 1744s ~~~~~^^ 1744s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py", line 370, in tst_1 1744s assert os.path.isfile('%s.cif_%s_000.mtz' % (prefix, bn)) 1744s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1744s AssertionError 1744s Standard error: 1744s *** buffer overflow detected ***: terminated 1744s Aborted (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s *** buffer overflow detected ***: terminated 1744s Aborted (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Time: 4.33 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex.py" [FAIL] 5.1s 1744s Time: 5.08 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_numpy_bridge.py" [FAIL] 5.0s 1744s Time: 5.04 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_smart_selection.py" [FAIL] 4.5s 1744s Time: 4.51 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_shared.py" [FAIL] 4.6s 1744s Time: 4.59 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/__init__.py" [FAIL] 2.8s 1744s Time: 2.85 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_random_transform.py" [FAIL] 2.6s 1744s Time: 2.60 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/superpose.py" [FAIL] 2.4s 1744s Time: 2.37 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/spe.py" [FAIL] 2.4s 1744s Time: 2.43 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/incremental_SO3_sampling.py" [FAIL] 4.2s 1744s Time: 4.24 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_curve_fitting.py" [FAIL] 6.3s 1744s Time: 6.33 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_weighted_correlation.py" [FAIL] 4.6s 1744s Time: 4.59 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_exp_functions.py" [FAIL] 4.4s 1744s Time: 4.38 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_math.py" [FAIL] 4.2s 1744s Time: 4.24 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_resample.py" [FAIL] 2.4s 1744s Time: 2.38 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian.py" [FAIL] 4.0s 1744s Time: 4.04 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_quadrature.py" [FAIL] 4.7s 1744s Time: 4.65 1744s Return code: 139 1744s OKs: 0 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_halton.py" [FAIL] 4.4s 1744s Time: 4.36 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/scale_curves.py" [FAIL] 2.5s 1744s Time: 2.48 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_fit_peak.py" [FAIL] 2.6s 1744s Time: 2.57 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_clustering.py" [FAIL] 2.3s 1744s Time: 2.25 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike.py" [FAIL] 11.5s 1744s Time: 11.46 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_periodogram.py" [FAIL] 4.6s 1744s Time: 4.59 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_error_propagation_matrix_inverse.py" [FAIL] 4.6s 1744s Time: 4.65 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_curvatures.py" [FAIL] 4.0s 1744s Time: 3.95 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgsb/boost_python/tst_lbfgsb.py" [FAIL] 2.8s 1744s Time: 2.81 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/fftpack/boost_python/tst_fftpack.py" [FAIL] 2.5s 1744s Time: 2.48 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_grid.py" [FAIL] 2.2s 1744s Time: 2.16 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_linear_least_squares_fit.py" [FAIL] 2.2s 1744s Time: 2.18 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/chebyshev_lsq_example.py" [FAIL] 4.0s 1744s Time: 4.03 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/immoptibox_ports.py" [FAIL] 4.3s 1744s Time: 4.27 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/integrating_a_weighted_sinc_function.py" [FAIL] 4.2s 1744s Time: 4.17 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/minimizer_comparisons.py" [FAIL] 4.2s 1744s Time: 4.17 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree.py" [FAIL] 2.6s 1744s Time: 2.60 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_basic.py" [FAIL] 4.4s 1744s Time: 4.44 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_tardy.py" [FAIL] 4.4s 1744s Time: 4.38 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_energy_plots.py" [FAIL] 4.4s 1744s Time: 4.45 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/tst.py" [FAIL] 4.4s 1744s Time: 4.41 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_featherstone.py" [FAIL] 4.4s 1744s Time: 4.39 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion.py" [FAIL] 4.4s 1744s Time: 4.37 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion_hard.py" [FAIL] 4.3s 1744s Time: 4.33 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_joint_lib.py" [FAIL] 4.4s 1744s Time: 4.41 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_singular.py" [FAIL] 4.4s 1744s Time: 4.35 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_molecules.py" [FAIL] 4.0s 1744s Time: 4.05 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_sparse.py" [FAIL] 4.3s 1744s Time: 4.30 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_lu_factorization.py" [FAIL] 4.2s 1744s Time: 4.21 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/iso_surface/tst_iso_surface.py" [FAIL] 4.2s 1744s Time: 4.20 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/simplex.py" [FAIL] 4.2s 1744s Time: 4.21 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/differential_evolution.py" [FAIL] 4.0s 1744s Time: 4.02 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/direct_search_simulated_annealing.py" [FAIL] 3.9s 1744s Time: 3.91 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/random/tests/tst_random.py" [FAIL] 4.5s 1744s Time: 4.52 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/tst_normal_equations.py" [FAIL] 4.6s 1744s Time: 4.65 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_basic.py" [FAIL] 2.4s 1744s Time: 2.45 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_booth.py" [FAIL] 4.0s 1744s Time: 3.97 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_twisted.py" [FAIL] 4.0s 1744s Time: 4.02 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/smtbx/absolute_structure/tests/tst_absolute_structure.py" --fix_random_seeds [FAIL] 4.6s 1744s Time: 4.56 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/smtbx/ab_initio/tests/tst_ab_initio_ext.py" [FAIL] 5.0s 1744s Time: 4.95 1744s Return code: 139 1744s OKs: 0 1744s 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] 4.8s 1744s Time: 4.82 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/smtbx/masks/tests/tst_masks.py" [FAIL] 5.1s 1744s Time: 5.06 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/smtbx/structure_factors/direct/tests/tst_standard_xray.py" [FAIL] 5.2s 1744s Time: 5.16 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_weighting_schemes.py" --fix_random_seeds [FAIL] 5.0s 1744s Time: 5.03 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_lbfgs.py" [FAIL] 5.1s 1744s Time: 5.14 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_occupancies.py" [FAIL] 5.4s 1744s Time: 5.39 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_same_group.py" [FAIL] 5.3s 1744s Time: 5.27 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_reparametrisation.py" [FAIL] 5.1s 1744s Time: 5.05 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=naive [FAIL] 5.2s 1744s Time: 5.20 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_disorder.py" [FAIL] 5.3s 1744s Time: 5.28 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=levenberg-marquardt [FAIL] 2.7s 1744s Time: 2.66 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_direction.py" [FAIL] 2.8s 1744s Time: 2.77 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_rigid.py" [FAIL] 5.3s 1744s Time: 5.30 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_adp_restraints.py" [FAIL] 5.0s 1744s Time: 5.04 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_manager.py" [FAIL] 5.0s 1744s Time: 5.03 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_restraints.py" --verbose --scatterers=5 --resolution=0.2 [FAIL] 5.1s 1744s Time: 5.06 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_refine.py" [FAIL] 5.4s 1744s Time: 5.37 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py" [FAIL] 6.8s 1744s Time: 6.81 1744s Return code: 1 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/smtbx/tests/tst_utils.py" [FAIL] 5.3s 1744s Time: 5.26 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/rstbx/dps_core/tst_iotbx_converter.py" [FAIL] 4.9s 1744s Time: 4.89 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/fastbragg/tst_bragg_minimal.py" [FAIL] 4.4s 1744s Time: 4.41 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python "/usr/lib/python3/dist-packages/rstbx/sublattice_support/tst_sublattice.py" [FAIL] 4.8s 1744s Time: 4.83 1744s Return code: 139 1744s OKs: 0 1744s libtbx.python -c "from rstbx.run_tests import run; run()" [FAIL] 3.7s 1744s Time: 3.68 1744s Return code: 139 1744s OKs: 0 1744s 1744s Please verify these tests manually. 1744s 1744s Summary: 1744s Tests run : 546 1744s Failures : 284 1744s Warnings (possible failures) : 0 1744s Known Failures ( 4) : 4 1744s Known Unstable ( 3) : 2 1744s Stderr output (discouraged) : 291 1744s 1744s See run_tests_parallel_zlog for full output. 1744s 1744s 1744s ******************************************************************************** 1744s ERROR: 284 TEST FAILURES. PLEASE FIX BEFORE COMMITTING CODE. 1744s ******************************************************************************** 1744s 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Traceback (most recent call last): 1744s File "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py", line 37, in 1744s run() 1744s ~~~^^ 1744s File "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py", line 27, in run 1744s run_buf.raise_if_errors() 1744s ~~~~~~~~~~~~~~~~~~~~~~~^^ 1744s File "/usr/lib/python3/dist-packages/libtbx/easy_run.py", line 46, in raise_if_errors 1744s raise Error(msg) 1744s RuntimeError: child process stderr output: 1744s 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' 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s Standard error: 1744s Segmentation fault (core dumped) 1744s autopkgtest [13:35:04]: test cctbx: -----------------------] 1745s autopkgtest [13:35:05]: test cctbx: - - - - - - - - - - results - - - - - - - - - - 1745s cctbx FAIL non-zero exit status 1 1745s autopkgtest [13:35:05]: test dxtbx: preparing testbed 1823s autopkgtest [13:36:23]: testbed dpkg architecture: s390x 1824s autopkgtest [13:36:24]: testbed apt version: 2.9.33 1824s autopkgtest [13:36:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup 1824s autopkgtest [13:36:24]: testbed release detected to be: plucky 1825s autopkgtest [13:36:25]: updating testbed package index (apt update) 1825s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 1825s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 1825s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 1825s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 1826s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [292 kB] 1826s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [1232 B] 1826s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [12.2 kB] 1826s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [30.7 kB] 1826s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [41.9 kB] 1826s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1264 B] 1826s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 1826s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [187 kB] 1826s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [10.7 kB] 1826s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [2992 B] 1826s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [220 B] 1826s Fetched 706 kB in 1s (943 kB/s) 1827s Reading package lists... 1827s autopkgtest [13:36:27]: upgrading testbed (apt dist-upgrade and autopurge) 1828s Reading package lists... 1828s Building dependency tree... 1828s Reading state information... 1828s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 1828s Starting 2 pkgProblemResolver with broken count: 0 1828s Done 1828s Entering ResolveByKeep 1828s 1828s Calculating upgrade... 1828s The following packages will be upgraded: 1828s apparmor apt apt-utils dpkg dpkg-dev fwupd gcc-14-base gcc-15-base 1828s ibverbs-providers libapparmor1 libapt-pkg7.0 libatomic1 libdpkg-perl 1828s libfwupd3 libgcc-s1 libibverbs1 libldap-common libldap2 libstdc++6 libxmlb2 1828s ubuntu-pro-client ubuntu-pro-client-l10n 1828s 22 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1828s Need to get 13.7 MB of archives. 1828s After this operation, 180 kB of additional disk space will be used. 1828s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libatomic1 s390x 15-20250319-1ubuntu1 [9366 B] 1829s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-15-base s390x 15-20250319-1ubuntu1 [53.6 kB] 1829s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libgcc-s1 s390x 15-20250319-1ubuntu1 [35.8 kB] 1829s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libstdc++6 s390x 15-20250319-1ubuntu1 [898 kB] 1829s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libapt-pkg7.0 s390x 2.9.34 [1114 kB] 1829s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x dpkg s390x 1.22.18ubuntu2 [1300 kB] 1829s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x apt s390x 2.9.34 [1424 kB] 1829s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x apt-utils s390x 2.9.34 [215 kB] 1829s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14-base s390x 14.2.0-19ubuntu1 [53.9 kB] 1829s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libapparmor1 s390x 4.1.0~beta5-0ubuntu11 [55.0 kB] 1829s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x ubuntu-pro-client-l10n s390x 35 [19.7 kB] 1829s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x ubuntu-pro-client s390x 35 [257 kB] 1829s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x apparmor s390x 4.1.0~beta5-0ubuntu11 [759 kB] 1829s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libibverbs1 s390x 56.0-3ubuntu1 [70.0 kB] 1829s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x ibverbs-providers s390x 56.0-3ubuntu1 [415 kB] 1829s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x dpkg-dev all 1.22.18ubuntu2 [1089 kB] 1829s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libdpkg-perl all 1.22.18ubuntu2 [281 kB] 1829s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x fwupd s390x 2.0.6-7 [5235 kB] 1829s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x libfwupd3 s390x 2.0.6-7 [134 kB] 1829s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libxmlb2 s390x 0.3.22-1 [69.2 kB] 1829s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x libldap-common all 2.6.9+dfsg-2ubuntu1 [35.5 kB] 1829s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libldap2 s390x 2.6.9+dfsg-2ubuntu1 [206 kB] 1830s Preconfiguring packages ... 1830s Fetched 13.7 MB in 1s (13.6 MB/s) 1830s (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 ... 81426 files and directories currently installed.) 1830s Preparing to unpack .../libatomic1_15-20250319-1ubuntu1_s390x.deb ... 1830s Unpacking libatomic1:s390x (15-20250319-1ubuntu1) over (15-20250315-1ubuntu1) ... 1830s Preparing to unpack .../gcc-15-base_15-20250319-1ubuntu1_s390x.deb ... 1830s Unpacking gcc-15-base:s390x (15-20250319-1ubuntu1) over (15-20250315-1ubuntu1) ... 1830s Setting up gcc-15-base:s390x (15-20250319-1ubuntu1) ... 1830s (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 ... 81426 files and directories currently installed.) 1830s Preparing to unpack .../libgcc-s1_15-20250319-1ubuntu1_s390x.deb ... 1830s Unpacking libgcc-s1:s390x (15-20250319-1ubuntu1) over (15-20250315-1ubuntu1) ... 1830s Setting up libgcc-s1:s390x (15-20250319-1ubuntu1) ... 1830s (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 ... 81426 files and directories currently installed.) 1830s Preparing to unpack .../libstdc++6_15-20250319-1ubuntu1_s390x.deb ... 1830s Unpacking libstdc++6:s390x (15-20250319-1ubuntu1) over (15-20250315-1ubuntu1) ... 1830s Setting up libstdc++6:s390x (15-20250319-1ubuntu1) ... 1830s (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 ... 81426 files and directories currently installed.) 1830s Preparing to unpack .../libapt-pkg7.0_2.9.34_s390x.deb ... 1830s Unpacking libapt-pkg7.0:s390x (2.9.34) over (2.9.33) ... 1830s Setting up libapt-pkg7.0:s390x (2.9.34) ... 1830s (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 ... 81426 files and directories currently installed.) 1830s Preparing to unpack .../dpkg_1.22.18ubuntu2_s390x.deb ... 1830s Unpacking dpkg (1.22.18ubuntu2) over (1.22.15ubuntu1) ... 1830s Setting up dpkg (1.22.18ubuntu2) ... 1830s (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 ... 81425 files and directories currently installed.) 1830s Preparing to unpack .../archives/apt_2.9.34_s390x.deb ... 1830s Unpacking apt (2.9.34) over (2.9.33) ... 1831s Setting up apt (2.9.34) ... 1831s (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 ... 81425 files and directories currently installed.) 1831s Preparing to unpack .../00-apt-utils_2.9.34_s390x.deb ... 1831s Unpacking apt-utils (2.9.34) over (2.9.33) ... 1831s Preparing to unpack .../01-gcc-14-base_14.2.0-19ubuntu1_s390x.deb ... 1831s Unpacking gcc-14-base:s390x (14.2.0-19ubuntu1) over (14.2.0-17ubuntu3) ... 1831s Preparing to unpack .../02-libapparmor1_4.1.0~beta5-0ubuntu11_s390x.deb ... 1831s Unpacking libapparmor1:s390x (4.1.0~beta5-0ubuntu11) over (4.1.0~beta5-0ubuntu9) ... 1831s Preparing to unpack .../03-ubuntu-pro-client-l10n_35_s390x.deb ... 1831s Unpacking ubuntu-pro-client-l10n (35) over (34.1.3) ... 1831s Preparing to unpack .../04-ubuntu-pro-client_35_s390x.deb ... 1831s Unpacking ubuntu-pro-client (35) over (34.1.3) ... 1831s Preparing to unpack .../05-apparmor_4.1.0~beta5-0ubuntu11_s390x.deb ... 1831s Unpacking apparmor (4.1.0~beta5-0ubuntu11) over (4.1.0~beta5-0ubuntu9) ... 1832s Preparing to unpack .../06-libibverbs1_56.0-3ubuntu1_s390x.deb ... 1832s Unpacking libibverbs1:s390x (56.0-3ubuntu1) over (55.0-1ubuntu1) ... 1832s Preparing to unpack .../07-ibverbs-providers_56.0-3ubuntu1_s390x.deb ... 1832s Unpacking ibverbs-providers:s390x (56.0-3ubuntu1) over (55.0-1ubuntu1) ... 1832s Preparing to unpack .../08-dpkg-dev_1.22.18ubuntu2_all.deb ... 1832s Unpacking dpkg-dev (1.22.18ubuntu2) over (1.22.15ubuntu1) ... 1832s Preparing to unpack .../09-libdpkg-perl_1.22.18ubuntu2_all.deb ... 1832s Unpacking libdpkg-perl (1.22.18ubuntu2) over (1.22.15ubuntu1) ... 1832s Preparing to unpack .../10-fwupd_2.0.6-7_s390x.deb ... 1832s Unpacking fwupd (2.0.6-7) over (2.0.6-5) ... 1832s Preparing to unpack .../11-libfwupd3_2.0.6-7_s390x.deb ... 1832s Unpacking libfwupd3:s390x (2.0.6-7) over (2.0.6-5) ... 1832s Preparing to unpack .../12-libxmlb2_0.3.22-1_s390x.deb ... 1832s Unpacking libxmlb2:s390x (0.3.22-1) over (0.3.21-1) ... 1832s Preparing to unpack .../13-libldap-common_2.6.9+dfsg-2ubuntu1_all.deb ... 1832s Unpacking libldap-common (2.6.9+dfsg-2ubuntu1) over (2.6.9+dfsg-1~exp2ubuntu1) ... 1832s Preparing to unpack .../14-libldap2_2.6.9+dfsg-2ubuntu1_s390x.deb ... 1832s Unpacking libldap2:s390x (2.6.9+dfsg-2ubuntu1) over (2.6.9+dfsg-1~exp2ubuntu1) ... 1832s Setting up libibverbs1:s390x (56.0-3ubuntu1) ... 1832s Setting up libapparmor1:s390x (4.1.0~beta5-0ubuntu11) ... 1832s Setting up apt-utils (2.9.34) ... 1832s Setting up ibverbs-providers:s390x (56.0-3ubuntu1) ... 1832s Setting up gcc-14-base:s390x (14.2.0-19ubuntu1) ... 1832s Setting up libxmlb2:s390x (0.3.22-1) ... 1832s Setting up libfwupd3:s390x (2.0.6-7) ... 1832s Setting up libldap-common (2.6.9+dfsg-2ubuntu1) ... 1832s Setting up apparmor (4.1.0~beta5-0ubuntu11) ... 1833s Reloading AppArmor profiles 1834s Setting up libatomic1:s390x (15-20250319-1ubuntu1) ... 1834s Setting up libdpkg-perl (1.22.18ubuntu2) ... 1834s Setting up ubuntu-pro-client (35) ... 1834s Installing new version of config file /etc/apparmor.d/ubuntu_pro_apt_news ... 1834s Installing new version of config file /etc/apt/apt.conf.d/20apt-esm-hook.conf ... 1835s Setting up libldap2:s390x (2.6.9+dfsg-2ubuntu1) ... 1835s Setting up fwupd (2.0.6-7) ... 1836s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 1836s fwupd.service is a disabled or a static unit not running, not starting it. 1836s Setting up ubuntu-pro-client-l10n (35) ... 1836s Setting up dpkg-dev (1.22.18ubuntu2) ... 1836s Processing triggers for libc-bin (2.41-1ubuntu2) ... 1836s Processing triggers for systemd (257.4-1ubuntu1) ... 1836s Processing triggers for man-db (2.13.0-1) ... 1837s Processing triggers for dbus (1.16.2-2ubuntu1) ... 1838s Reading package lists... 1838s Building dependency tree... 1838s Reading state information... 1838s Starting pkgProblemResolver with broken count: 0 1838s Starting 2 pkgProblemResolver with broken count: 0 1838s Done 1838s Solving dependencies... 1838s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1839s autopkgtest [13:36:39]: rebooting testbed after setup commands that affected boot 1852s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 1861s Reading package lists... 1861s Building dependency tree... 1861s Reading state information... 1861s Starting pkgProblemResolver with broken count: 0 1861s Starting 2 pkgProblemResolver with broken count: 0 1861s Done 1861s The following NEW packages will be installed: 1861s adwaita-icon-theme at-spi2-common bitshuffle blt dconf-gsettings-backend 1861s dconf-service fontconfig fontconfig-config fonts-dejavu-core 1861s fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lyx 1861s gtk-update-icon-cache hicolor-icon-theme libaec0 libann-cctbx-dev 1861s libann-cctbx0 libantlr3c-3.4-0 libasan8 libatk-bridge2.0-0t64 libatk1.0-0t64 1861s libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 1861s libblas3 libboost-numpy1.83.0 libboost-python-dev libboost-python1.83-dev 1861s libboost-python1.83.0 libboost-thread1.83.0 libboost-timer1.83.0 1861s libboost1.83-dev libcairo-gobject2 libcairo2 libcbf1t64 libccp4-data 1861s libccp4-dev libccp4c0t64 libccp4f0t64 libcctbx-dev libcctbx0 libcolord2 1861s libcups2t64 libdatrie1 libdconf1 libdeflate0 libdouble-conversion3 1861s libegl-mesa0 libegl1 libepoxy0 libevent-pthreads-2.1-7t64 libexpat1-dev 1861s libfabric1 libfontconfig1 libfreetype6 libgbm1 libgcc-14-dev 1861s libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgl1 1861s libgl1-mesa-dri libglew2.2 libglu1-mesa libglut3.12 libglvnd0 libglx-mesa0 1861s libglx0 libgomp1 libgraphite2-3 libgtk-3-0t64 libgtk-3-common libharfbuzz0b 1861s libhdf5-310 libhdf5-hl-310 libhdf5-openmpi-310 libhwloc-plugins libhwloc15 1861s libice6 libimagequant0 libinput-bin libinput10 libitm1 libjbig0 1861s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc 1861s libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 liblzf1 libmd4c0 1861s libmmdb2-0 libmtdev1t64 libmunge2 libnetcdf22 libnotify4 libopengl0 1861s libopenjp2-7 libopenmpi40 libpango-1.0-0 libpangocairo-1.0-0 1861s libpangoft2-1.0-0 libpciaccess0 libpcre2-16-0 libpcre2-32-0 libpixman-1-0 1861s libpmix2t64 libpython3-dev libpython3.13-dev libqhull-r8.0 libqt5core5t64 1861s libqt5dbus5t64 libqt5designer5 libqt5gui5t64 libqt5help5 libqt5network5t64 1861s libqt5opengl5t64 libqt5printsupport5t64 libqt5sql5t64 libqt5test5t64 1861s libqt5widgets5t64 libqt5xml5t64 libraqm0 librdmacm1t64 libsharpyuv0 libsm6 1861s libssm2 libstdc++-14-dev libsz2 libtcl8.6 libthai-data libthai0 libtiff6 1861s libtk8.6 libubsan1 libvulkan1 libwacom-common libwacom9 libwayland-client0 1861s libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 1861s libwebpmux3 libwxbase3.2-1t64 libwxgtk-gl3.2-1t64 libwxgtk3.2-1t64 1861s libx11-xcb1 libxcb-dri3-0 libxcb-glx0 libxcb-icccm4 libxcb-image0 1861s libxcb-keysyms1 libxcb-present0 libxcb-randr0 libxcb-render-util0 1861s libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-util1 1861s libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxcomposite1 1861s libxcursor1 libxdamage1 libxfixes3 libxft2 libxi6 libxinerama1 1861s libxkbcommon-x11-0 libxnvctrl0 libxrandr2 libxrender1 libxshmfence1 1861s libxslt1.1 libxss1 libxtst6 libxxf86vm1 mesa-libgallium ocl-icd-libopencl1 1861s pymol-data python-matplotlib-data python3-all python3-brotli python3-cctbx 1861s python3-contourpy python3-cycler python3-dateutil python3-decorator 1861s python3-dev python3-dials-data python3-flexcache python3-flexparser 1861s python3-fonttools python3-fs python3-h5py python3-h5py-serial 1861s python3-hdf5plugin python3-importlib-resources python3-iniconfig 1861s python3-kiwisolver python3-legacy-cgi python3-lxml python3-lz4 1861s python3-matplotlib python3-mpmath python3-mrcfile python3-natsort 1861s python3-numpy python3-numpy-dev python3-nxmx python3-opengl 1861s python3-ordered-set python3-packaging python3-pil python3-pil.imagetk 1861s python3-pint python3-platformdirs python3-pluggy python3-procrunner 1861s python3-pycbf python3-pymol python3-pyqt5 python3-pyqt5.qtopengl 1861s python3-pyqt5.sip python3-pytest python3-pytest-datadir python3-pytest-mock 1861s python3-pytest-regressions python3-scipy python3-six python3-sympy 1861s python3-tk python3-tqdm python3-ufolib2 python3-wxgtk4.0 python3.13-dev 1861s python3.13-tk sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data x11-common 1861s zlib1g-dev 1862s 0 upgraded, 253 newly installed, 0 to remove and 0 not upgraded. 1862s Need to get 202 MB of archives. 1862s After this operation, 1022 MB of additional disk space will be used. 1862s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-lato all 2.015-1 [2781 kB] 1863s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy-dev s390x 1:2.2.3+ds-5 [147 kB] 1863s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 1864s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250319-1ubuntu1 [620 kB] 1864s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 1864s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:2.2.3+ds-5 [4396 kB] 1865s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [8004 B] 1865s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB] 1865s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 1865s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 1865s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 1865s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 1865s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 1865s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 1865s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libgdk-pixbuf-2.0-0 s390x 2.42.12+dfsg-2 [154 kB] 1865s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x gtk-update-icon-cache s390x 4.18.2+ds-1 [53.2 kB] 1865s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x hicolor-icon-theme all 0.18-2 [13.3 kB] 1865s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x adwaita-icon-theme all 48.0-1 [578 kB] 1865s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x at-spi2-common all 2.56.0-2 [9108 B] 1865s Get:20 http://ftpmaster.internal/ubuntu plucky/universe s390x libaec0 s390x 1.1.3-1 [25.7 kB] 1865s Get:21 http://ftpmaster.internal/ubuntu plucky/universe s390x libsz2 s390x 1.1.3-1 [5442 B] 1865s Get:22 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-310 s390x 1.14.5+repack-3 [1477 kB] 1865s Get:23 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-hl-310 s390x 1.14.5+repack-3 [61.0 kB] 1865s Get:24 http://ftpmaster.internal/ubuntu plucky/universe s390x liblzf1 s390x 3.6-4 [7020 B] 1865s Get:25 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py-serial s390x 3.13.0-1 [1185 kB] 1865s Get:26 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py all 3.13.0-1 [7978 B] 1865s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250319-1ubuntu1 [151 kB] 1865s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x libevent-pthreads-2.1-7t64 s390x 2.1.12-stable-10 [7870 B] 1865s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x librdmacm1t64 s390x 56.0-3ubuntu1 [73.8 kB] 1865s Get:30 http://ftpmaster.internal/ubuntu plucky/universe s390x libfabric1 s390x 1.17.0-3.1 [558 kB] 1865s Get:31 http://ftpmaster.internal/ubuntu plucky/universe s390x libhwloc15 s390x 2.12.0-1 [176 kB] 1866s Get:32 http://ftpmaster.internal/ubuntu plucky/universe s390x libmunge2 s390x 0.5.16-1 [15.2 kB] 1866s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libpciaccess0 s390x 0.17-3build1 [19.0 kB] 1866s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libxnvctrl0 s390x 510.47.03-0ubuntu4 [12.7 kB] 1866s Get:35 http://ftpmaster.internal/ubuntu plucky/universe s390x ocl-icd-libopencl1 s390x 2.3.2-1build1 [41.1 kB] 1866s Get:36 http://ftpmaster.internal/ubuntu plucky/universe s390x libhwloc-plugins s390x 2.12.0-1 [16.1 kB] 1866s Get:37 http://ftpmaster.internal/ubuntu plucky/universe s390x libpmix2t64 s390x 5.0.6-5 [715 kB] 1866s Get:38 http://ftpmaster.internal/ubuntu plucky/universe s390x libopenmpi40 s390x 5.0.7-1 [2196 kB] 1866s Get:39 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-openmpi-310 s390x 1.14.5+repack-3 [1539 kB] 1866s Get:40 http://ftpmaster.internal/ubuntu plucky/universe s390x bitshuffle s390x 0.5.2-1build2 [152 kB] 1866s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libtcl8.6 s390x 8.6.16+dfsg-1 [1034 kB] 1866s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 1866s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 1866s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 1866s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-2.1ubuntu1 [37.7 kB] 1866s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-2.1ubuntu1 [150 kB] 1866s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 1866s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB] 1866s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] 1866s Get:50 http://ftpmaster.internal/ubuntu plucky/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B] 1866s Get:51 http://ftpmaster.internal/ubuntu plucky/main s390x libtk8.6 s390x 8.6.16-1 [830 kB] 1866s Get:52 http://ftpmaster.internal/ubuntu plucky/main s390x tk8.6-blt2.5 s390x 2.5.3+dfsg-8 [657 kB] 1866s Get:53 http://ftpmaster.internal/ubuntu plucky/main s390x blt s390x 2.5.3+dfsg-8 [4826 B] 1866s Get:54 http://ftpmaster.internal/ubuntu plucky/main s390x libdconf1 s390x 0.40.0-5 [40.0 kB] 1866s Get:55 http://ftpmaster.internal/ubuntu plucky/main s390x dconf-service s390x 0.40.0-5 [28.4 kB] 1866s Get:56 http://ftpmaster.internal/ubuntu plucky/main s390x dconf-gsettings-backend s390x 0.40.0-5 [22.8 kB] 1866s Get:57 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig s390x 2.15.0-2.1ubuntu1 [191 kB] 1866s Get:58 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 1866s Get:59 http://ftpmaster.internal/ubuntu plucky/universe s390x fonts-lyx all 2.4.3-1 [171 kB] 1866s Get:60 http://ftpmaster.internal/ubuntu plucky/universe s390x libann-cctbx0 s390x 1.1.2+doc-9build1 [36.2 kB] 1866s Get:61 http://ftpmaster.internal/ubuntu plucky/universe s390x libann-cctbx-dev s390x 1.1.2+doc-9build1 [48.1 kB] 1866s Get:62 http://ftpmaster.internal/ubuntu plucky/universe s390x libantlr3c-3.4-0 s390x 3.4+dfsg-4build2 [51.3 kB] 1866s Get:63 http://ftpmaster.internal/ubuntu plucky/main s390x libasan8 s390x 15-20250319-1ubuntu1 [2966 kB] 1866s Get:64 http://ftpmaster.internal/ubuntu plucky/main s390x libatk1.0-0t64 s390x 2.56.0-2 [54.9 kB] 1866s Get:65 http://ftpmaster.internal/ubuntu plucky/main s390x libxi6 s390x 2:1.8.2-1 [35.4 kB] 1866s Get:66 http://ftpmaster.internal/ubuntu plucky/main s390x libatspi2.0-0t64 s390x 2.56.0-2 [84.0 kB] 1866s Get:67 http://ftpmaster.internal/ubuntu plucky/main s390x libatk-bridge2.0-0t64 s390x 2.56.0-2 [66.7 kB] 1866s Get:68 http://ftpmaster.internal/ubuntu plucky/main s390x libavahi-common-data s390x 0.8-16ubuntu2 [31.0 kB] 1866s Get:69 http://ftpmaster.internal/ubuntu plucky/main s390x libavahi-common3 s390x 0.8-16ubuntu2 [23.5 kB] 1866s Get:70 http://ftpmaster.internal/ubuntu plucky/main s390x libavahi-client3 s390x 0.8-16ubuntu2 [26.3 kB] 1866s Get:71 http://ftpmaster.internal/ubuntu plucky/main s390x libboost-python1.83.0 s390x 1.83.0-4.1ubuntu2 [313 kB] 1866s Get:72 http://ftpmaster.internal/ubuntu plucky/universe s390x libboost-numpy1.83.0 s390x 1.83.0-4.1ubuntu2 [243 kB] 1866s Get:73 http://ftpmaster.internal/ubuntu plucky/main s390x libitm1 s390x 15-20250319-1ubuntu1 [31.2 kB] 1866s Get:74 http://ftpmaster.internal/ubuntu plucky/main s390x libubsan1 s390x 15-20250319-1ubuntu1 [1210 kB] 1866s Get:75 http://ftpmaster.internal/ubuntu plucky/main s390x libgcc-14-dev s390x 14.2.0-19ubuntu1 [1037 kB] 1867s Get:76 http://ftpmaster.internal/ubuntu plucky/main s390x libstdc++-14-dev s390x 14.2.0-19ubuntu1 [2615 kB] 1867s Get:77 http://ftpmaster.internal/ubuntu plucky/main s390x libboost1.83-dev s390x 1.83.0-4.1ubuntu2 [10.7 MB] 1867s Get:78 http://ftpmaster.internal/ubuntu plucky/main s390x libexpat1-dev s390x 2.6.4-1 [146 kB] 1867s Get:79 http://ftpmaster.internal/ubuntu plucky/main s390x zlib1g-dev s390x 1:1.3.dfsg+really1.3.1-1ubuntu1 [898 kB] 1867s Get:80 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-dev s390x 3.13.2-2 [5597 kB] 1867s Get:81 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3-dev s390x 3.13.2-2 [10.7 kB] 1867s Get:82 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-dev s390x 3.13.2-2 [513 kB] 1867s Get:83 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 1867s Get:84 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 1867s Get:85 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 1867s Get:86 http://ftpmaster.internal/ubuntu plucky/main s390x python3-dev s390x 3.13.2-2 [26.7 kB] 1867s Get:87 http://ftpmaster.internal/ubuntu plucky/universe s390x libboost-python1.83-dev s390x 1.83.0-4.1ubuntu2 [335 kB] 1867s Get:88 http://ftpmaster.internal/ubuntu plucky/universe s390x libboost-python-dev s390x 1.83.0.2ubuntu1 [4518 B] 1867s Get:89 http://ftpmaster.internal/ubuntu plucky/main s390x libboost-thread1.83.0 s390x 1.83.0-4.1ubuntu2 [279 kB] 1867s Get:90 http://ftpmaster.internal/ubuntu plucky/universe s390x libboost-timer1.83.0 s390x 1.83.0-4.1ubuntu2 [241 kB] 1867s Get:91 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 1867s Get:92 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 1867s Get:93 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 1867s Get:94 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.4-1 [580 kB] 1867s Get:95 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo-gobject2 s390x 1.18.4-1 [127 kB] 1867s Get:96 http://ftpmaster.internal/ubuntu plucky/universe s390x libcbf1t64 s390x 0.9.7+dfsg1-5build1 [391 kB] 1867s Get:97 http://ftpmaster.internal/ubuntu plucky/universe s390x libccp4-data all 8.0.0-4 [65.2 kB] 1867s Get:98 http://ftpmaster.internal/ubuntu plucky/universe s390x libccp4c0t64 s390x 8.0.0-4 [104 kB] 1867s Get:99 http://ftpmaster.internal/ubuntu plucky/universe s390x libmmdb2-0 s390x 2.0.22-1 [351 kB] 1867s Get:100 http://ftpmaster.internal/ubuntu plucky/universe s390x libccp4f0t64 s390x 8.0.0-4 [224 kB] 1867s Get:101 http://ftpmaster.internal/ubuntu plucky/universe s390x libccp4-dev s390x 8.0.0-4 [42.4 kB] 1868s Get:102 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x libcctbx0 s390x 2024.10+ds2+~3.22.1+ds1-4build2 [2003 kB] 1868s Get:103 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x libcctbx-dev s390x 2024.10+ds2+~3.22.1+ds1-4build2 [1192 kB] 1868s Get:104 http://ftpmaster.internal/ubuntu plucky/main s390x liblcms2-2 s390x 2.16-2 [175 kB] 1868s Get:105 http://ftpmaster.internal/ubuntu plucky/main s390x libcolord2 s390x 1.4.7-3 [149 kB] 1868s Get:106 http://ftpmaster.internal/ubuntu plucky/main s390x libcups2t64 s390x 2.4.11-0ubuntu2 [282 kB] 1868s Get:107 http://ftpmaster.internal/ubuntu plucky/main s390x libdatrie1 s390x 0.2.13-3build1 [20.6 kB] 1868s Get:108 http://ftpmaster.internal/ubuntu plucky/universe s390x libdouble-conversion3 s390x 3.3.1-1 [43.3 kB] 1868s Get:109 http://ftpmaster.internal/ubuntu plucky/main s390x libwayland-server0 s390x 1.23.1-3 [37.3 kB] 1868s Get:110 http://ftpmaster.internal/ubuntu plucky/main s390x libx11-xcb1 s390x 2:1.8.10-2 [7954 B] 1868s Get:111 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-dri3-0 s390x 1.17.0-2 [7616 B] 1868s Get:112 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-present0 s390x 1.17.0-2 [6244 B] 1868s Get:113 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-randr0 s390x 1.17.0-2 [19.2 kB] 1868s Get:114 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-sync1 s390x 1.17.0-2 [9488 B] 1868s Get:115 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-xfixes0 s390x 1.17.0-2 [10.5 kB] 1868s Get:116 http://ftpmaster.internal/ubuntu plucky/main s390x libxshmfence1 s390x 1.3-1build5 [4772 B] 1868s Get:117 http://ftpmaster.internal/ubuntu plucky/main s390x mesa-libgallium s390x 25.0.1-2ubuntu2 [8056 kB] 1869s Get:118 http://ftpmaster.internal/ubuntu plucky/main s390x libgbm1 s390x 25.0.1-2ubuntu2 [34.5 kB] 1869s Get:119 http://ftpmaster.internal/ubuntu plucky/main s390x libwayland-client0 s390x 1.23.1-3 [28.2 kB] 1869s Get:120 http://ftpmaster.internal/ubuntu plucky/main s390x libegl-mesa0 s390x 25.0.1-2ubuntu2 [126 kB] 1869s Get:121 http://ftpmaster.internal/ubuntu plucky/main s390x libepoxy0 s390x 1.5.10-2 [222 kB] 1869s Get:122 http://ftpmaster.internal/ubuntu plucky/main s390x libvulkan1 s390x 1.4.304.0-1 [147 kB] 1869s Get:123 http://ftpmaster.internal/ubuntu plucky/main s390x libgl1-mesa-dri s390x 25.0.1-2ubuntu2 [35.4 kB] 1869s Get:124 http://ftpmaster.internal/ubuntu plucky/main s390x libglvnd0 s390x 1.7.0-1build1 [110 kB] 1869s Get:125 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-glx0 s390x 1.17.0-2 [26.0 kB] 1869s Get:126 http://ftpmaster.internal/ubuntu plucky/main s390x libxxf86vm1 s390x 1:1.1.4-1build4 [9630 B] 1869s Get:127 http://ftpmaster.internal/ubuntu plucky/main s390x libglx-mesa0 s390x 25.0.1-2ubuntu2 [161 kB] 1869s Get:128 http://ftpmaster.internal/ubuntu plucky/main s390x libglx0 s390x 1.7.0-1build1 [32.2 kB] 1869s Get:129 http://ftpmaster.internal/ubuntu plucky/main s390x libgl1 s390x 1.7.0-1build1 [142 kB] 1869s Get:130 http://ftpmaster.internal/ubuntu plucky/universe s390x libglew2.2 s390x 2.2.0-4build1 [195 kB] 1869s Get:131 http://ftpmaster.internal/ubuntu plucky/universe s390x libglut3.12 s390x 3.4.0-4 [99.3 kB] 1869s Get:132 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 1869s Get:133 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB] 1869s Get:134 http://ftpmaster.internal/ubuntu plucky/main s390x libthai-data all 0.1.29-2build1 [158 kB] 1869s Get:135 http://ftpmaster.internal/ubuntu plucky/main s390x libthai0 s390x 0.1.29-2build1 [20.7 kB] 1869s Get:136 http://ftpmaster.internal/ubuntu plucky/main s390x libpango-1.0-0 s390x 1.56.3-1 [254 kB] 1869s Get:137 http://ftpmaster.internal/ubuntu plucky/main s390x libpangoft2-1.0-0 s390x 1.56.3-1 [50.5 kB] 1869s Get:138 http://ftpmaster.internal/ubuntu plucky/main s390x libpangocairo-1.0-0 s390x 1.56.3-1 [28.2 kB] 1869s Get:139 http://ftpmaster.internal/ubuntu plucky/main s390x libwayland-cursor0 s390x 1.23.1-3 [11.5 kB] 1869s Get:140 http://ftpmaster.internal/ubuntu plucky/main s390x libwayland-egl1 s390x 1.23.1-3 [6078 B] 1869s Get:141 http://ftpmaster.internal/ubuntu plucky/main s390x libxcomposite1 s390x 1:0.4.6-1 [6588 B] 1869s Get:142 http://ftpmaster.internal/ubuntu plucky/main s390x libxfixes3 s390x 1:6.0.0-2build1 [11.3 kB] 1869s Get:143 http://ftpmaster.internal/ubuntu plucky/main s390x libxcursor1 s390x 1:1.2.3-1 [23.4 kB] 1869s Get:144 http://ftpmaster.internal/ubuntu plucky/main s390x libxdamage1 s390x 1:1.1.6-1build1 [6156 B] 1869s Get:145 http://ftpmaster.internal/ubuntu plucky/main s390x libxinerama1 s390x 2:1.1.4-3build1 [6476 B] 1869s Get:146 http://ftpmaster.internal/ubuntu plucky/main s390x libxrandr2 s390x 2:1.5.4-1 [20.8 kB] 1869s Get:147 http://ftpmaster.internal/ubuntu plucky/main s390x libgtk-3-common all 3.24.49-2ubuntu1 [1424 kB] 1869s Get:148 http://ftpmaster.internal/ubuntu plucky/main s390x libgtk-3-0t64 s390x 3.24.49-2ubuntu1 [2950 kB] 1869s Get:149 http://ftpmaster.internal/ubuntu plucky/main s390x libice6 s390x 2:1.1.1-1 [45.4 kB] 1869s Get:150 http://ftpmaster.internal/ubuntu plucky/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 1869s Get:151 http://ftpmaster.internal/ubuntu plucky/main s390x libwacom-common all 2.14.0-1 [103 kB] 1869s Get:152 http://ftpmaster.internal/ubuntu plucky/main s390x libwacom9 s390x 2.14.0-1 [27.1 kB] 1869s Get:153 http://ftpmaster.internal/ubuntu plucky/main s390x libinput-bin s390x 1.27.1-1 [23.3 kB] 1869s Get:154 http://ftpmaster.internal/ubuntu plucky/main s390x libmtdev1t64 s390x 1.1.7-1 [15.6 kB] 1869s Get:155 http://ftpmaster.internal/ubuntu plucky/main s390x libinput10 s390x 1.27.1-1 [139 kB] 1869s Get:156 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 1869s Get:157 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 1869s Get:158 http://ftpmaster.internal/ubuntu plucky/universe s390x libmd4c0 s390x 0.5.2-2 [47.7 kB] 1869s Get:159 http://ftpmaster.internal/ubuntu plucky/universe s390x libnetcdf22 s390x 1:4.9.3-1 [533 kB] 1869s Get:160 http://ftpmaster.internal/ubuntu plucky/main s390x libnotify4 s390x 0.8.4-1 [25.9 kB] 1869s Get:161 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-16-0 s390x 10.45-1 [259 kB] 1869s Get:162 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-32-0 s390x 10.45-1 [245 kB] 1869s Get:163 http://ftpmaster.internal/ubuntu plucky/universe s390x libqhull-r8.0 s390x 2020.2-6build1 [199 kB] 1869s Get:164 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5core5t64 s390x 5.15.15+dfsg-4ubuntu1 [2242 kB] 1869s Get:165 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5dbus5t64 s390x 5.15.15+dfsg-4ubuntu1 [240 kB] 1869s Get:166 http://ftpmaster.internal/ubuntu plucky/main s390x libegl1 s390x 1.7.0-1build1 [31.8 kB] 1869s Get:167 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5network5t64 s390x 5.15.15+dfsg-4ubuntu1 [788 kB] 1870s Get:168 http://ftpmaster.internal/ubuntu plucky/main s390x libsm6 s390x 2:1.2.4-1 [18.4 kB] 1870s Get:169 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-icccm4 s390x 0.4.2-1 [11.4 kB] 1870s Get:170 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-util1 s390x 0.4.1-1 [10.7 kB] 1870s Get:171 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-image0 s390x 0.4.0-2build1 [12.0 kB] 1870s Get:172 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-keysyms1 s390x 0.4.1-1 [8908 B] 1870s Get:173 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render-util0 s390x 0.3.10-1 [10.3 kB] 1870s Get:174 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shape0 s390x 1.17.0-2 [6202 B] 1870s Get:175 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-xinerama0 s390x 1.17.0-2 [5430 B] 1870s Get:176 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-xinput0 s390x 1.17.0-2 [35.8 kB] 1870s Get:177 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-xkb1 s390x 1.17.0-2 [34.5 kB] 1870s Get:178 http://ftpmaster.internal/ubuntu plucky/main s390x libxkbcommon-x11-0 s390x 1.7.0-2 [14.8 kB] 1870s Get:179 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5gui5t64 s390x 5.15.15+dfsg-4ubuntu1 [4187 kB] 1870s Get:180 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5widgets5t64 s390x 5.15.15+dfsg-4ubuntu1 [2718 kB] 1870s Get:181 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5xml5t64 s390x 5.15.15+dfsg-4ubuntu1 [129 kB] 1870s Get:182 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5designer5 s390x 5.15.15-6build1 [2900 kB] 1870s Get:183 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5sql5t64 s390x 5.15.15+dfsg-4ubuntu1 [130 kB] 1870s Get:184 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5help5 s390x 5.15.15-6build1 [172 kB] 1870s Get:185 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5opengl5t64 s390x 5.15.15+dfsg-4ubuntu1 [156 kB] 1870s Get:186 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5printsupport5t64 s390x 5.15.15+dfsg-4ubuntu1 [218 kB] 1870s Get:187 http://ftpmaster.internal/ubuntu plucky/universe s390x libqt5test5t64 s390x 5.15.15+dfsg-4ubuntu1 [156 kB] 1870s Get:188 http://ftpmaster.internal/ubuntu plucky/main s390x libraqm0 s390x 0.10.2-1 [15.8 kB] 1870s Get:189 http://ftpmaster.internal/ubuntu plucky/universe s390x libssm2 s390x 1.4.0-2build1 [97.8 kB] 1870s Get:190 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpdemux2 s390x 1.5.0-0.1 [12.6 kB] 1870s Get:191 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpmux3 s390x 1.5.0-0.1 [25.8 kB] 1870s Get:192 http://ftpmaster.internal/ubuntu plucky/universe s390x libwxbase3.2-1t64 s390x 3.2.6+dfsg-2ubuntu1 [915 kB] 1870s Get:193 http://ftpmaster.internal/ubuntu plucky/main s390x libxtst6 s390x 2:1.2.5-1 [13.5 kB] 1870s Get:194 http://ftpmaster.internal/ubuntu plucky/universe s390x libwxgtk3.2-1t64 s390x 3.2.6+dfsg-2ubuntu1 [4737 kB] 1870s Get:195 http://ftpmaster.internal/ubuntu plucky/universe s390x libwxgtk-gl3.2-1t64 s390x 3.2.6+dfsg-2ubuntu1 [52.9 kB] 1870s Get:196 http://ftpmaster.internal/ubuntu plucky/main s390x libxslt1.1 s390x 1.1.39-0exp1ubuntu4 [170 kB] 1870s Get:197 http://ftpmaster.internal/ubuntu plucky/universe s390x pymol-data all 3.1.0+dfsg-1 [1394 kB] 1870s Get:198 http://ftpmaster.internal/ubuntu plucky/universe s390x python-matplotlib-data all 3.8.3-7build1 [2934 kB] 1871s Get:199 http://ftpmaster.internal/ubuntu plucky/main s390x python3-all s390x 3.13.2-2 [886 B] 1871s Get:200 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-brotli s390x 1.1.0-2build4 [380 kB] 1871s Get:201 http://ftpmaster.internal/ubuntu plucky/main s390x python3-legacy-cgi all 2.6.2-1 [16.6 kB] 1871s Get:202 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pycbf s390x 0.9.7+dfsg1-5build1 [152 kB] 1871s Get:203 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-hdf5plugin all 5.0.0-1 [23.1 kB] 1871s Get:204 http://ftpmaster.internal/ubuntu plucky/main s390x python3-dateutil all 2.9.0-4 [80.3 kB] 1871s Get:205 http://ftpmaster.internal/ubuntu plucky/main s390x libopenjp2-7 s390x 2.5.3-2 [207 kB] 1871s Get:206 http://ftpmaster.internal/ubuntu plucky/main s390x python3-pil s390x 11.1.0-5build1 [498 kB] 1871s Get:207 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-tk s390x 3.13.2-2 [108 kB] 1871s Get:208 http://ftpmaster.internal/ubuntu plucky/main s390x python3-tk s390x 3.13.2-1 [9820 B] 1871s Get:209 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pil.imagetk s390x 11.1.0-5build1 [9668 B] 1871s Get:210 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-contourpy s390x 1.3.1-1build1 [197 kB] 1871s Get:211 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-cycler all 0.12.1-1 [9716 B] 1871s Get:212 http://ftpmaster.internal/ubuntu plucky/main s390x python3-platformdirs all 4.3.6-1 [16.8 kB] 1871s Get:213 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-fs all 2.4.16-7 [90.8 kB] 1871s Get:214 http://ftpmaster.internal/ubuntu plucky/main s390x python3-lxml s390x 5.3.1-1build1 [1370 kB] 1871s Get:215 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-lz4 s390x 4.4.0+dfsg-1build1 [26.6 kB] 1871s Get:216 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 1871s Get:217 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.14.1-4ubuntu2 [18.0 MB] 1873s Get:218 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-mpmath all 1.3.0-1 [425 kB] 1873s Get:219 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-sympy all 1.13.3-5 [4229 kB] 1873s Get:220 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 1873s Get:221 http://ftpmaster.internal/ubuntu plucky/universe s390x unicode-data all 15.1.0-1 [8878 kB] 1874s Get:222 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-fonttools s390x 4.55.3-2build1 [1496 kB] 1874s Get:223 http://ftpmaster.internal/ubuntu plucky/main s390x python3-importlib-resources all 6.5.2-1 [24.5 kB] 1874s Get:224 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-kiwisolver s390x 1.4.7-3build1 [55.0 kB] 1874s Get:225 http://ftpmaster.internal/ubuntu plucky/main s390x python3-packaging all 24.2-1 [51.5 kB] 1874s Get:226 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-matplotlib s390x 3.8.3-7build1 [17.3 MB] 1875s Get:227 http://ftpmaster.internal/ubuntu plucky/main s390x sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 1875s Get:228 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-mrcfile all 1.5.4-2 [116 kB] 1875s Get:229 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-natsort all 8.0.2-2 [33.8 kB] 1875s Get:230 http://ftpmaster.internal/ubuntu plucky/main s390x python3-flexcache all 0.3-2 [13.4 kB] 1875s Get:231 http://ftpmaster.internal/ubuntu plucky/main s390x python3-flexparser all 0.4-1 [43.8 kB] 1875s Get:232 http://ftpmaster.internal/ubuntu plucky/main s390x python3-pint all 0.24.4-1 [203 kB] 1875s Get:233 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-nxmx all 0.0.4-1 [16.4 kB] 1875s Get:234 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-ordered-set all 4.1.0-1 [9778 B] 1875s Get:235 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-procrunner all 2.3.3-2 [12.0 kB] 1875s Get:236 http://ftpmaster.internal/ubuntu plucky/main s390x libopengl0 s390x 1.7.0-1build1 [48.0 kB] 1875s Get:237 http://ftpmaster.internal/ubuntu plucky/main s390x libglu1-mesa s390x 9.0.2-1.1build1 [176 kB] 1875s Get:238 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-opengl all 3.1.9+dfsg-1syncable1 [631 kB] 1875s Get:239 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pyqt5.sip s390x 12.17.0-1build1 [66.5 kB] 1875s Get:240 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pyqt5 s390x 5.15.11+dfsg-2 [2880 kB] 1876s Get:241 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pyqt5.qtopengl s390x 5.15.11+dfsg-2 [140 kB] 1876s Get:242 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pymol s390x 3.1.0+dfsg-1 [4292 kB] 1876s Get:243 http://ftpmaster.internal/ubuntu plucky/main s390x python3-six all 1.17.0-1 [13.2 kB] 1876s Get:244 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-tqdm all 4.67.1-2 [92.5 kB] 1876s Get:245 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-wxgtk4.0 s390x 4.2.2+dfsg-3build1 [7757 kB] 1877s Get:246 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x python3-cctbx s390x 2024.10+ds2+~3.22.1+ds1-4build2 [28.1 MB] 1879s Get:247 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-iniconfig all 1.1.1-2 [6024 B] 1879s Get:248 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pluggy all 1.5.0-1 [21.0 kB] 1879s Get:249 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pytest all 8.3.5-1 [252 kB] 1879s Get:250 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-dials-data all 2.4.0-2 [110 kB] 1879s Get:251 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pytest-datadir all 1.4.1+ds-1 [5386 B] 1879s Get:252 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pytest-mock all 3.14.0-2 [11.7 kB] 1879s Get:253 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pytest-regressions all 2.5.0+ds-2 [39.2 kB] 1879s Fetched 202 MB in 17s (11.7 MB/s) 1879s Selecting previously unselected package fonts-lato. 1879s (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 ... 81447 files and directories currently installed.) 1879s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ... 1879s Unpacking fonts-lato (2.015-1) ... 1880s Selecting previously unselected package python3-numpy-dev:s390x. 1880s Preparing to unpack .../001-python3-numpy-dev_1%3a2.2.3+ds-5_s390x.deb ... 1880s Unpacking python3-numpy-dev:s390x (1:2.2.3+ds-5) ... 1880s Selecting previously unselected package libblas3:s390x. 1880s Preparing to unpack .../002-libblas3_3.12.1-2_s390x.deb ... 1880s Unpacking libblas3:s390x (3.12.1-2) ... 1880s Selecting previously unselected package libgfortran5:s390x. 1880s Preparing to unpack .../003-libgfortran5_15-20250319-1ubuntu1_s390x.deb ... 1880s Unpacking libgfortran5:s390x (15-20250319-1ubuntu1) ... 1880s Selecting previously unselected package liblapack3:s390x. 1880s Preparing to unpack .../004-liblapack3_3.12.1-2_s390x.deb ... 1880s Unpacking liblapack3:s390x (3.12.1-2) ... 1880s Selecting previously unselected package python3-numpy. 1880s Preparing to unpack .../005-python3-numpy_1%3a2.2.3+ds-5_s390x.deb ... 1880s Unpacking python3-numpy (1:2.2.3+ds-5) ... 1880s Selecting previously unselected package libgdk-pixbuf2.0-common. 1880s Preparing to unpack .../006-libgdk-pixbuf2.0-common_2.42.12+dfsg-2_all.deb ... 1880s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... 1880s Selecting previously unselected package libjpeg-turbo8:s390x. 1880s Preparing to unpack .../007-libjpeg-turbo8_2.1.5-3ubuntu2_s390x.deb ... 1880s Unpacking libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 1880s Selecting previously unselected package libjpeg8:s390x. 1880s Preparing to unpack .../008-libjpeg8_8c-2ubuntu11_s390x.deb ... 1880s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 1880s Selecting previously unselected package libdeflate0:s390x. 1880s Preparing to unpack .../009-libdeflate0_1.23-1_s390x.deb ... 1880s Unpacking libdeflate0:s390x (1.23-1) ... 1880s Selecting previously unselected package libjbig0:s390x. 1880s Preparing to unpack .../010-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 1880s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 1880s Selecting previously unselected package libsharpyuv0:s390x. 1880s Preparing to unpack .../011-libsharpyuv0_1.5.0-0.1_s390x.deb ... 1880s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ... 1880s Selecting previously unselected package libwebp7:s390x. 1880s Preparing to unpack .../012-libwebp7_1.5.0-0.1_s390x.deb ... 1880s Unpacking libwebp7:s390x (1.5.0-0.1) ... 1880s Selecting previously unselected package libtiff6:s390x. 1880s Preparing to unpack .../013-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ... 1880s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 1880s Selecting previously unselected package libgdk-pixbuf-2.0-0:s390x. 1880s Preparing to unpack .../014-libgdk-pixbuf-2.0-0_2.42.12+dfsg-2_s390x.deb ... 1880s Unpacking libgdk-pixbuf-2.0-0:s390x (2.42.12+dfsg-2) ... 1880s Selecting previously unselected package gtk-update-icon-cache. 1880s Preparing to unpack .../015-gtk-update-icon-cache_4.18.2+ds-1_s390x.deb ... 1880s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 1880s 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. 1880s Unpacking gtk-update-icon-cache (4.18.2+ds-1) ... 1880s Selecting previously unselected package hicolor-icon-theme. 1880s Preparing to unpack .../016-hicolor-icon-theme_0.18-2_all.deb ... 1880s Unpacking hicolor-icon-theme (0.18-2) ... 1880s Selecting previously unselected package adwaita-icon-theme. 1880s Preparing to unpack .../017-adwaita-icon-theme_48.0-1_all.deb ... 1880s Unpacking adwaita-icon-theme (48.0-1) ... 1880s Selecting previously unselected package at-spi2-common. 1880s Preparing to unpack .../018-at-spi2-common_2.56.0-2_all.deb ... 1880s Unpacking at-spi2-common (2.56.0-2) ... 1880s Selecting previously unselected package libaec0:s390x. 1880s Preparing to unpack .../019-libaec0_1.1.3-1_s390x.deb ... 1880s Unpacking libaec0:s390x (1.1.3-1) ... 1880s Selecting previously unselected package libsz2:s390x. 1880s Preparing to unpack .../020-libsz2_1.1.3-1_s390x.deb ... 1880s Unpacking libsz2:s390x (1.1.3-1) ... 1880s Selecting previously unselected package libhdf5-310:s390x. 1880s Preparing to unpack .../021-libhdf5-310_1.14.5+repack-3_s390x.deb ... 1880s Unpacking libhdf5-310:s390x (1.14.5+repack-3) ... 1880s Selecting previously unselected package libhdf5-hl-310:s390x. 1880s Preparing to unpack .../022-libhdf5-hl-310_1.14.5+repack-3_s390x.deb ... 1880s Unpacking libhdf5-hl-310:s390x (1.14.5+repack-3) ... 1880s Selecting previously unselected package liblzf1:s390x. 1880s Preparing to unpack .../023-liblzf1_3.6-4_s390x.deb ... 1880s Unpacking liblzf1:s390x (3.6-4) ... 1880s Selecting previously unselected package python3-h5py-serial. 1880s Preparing to unpack .../024-python3-h5py-serial_3.13.0-1_s390x.deb ... 1880s Unpacking python3-h5py-serial (3.13.0-1) ... 1880s Selecting previously unselected package python3-h5py. 1880s Preparing to unpack .../025-python3-h5py_3.13.0-1_all.deb ... 1880s Unpacking python3-h5py (3.13.0-1) ... 1880s Selecting previously unselected package libgomp1:s390x. 1880s Preparing to unpack .../026-libgomp1_15-20250319-1ubuntu1_s390x.deb ... 1880s Unpacking libgomp1:s390x (15-20250319-1ubuntu1) ... 1880s Selecting previously unselected package libevent-pthreads-2.1-7t64:s390x. 1880s Preparing to unpack .../027-libevent-pthreads-2.1-7t64_2.1.12-stable-10_s390x.deb ... 1880s Unpacking libevent-pthreads-2.1-7t64:s390x (2.1.12-stable-10) ... 1880s Selecting previously unselected package librdmacm1t64:s390x. 1880s Preparing to unpack .../028-librdmacm1t64_56.0-3ubuntu1_s390x.deb ... 1880s Unpacking librdmacm1t64:s390x (56.0-3ubuntu1) ... 1880s Selecting previously unselected package libfabric1:s390x. 1880s Preparing to unpack .../029-libfabric1_1.17.0-3.1_s390x.deb ... 1880s Unpacking libfabric1:s390x (1.17.0-3.1) ... 1880s Selecting previously unselected package libhwloc15:s390x. 1880s Preparing to unpack .../030-libhwloc15_2.12.0-1_s390x.deb ... 1880s Unpacking libhwloc15:s390x (2.12.0-1) ... 1880s Selecting previously unselected package libmunge2:s390x. 1880s Preparing to unpack .../031-libmunge2_0.5.16-1_s390x.deb ... 1880s Unpacking libmunge2:s390x (0.5.16-1) ... 1880s Selecting previously unselected package libpciaccess0:s390x. 1880s Preparing to unpack .../032-libpciaccess0_0.17-3build1_s390x.deb ... 1880s Unpacking libpciaccess0:s390x (0.17-3build1) ... 1880s Selecting previously unselected package libxnvctrl0:s390x. 1880s Preparing to unpack .../033-libxnvctrl0_510.47.03-0ubuntu4_s390x.deb ... 1880s Unpacking libxnvctrl0:s390x (510.47.03-0ubuntu4) ... 1880s Selecting previously unselected package ocl-icd-libopencl1:s390x. 1880s Preparing to unpack .../034-ocl-icd-libopencl1_2.3.2-1build1_s390x.deb ... 1880s Unpacking ocl-icd-libopencl1:s390x (2.3.2-1build1) ... 1880s Selecting previously unselected package libhwloc-plugins:s390x. 1880s Preparing to unpack .../035-libhwloc-plugins_2.12.0-1_s390x.deb ... 1880s Unpacking libhwloc-plugins:s390x (2.12.0-1) ... 1880s Selecting previously unselected package libpmix2t64:s390x. 1880s Preparing to unpack .../036-libpmix2t64_5.0.6-5_s390x.deb ... 1880s Unpacking libpmix2t64:s390x (5.0.6-5) ... 1880s Selecting previously unselected package libopenmpi40:s390x. 1880s Preparing to unpack .../037-libopenmpi40_5.0.7-1_s390x.deb ... 1880s Unpacking libopenmpi40:s390x (5.0.7-1) ... 1880s Selecting previously unselected package libhdf5-openmpi-310:s390x. 1880s Preparing to unpack .../038-libhdf5-openmpi-310_1.14.5+repack-3_s390x.deb ... 1880s Unpacking libhdf5-openmpi-310:s390x (1.14.5+repack-3) ... 1880s Selecting previously unselected package bitshuffle. 1880s Preparing to unpack .../039-bitshuffle_0.5.2-1build2_s390x.deb ... 1880s Unpacking bitshuffle (0.5.2-1build2) ... 1880s Selecting previously unselected package libtcl8.6:s390x. 1880s Preparing to unpack .../040-libtcl8.6_8.6.16+dfsg-1_s390x.deb ... 1880s Unpacking libtcl8.6:s390x (8.6.16+dfsg-1) ... 1880s Selecting previously unselected package libfreetype6:s390x. 1880s Preparing to unpack .../041-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 1880s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 1880s Selecting previously unselected package fonts-dejavu-mono. 1880s Preparing to unpack .../042-fonts-dejavu-mono_2.37-8_all.deb ... 1880s Unpacking fonts-dejavu-mono (2.37-8) ... 1880s Selecting previously unselected package fonts-dejavu-core. 1880s Preparing to unpack .../043-fonts-dejavu-core_2.37-8_all.deb ... 1880s Unpacking fonts-dejavu-core (2.37-8) ... 1881s Selecting previously unselected package fontconfig-config. 1881s Preparing to unpack .../044-fontconfig-config_2.15.0-2.1ubuntu1_s390x.deb ... 1881s Unpacking fontconfig-config (2.15.0-2.1ubuntu1) ... 1881s Selecting previously unselected package libfontconfig1:s390x. 1881s Preparing to unpack .../045-libfontconfig1_2.15.0-2.1ubuntu1_s390x.deb ... 1881s Unpacking libfontconfig1:s390x (2.15.0-2.1ubuntu1) ... 1881s Selecting previously unselected package libxrender1:s390x. 1881s Preparing to unpack .../046-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 1881s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 1881s Selecting previously unselected package libxft2:s390x. 1881s Preparing to unpack .../047-libxft2_2.3.6-1build1_s390x.deb ... 1881s Unpacking libxft2:s390x (2.3.6-1build1) ... 1881s Selecting previously unselected package x11-common. 1881s Preparing to unpack .../048-x11-common_1%3a7.7+23ubuntu3_all.deb ... 1881s Unpacking x11-common (1:7.7+23ubuntu3) ... 1881s Selecting previously unselected package libxss1:s390x. 1881s Preparing to unpack .../049-libxss1_1%3a1.2.3-1build3_s390x.deb ... 1881s Unpacking libxss1:s390x (1:1.2.3-1build3) ... 1881s Selecting previously unselected package libtk8.6:s390x. 1881s Preparing to unpack .../050-libtk8.6_8.6.16-1_s390x.deb ... 1881s Unpacking libtk8.6:s390x (8.6.16-1) ... 1881s Selecting previously unselected package tk8.6-blt2.5. 1881s Preparing to unpack .../051-tk8.6-blt2.5_2.5.3+dfsg-8_s390x.deb ... 1881s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 1881s Selecting previously unselected package blt. 1881s Preparing to unpack .../052-blt_2.5.3+dfsg-8_s390x.deb ... 1881s Unpacking blt (2.5.3+dfsg-8) ... 1881s Selecting previously unselected package libdconf1:s390x. 1881s Preparing to unpack .../053-libdconf1_0.40.0-5_s390x.deb ... 1881s Unpacking libdconf1:s390x (0.40.0-5) ... 1881s Selecting previously unselected package dconf-service. 1881s Preparing to unpack .../054-dconf-service_0.40.0-5_s390x.deb ... 1881s Unpacking dconf-service (0.40.0-5) ... 1881s Selecting previously unselected package dconf-gsettings-backend:s390x. 1881s Preparing to unpack .../055-dconf-gsettings-backend_0.40.0-5_s390x.deb ... 1881s Unpacking dconf-gsettings-backend:s390x (0.40.0-5) ... 1881s Selecting previously unselected package fontconfig. 1881s Preparing to unpack .../056-fontconfig_2.15.0-2.1ubuntu1_s390x.deb ... 1881s Unpacking fontconfig (2.15.0-2.1ubuntu1) ... 1881s Selecting previously unselected package fonts-font-awesome. 1881s Preparing to unpack .../057-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 1881s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 1881s Selecting previously unselected package fonts-lyx. 1881s Preparing to unpack .../058-fonts-lyx_2.4.3-1_all.deb ... 1881s Unpacking fonts-lyx (2.4.3-1) ... 1881s Selecting previously unselected package libann-cctbx0. 1881s Preparing to unpack .../059-libann-cctbx0_1.1.2+doc-9build1_s390x.deb ... 1881s Unpacking libann-cctbx0 (1.1.2+doc-9build1) ... 1881s Selecting previously unselected package libann-cctbx-dev. 1881s Preparing to unpack .../060-libann-cctbx-dev_1.1.2+doc-9build1_s390x.deb ... 1881s Unpacking libann-cctbx-dev (1.1.2+doc-9build1) ... 1881s Selecting previously unselected package libantlr3c-3.4-0:s390x. 1881s Preparing to unpack .../061-libantlr3c-3.4-0_3.4+dfsg-4build2_s390x.deb ... 1881s Unpacking libantlr3c-3.4-0:s390x (3.4+dfsg-4build2) ... 1881s Selecting previously unselected package libasan8:s390x. 1881s Preparing to unpack .../062-libasan8_15-20250319-1ubuntu1_s390x.deb ... 1881s Unpacking libasan8:s390x (15-20250319-1ubuntu1) ... 1881s Selecting previously unselected package libatk1.0-0t64:s390x. 1881s Preparing to unpack .../063-libatk1.0-0t64_2.56.0-2_s390x.deb ... 1881s Unpacking libatk1.0-0t64:s390x (2.56.0-2) ... 1881s Selecting previously unselected package libxi6:s390x. 1881s Preparing to unpack .../064-libxi6_2%3a1.8.2-1_s390x.deb ... 1881s Unpacking libxi6:s390x (2:1.8.2-1) ... 1881s Selecting previously unselected package libatspi2.0-0t64:s390x. 1881s Preparing to unpack .../065-libatspi2.0-0t64_2.56.0-2_s390x.deb ... 1881s Unpacking libatspi2.0-0t64:s390x (2.56.0-2) ... 1881s Selecting previously unselected package libatk-bridge2.0-0t64:s390x. 1881s Preparing to unpack .../066-libatk-bridge2.0-0t64_2.56.0-2_s390x.deb ... 1881s Unpacking libatk-bridge2.0-0t64:s390x (2.56.0-2) ... 1881s Selecting previously unselected package libavahi-common-data:s390x. 1881s Preparing to unpack .../067-libavahi-common-data_0.8-16ubuntu2_s390x.deb ... 1881s Unpacking libavahi-common-data:s390x (0.8-16ubuntu2) ... 1881s Selecting previously unselected package libavahi-common3:s390x. 1881s Preparing to unpack .../068-libavahi-common3_0.8-16ubuntu2_s390x.deb ... 1881s Unpacking libavahi-common3:s390x (0.8-16ubuntu2) ... 1881s Selecting previously unselected package libavahi-client3:s390x. 1881s Preparing to unpack .../069-libavahi-client3_0.8-16ubuntu2_s390x.deb ... 1881s Unpacking libavahi-client3:s390x (0.8-16ubuntu2) ... 1881s Selecting previously unselected package libboost-python1.83.0. 1881s Preparing to unpack .../070-libboost-python1.83.0_1.83.0-4.1ubuntu2_s390x.deb ... 1881s Unpacking libboost-python1.83.0 (1.83.0-4.1ubuntu2) ... 1881s Selecting previously unselected package libboost-numpy1.83.0. 1881s Preparing to unpack .../071-libboost-numpy1.83.0_1.83.0-4.1ubuntu2_s390x.deb ... 1881s Unpacking libboost-numpy1.83.0 (1.83.0-4.1ubuntu2) ... 1881s Selecting previously unselected package libitm1:s390x. 1881s Preparing to unpack .../072-libitm1_15-20250319-1ubuntu1_s390x.deb ... 1881s Unpacking libitm1:s390x (15-20250319-1ubuntu1) ... 1881s Selecting previously unselected package libubsan1:s390x. 1881s Preparing to unpack .../073-libubsan1_15-20250319-1ubuntu1_s390x.deb ... 1881s Unpacking libubsan1:s390x (15-20250319-1ubuntu1) ... 1881s Selecting previously unselected package libgcc-14-dev:s390x. 1881s Preparing to unpack .../074-libgcc-14-dev_14.2.0-19ubuntu1_s390x.deb ... 1881s Unpacking libgcc-14-dev:s390x (14.2.0-19ubuntu1) ... 1881s Selecting previously unselected package libstdc++-14-dev:s390x. 1881s Preparing to unpack .../075-libstdc++-14-dev_14.2.0-19ubuntu1_s390x.deb ... 1881s Unpacking libstdc++-14-dev:s390x (14.2.0-19ubuntu1) ... 1881s Selecting previously unselected package libboost1.83-dev:s390x. 1881s Preparing to unpack .../076-libboost1.83-dev_1.83.0-4.1ubuntu2_s390x.deb ... 1881s Unpacking libboost1.83-dev:s390x (1.83.0-4.1ubuntu2) ... 1882s Selecting previously unselected package libexpat1-dev:s390x. 1882s Preparing to unpack .../077-libexpat1-dev_2.6.4-1_s390x.deb ... 1882s Unpacking libexpat1-dev:s390x (2.6.4-1) ... 1882s Selecting previously unselected package zlib1g-dev:s390x. 1882s Preparing to unpack .../078-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_s390x.deb ... 1882s Unpacking zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 1882s Selecting previously unselected package libpython3.13-dev:s390x. 1882s Preparing to unpack .../079-libpython3.13-dev_3.13.2-2_s390x.deb ... 1882s Unpacking libpython3.13-dev:s390x (3.13.2-2) ... 1882s Selecting previously unselected package libpython3-dev:s390x. 1882s Preparing to unpack .../080-libpython3-dev_3.13.2-2_s390x.deb ... 1882s Unpacking libpython3-dev:s390x (3.13.2-2) ... 1882s Selecting previously unselected package python3.13-dev. 1882s Preparing to unpack .../081-python3.13-dev_3.13.2-2_s390x.deb ... 1882s Unpacking python3.13-dev (3.13.2-2) ... 1882s Selecting previously unselected package libjs-jquery. 1882s Preparing to unpack .../082-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 1882s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 1882s Selecting previously unselected package libjs-underscore. 1882s Preparing to unpack .../083-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 1882s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 1882s Selecting previously unselected package libjs-sphinxdoc. 1882s Preparing to unpack .../084-libjs-sphinxdoc_8.1.3-5_all.deb ... 1882s Unpacking libjs-sphinxdoc (8.1.3-5) ... 1882s Selecting previously unselected package python3-dev. 1882s Preparing to unpack .../085-python3-dev_3.13.2-2_s390x.deb ... 1882s Unpacking python3-dev (3.13.2-2) ... 1882s Selecting previously unselected package libboost-python1.83-dev. 1882s Preparing to unpack .../086-libboost-python1.83-dev_1.83.0-4.1ubuntu2_s390x.deb ... 1882s Unpacking libboost-python1.83-dev (1.83.0-4.1ubuntu2) ... 1882s Selecting previously unselected package libboost-python-dev. 1882s Preparing to unpack .../087-libboost-python-dev_1.83.0.2ubuntu1_s390x.deb ... 1882s Unpacking libboost-python-dev (1.83.0.2ubuntu1) ... 1882s Selecting previously unselected package libboost-thread1.83.0:s390x. 1882s Preparing to unpack .../088-libboost-thread1.83.0_1.83.0-4.1ubuntu2_s390x.deb ... 1882s Unpacking libboost-thread1.83.0:s390x (1.83.0-4.1ubuntu2) ... 1882s Selecting previously unselected package libboost-timer1.83.0:s390x. 1882s Preparing to unpack .../089-libboost-timer1.83.0_1.83.0-4.1ubuntu2_s390x.deb ... 1882s Unpacking libboost-timer1.83.0:s390x (1.83.0-4.1ubuntu2) ... 1883s Selecting previously unselected package libpixman-1-0:s390x. 1883s Preparing to unpack .../090-libpixman-1-0_0.44.0-3_s390x.deb ... 1883s Unpacking libpixman-1-0:s390x (0.44.0-3) ... 1883s Selecting previously unselected package libxcb-render0:s390x. 1883s Preparing to unpack .../091-libxcb-render0_1.17.0-2_s390x.deb ... 1883s Unpacking libxcb-render0:s390x (1.17.0-2) ... 1883s Selecting previously unselected package libxcb-shm0:s390x. 1883s Preparing to unpack .../092-libxcb-shm0_1.17.0-2_s390x.deb ... 1883s Unpacking libxcb-shm0:s390x (1.17.0-2) ... 1883s Selecting previously unselected package libcairo2:s390x. 1883s Preparing to unpack .../093-libcairo2_1.18.4-1_s390x.deb ... 1883s Unpacking libcairo2:s390x (1.18.4-1) ... 1883s Selecting previously unselected package libcairo-gobject2:s390x. 1883s Preparing to unpack .../094-libcairo-gobject2_1.18.4-1_s390x.deb ... 1883s Unpacking libcairo-gobject2:s390x (1.18.4-1) ... 1883s Selecting previously unselected package libcbf1t64:s390x. 1883s Preparing to unpack .../095-libcbf1t64_0.9.7+dfsg1-5build1_s390x.deb ... 1883s Unpacking libcbf1t64:s390x (0.9.7+dfsg1-5build1) ... 1883s Selecting previously unselected package libccp4-data. 1883s Preparing to unpack .../096-libccp4-data_8.0.0-4_all.deb ... 1883s Unpacking libccp4-data (8.0.0-4) ... 1883s Selecting previously unselected package libccp4c0t64:s390x. 1883s Preparing to unpack .../097-libccp4c0t64_8.0.0-4_s390x.deb ... 1883s Unpacking libccp4c0t64:s390x (8.0.0-4) ... 1883s Selecting previously unselected package libmmdb2-0:s390x. 1883s Preparing to unpack .../098-libmmdb2-0_2.0.22-1_s390x.deb ... 1883s Unpacking libmmdb2-0:s390x (2.0.22-1) ... 1883s Selecting previously unselected package libccp4f0t64:s390x. 1883s Preparing to unpack .../099-libccp4f0t64_8.0.0-4_s390x.deb ... 1883s Unpacking libccp4f0t64:s390x (8.0.0-4) ... 1883s Selecting previously unselected package libccp4-dev:s390x. 1883s Preparing to unpack .../100-libccp4-dev_8.0.0-4_s390x.deb ... 1883s Unpacking libccp4-dev:s390x (8.0.0-4) ... 1883s Selecting previously unselected package libcctbx0. 1883s Preparing to unpack .../101-libcctbx0_2024.10+ds2+~3.22.1+ds1-4build2_s390x.deb ... 1883s Unpacking libcctbx0 (2024.10+ds2+~3.22.1+ds1-4build2) ... 1883s Selecting previously unselected package libcctbx-dev. 1883s Preparing to unpack .../102-libcctbx-dev_2024.10+ds2+~3.22.1+ds1-4build2_s390x.deb ... 1883s Unpacking libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4build2) ... 1883s Selecting previously unselected package liblcms2-2:s390x. 1883s Preparing to unpack .../103-liblcms2-2_2.16-2_s390x.deb ... 1883s Unpacking liblcms2-2:s390x (2.16-2) ... 1883s Selecting previously unselected package libcolord2:s390x. 1883s Preparing to unpack .../104-libcolord2_1.4.7-3_s390x.deb ... 1883s Unpacking libcolord2:s390x (1.4.7-3) ... 1883s Selecting previously unselected package libcups2t64:s390x. 1883s Preparing to unpack .../105-libcups2t64_2.4.11-0ubuntu2_s390x.deb ... 1883s Unpacking libcups2t64:s390x (2.4.11-0ubuntu2) ... 1883s Selecting previously unselected package libdatrie1:s390x. 1883s Preparing to unpack .../106-libdatrie1_0.2.13-3build1_s390x.deb ... 1883s Unpacking libdatrie1:s390x (0.2.13-3build1) ... 1883s Selecting previously unselected package libdouble-conversion3:s390x. 1883s Preparing to unpack .../107-libdouble-conversion3_3.3.1-1_s390x.deb ... 1883s Unpacking libdouble-conversion3:s390x (3.3.1-1) ... 1883s Selecting previously unselected package libwayland-server0:s390x. 1883s Preparing to unpack .../108-libwayland-server0_1.23.1-3_s390x.deb ... 1883s Unpacking libwayland-server0:s390x (1.23.1-3) ... 1883s Selecting previously unselected package libx11-xcb1:s390x. 1883s Preparing to unpack .../109-libx11-xcb1_2%3a1.8.10-2_s390x.deb ... 1883s Unpacking libx11-xcb1:s390x (2:1.8.10-2) ... 1883s Selecting previously unselected package libxcb-dri3-0:s390x. 1883s Preparing to unpack .../110-libxcb-dri3-0_1.17.0-2_s390x.deb ... 1883s Unpacking libxcb-dri3-0:s390x (1.17.0-2) ... 1883s Selecting previously unselected package libxcb-present0:s390x. 1883s Preparing to unpack .../111-libxcb-present0_1.17.0-2_s390x.deb ... 1883s Unpacking libxcb-present0:s390x (1.17.0-2) ... 1883s Selecting previously unselected package libxcb-randr0:s390x. 1883s Preparing to unpack .../112-libxcb-randr0_1.17.0-2_s390x.deb ... 1883s Unpacking libxcb-randr0:s390x (1.17.0-2) ... 1883s Selecting previously unselected package libxcb-sync1:s390x. 1883s Preparing to unpack .../113-libxcb-sync1_1.17.0-2_s390x.deb ... 1883s Unpacking libxcb-sync1:s390x (1.17.0-2) ... 1883s Selecting previously unselected package libxcb-xfixes0:s390x. 1883s Preparing to unpack .../114-libxcb-xfixes0_1.17.0-2_s390x.deb ... 1883s Unpacking libxcb-xfixes0:s390x (1.17.0-2) ... 1883s Selecting previously unselected package libxshmfence1:s390x. 1883s Preparing to unpack .../115-libxshmfence1_1.3-1build5_s390x.deb ... 1883s Unpacking libxshmfence1:s390x (1.3-1build5) ... 1883s Selecting previously unselected package mesa-libgallium:s390x. 1883s Preparing to unpack .../116-mesa-libgallium_25.0.1-2ubuntu2_s390x.deb ... 1883s Unpacking mesa-libgallium:s390x (25.0.1-2ubuntu2) ... 1883s Selecting previously unselected package libgbm1:s390x. 1883s Preparing to unpack .../117-libgbm1_25.0.1-2ubuntu2_s390x.deb ... 1883s Unpacking libgbm1:s390x (25.0.1-2ubuntu2) ... 1883s Selecting previously unselected package libwayland-client0:s390x. 1883s Preparing to unpack .../118-libwayland-client0_1.23.1-3_s390x.deb ... 1883s Unpacking libwayland-client0:s390x (1.23.1-3) ... 1883s Selecting previously unselected package libegl-mesa0:s390x. 1883s Preparing to unpack .../119-libegl-mesa0_25.0.1-2ubuntu2_s390x.deb ... 1883s Unpacking libegl-mesa0:s390x (25.0.1-2ubuntu2) ... 1883s Selecting previously unselected package libepoxy0:s390x. 1883s Preparing to unpack .../120-libepoxy0_1.5.10-2_s390x.deb ... 1883s Unpacking libepoxy0:s390x (1.5.10-2) ... 1883s Selecting previously unselected package libvulkan1:s390x. 1883s Preparing to unpack .../121-libvulkan1_1.4.304.0-1_s390x.deb ... 1883s Unpacking libvulkan1:s390x (1.4.304.0-1) ... 1883s Selecting previously unselected package libgl1-mesa-dri:s390x. 1883s Preparing to unpack .../122-libgl1-mesa-dri_25.0.1-2ubuntu2_s390x.deb ... 1883s Unpacking libgl1-mesa-dri:s390x (25.0.1-2ubuntu2) ... 1883s Selecting previously unselected package libglvnd0:s390x. 1883s Preparing to unpack .../123-libglvnd0_1.7.0-1build1_s390x.deb ... 1883s Unpacking libglvnd0:s390x (1.7.0-1build1) ... 1883s Selecting previously unselected package libxcb-glx0:s390x. 1883s Preparing to unpack .../124-libxcb-glx0_1.17.0-2_s390x.deb ... 1883s Unpacking libxcb-glx0:s390x (1.17.0-2) ... 1883s Selecting previously unselected package libxxf86vm1:s390x. 1883s Preparing to unpack .../125-libxxf86vm1_1%3a1.1.4-1build4_s390x.deb ... 1883s Unpacking libxxf86vm1:s390x (1:1.1.4-1build4) ... 1883s Selecting previously unselected package libglx-mesa0:s390x. 1883s Preparing to unpack .../126-libglx-mesa0_25.0.1-2ubuntu2_s390x.deb ... 1883s Unpacking libglx-mesa0:s390x (25.0.1-2ubuntu2) ... 1883s Selecting previously unselected package libglx0:s390x. 1883s Preparing to unpack .../127-libglx0_1.7.0-1build1_s390x.deb ... 1883s Unpacking libglx0:s390x (1.7.0-1build1) ... 1883s Selecting previously unselected package libgl1:s390x. 1883s Preparing to unpack .../128-libgl1_1.7.0-1build1_s390x.deb ... 1883s Unpacking libgl1:s390x (1.7.0-1build1) ... 1883s Selecting previously unselected package libglew2.2:s390x. 1883s Preparing to unpack .../129-libglew2.2_2.2.0-4build1_s390x.deb ... 1883s Unpacking libglew2.2:s390x (2.2.0-4build1) ... 1883s Selecting previously unselected package libglut3.12:s390x. 1883s Preparing to unpack .../130-libglut3.12_3.4.0-4_s390x.deb ... 1883s Unpacking libglut3.12:s390x (3.4.0-4) ... 1883s Selecting previously unselected package libgraphite2-3:s390x. 1883s Preparing to unpack .../131-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 1883s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 1883s Selecting previously unselected package libharfbuzz0b:s390x. 1883s Preparing to unpack .../132-libharfbuzz0b_10.2.0-1_s390x.deb ... 1883s Unpacking libharfbuzz0b:s390x (10.2.0-1) ... 1883s Selecting previously unselected package libthai-data. 1883s Preparing to unpack .../133-libthai-data_0.1.29-2build1_all.deb ... 1883s Unpacking libthai-data (0.1.29-2build1) ... 1883s Selecting previously unselected package libthai0:s390x. 1883s Preparing to unpack .../134-libthai0_0.1.29-2build1_s390x.deb ... 1883s Unpacking libthai0:s390x (0.1.29-2build1) ... 1883s Selecting previously unselected package libpango-1.0-0:s390x. 1883s Preparing to unpack .../135-libpango-1.0-0_1.56.3-1_s390x.deb ... 1883s Unpacking libpango-1.0-0:s390x (1.56.3-1) ... 1883s Selecting previously unselected package libpangoft2-1.0-0:s390x. 1883s Preparing to unpack .../136-libpangoft2-1.0-0_1.56.3-1_s390x.deb ... 1883s Unpacking libpangoft2-1.0-0:s390x (1.56.3-1) ... 1883s Selecting previously unselected package libpangocairo-1.0-0:s390x. 1883s Preparing to unpack .../137-libpangocairo-1.0-0_1.56.3-1_s390x.deb ... 1883s Unpacking libpangocairo-1.0-0:s390x (1.56.3-1) ... 1883s Selecting previously unselected package libwayland-cursor0:s390x. 1883s Preparing to unpack .../138-libwayland-cursor0_1.23.1-3_s390x.deb ... 1883s Unpacking libwayland-cursor0:s390x (1.23.1-3) ... 1883s Selecting previously unselected package libwayland-egl1:s390x. 1883s Preparing to unpack .../139-libwayland-egl1_1.23.1-3_s390x.deb ... 1883s Unpacking libwayland-egl1:s390x (1.23.1-3) ... 1883s Selecting previously unselected package libxcomposite1:s390x. 1883s Preparing to unpack .../140-libxcomposite1_1%3a0.4.6-1_s390x.deb ... 1883s Unpacking libxcomposite1:s390x (1:0.4.6-1) ... 1883s Selecting previously unselected package libxfixes3:s390x. 1883s Preparing to unpack .../141-libxfixes3_1%3a6.0.0-2build1_s390x.deb ... 1883s Unpacking libxfixes3:s390x (1:6.0.0-2build1) ... 1883s Selecting previously unselected package libxcursor1:s390x. 1883s Preparing to unpack .../142-libxcursor1_1%3a1.2.3-1_s390x.deb ... 1883s Unpacking libxcursor1:s390x (1:1.2.3-1) ... 1883s Selecting previously unselected package libxdamage1:s390x. 1883s Preparing to unpack .../143-libxdamage1_1%3a1.1.6-1build1_s390x.deb ... 1883s Unpacking libxdamage1:s390x (1:1.1.6-1build1) ... 1883s Selecting previously unselected package libxinerama1:s390x. 1883s Preparing to unpack .../144-libxinerama1_2%3a1.1.4-3build1_s390x.deb ... 1883s Unpacking libxinerama1:s390x (2:1.1.4-3build1) ... 1883s Selecting previously unselected package libxrandr2:s390x. 1883s Preparing to unpack .../145-libxrandr2_2%3a1.5.4-1_s390x.deb ... 1883s Unpacking libxrandr2:s390x (2:1.5.4-1) ... 1883s Selecting previously unselected package libgtk-3-common. 1883s Preparing to unpack .../146-libgtk-3-common_3.24.49-2ubuntu1_all.deb ... 1883s Unpacking libgtk-3-common (3.24.49-2ubuntu1) ... 1884s Selecting previously unselected package libgtk-3-0t64:s390x. 1884s Preparing to unpack .../147-libgtk-3-0t64_3.24.49-2ubuntu1_s390x.deb ... 1884s Unpacking libgtk-3-0t64:s390x (3.24.49-2ubuntu1) ... 1884s Selecting previously unselected package libice6:s390x. 1884s Preparing to unpack .../148-libice6_2%3a1.1.1-1_s390x.deb ... 1884s Unpacking libice6:s390x (2:1.1.1-1) ... 1884s Selecting previously unselected package libimagequant0:s390x. 1884s Preparing to unpack .../149-libimagequant0_2.18.0-1build1_s390x.deb ... 1884s Unpacking libimagequant0:s390x (2.18.0-1build1) ... 1884s Selecting previously unselected package libwacom-common. 1884s Preparing to unpack .../150-libwacom-common_2.14.0-1_all.deb ... 1884s Unpacking libwacom-common (2.14.0-1) ... 1884s Selecting previously unselected package libwacom9:s390x. 1884s Preparing to unpack .../151-libwacom9_2.14.0-1_s390x.deb ... 1884s Unpacking libwacom9:s390x (2.14.0-1) ... 1884s Selecting previously unselected package libinput-bin. 1884s Preparing to unpack .../152-libinput-bin_1.27.1-1_s390x.deb ... 1884s Unpacking libinput-bin (1.27.1-1) ... 1884s Selecting previously unselected package libmtdev1t64:s390x. 1884s Preparing to unpack .../153-libmtdev1t64_1.1.7-1_s390x.deb ... 1884s Unpacking libmtdev1t64:s390x (1.1.7-1) ... 1884s Selecting previously unselected package libinput10:s390x. 1884s Preparing to unpack .../154-libinput10_1.27.1-1_s390x.deb ... 1884s Unpacking libinput10:s390x (1.27.1-1) ... 1884s Selecting previously unselected package libjs-jquery-ui. 1884s Preparing to unpack .../155-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 1884s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 1884s Selecting previously unselected package liblbfgsb0:s390x. 1884s Preparing to unpack .../156-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 1884s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 1884s Selecting previously unselected package libmd4c0:s390x. 1884s Preparing to unpack .../157-libmd4c0_0.5.2-2_s390x.deb ... 1884s Unpacking libmd4c0:s390x (0.5.2-2) ... 1884s Selecting previously unselected package libnetcdf22:s390x. 1884s Preparing to unpack .../158-libnetcdf22_1%3a4.9.3-1_s390x.deb ... 1884s Unpacking libnetcdf22:s390x (1:4.9.3-1) ... 1884s Selecting previously unselected package libnotify4:s390x. 1884s Preparing to unpack .../159-libnotify4_0.8.4-1_s390x.deb ... 1884s Unpacking libnotify4:s390x (0.8.4-1) ... 1884s Selecting previously unselected package libpcre2-16-0:s390x. 1884s Preparing to unpack .../160-libpcre2-16-0_10.45-1_s390x.deb ... 1884s Unpacking libpcre2-16-0:s390x (10.45-1) ... 1884s Selecting previously unselected package libpcre2-32-0:s390x. 1884s Preparing to unpack .../161-libpcre2-32-0_10.45-1_s390x.deb ... 1884s Unpacking libpcre2-32-0:s390x (10.45-1) ... 1884s Selecting previously unselected package libqhull-r8.0:s390x. 1884s Preparing to unpack .../162-libqhull-r8.0_2020.2-6build1_s390x.deb ... 1884s Unpacking libqhull-r8.0:s390x (2020.2-6build1) ... 1884s Selecting previously unselected package libqt5core5t64:s390x. 1884s Preparing to unpack .../163-libqt5core5t64_5.15.15+dfsg-4ubuntu1_s390x.deb ... 1884s Unpacking libqt5core5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 1884s Selecting previously unselected package libqt5dbus5t64:s390x. 1884s Preparing to unpack .../164-libqt5dbus5t64_5.15.15+dfsg-4ubuntu1_s390x.deb ... 1884s Unpacking libqt5dbus5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 1884s Selecting previously unselected package libegl1:s390x. 1884s Preparing to unpack .../165-libegl1_1.7.0-1build1_s390x.deb ... 1884s Unpacking libegl1:s390x (1.7.0-1build1) ... 1884s Selecting previously unselected package libqt5network5t64:s390x. 1884s Preparing to unpack .../166-libqt5network5t64_5.15.15+dfsg-4ubuntu1_s390x.deb ... 1884s Unpacking libqt5network5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 1884s Selecting previously unselected package libsm6:s390x. 1884s Preparing to unpack .../167-libsm6_2%3a1.2.4-1_s390x.deb ... 1884s Unpacking libsm6:s390x (2:1.2.4-1) ... 1884s Selecting previously unselected package libxcb-icccm4:s390x. 1884s Preparing to unpack .../168-libxcb-icccm4_0.4.2-1_s390x.deb ... 1884s Unpacking libxcb-icccm4:s390x (0.4.2-1) ... 1884s Selecting previously unselected package libxcb-util1:s390x. 1884s Preparing to unpack .../169-libxcb-util1_0.4.1-1_s390x.deb ... 1884s Unpacking libxcb-util1:s390x (0.4.1-1) ... 1884s Selecting previously unselected package libxcb-image0:s390x. 1884s Preparing to unpack .../170-libxcb-image0_0.4.0-2build1_s390x.deb ... 1884s Unpacking libxcb-image0:s390x (0.4.0-2build1) ... 1884s Selecting previously unselected package libxcb-keysyms1:s390x. 1884s Preparing to unpack .../171-libxcb-keysyms1_0.4.1-1_s390x.deb ... 1884s Unpacking libxcb-keysyms1:s390x (0.4.1-1) ... 1884s Selecting previously unselected package libxcb-render-util0:s390x. 1884s Preparing to unpack .../172-libxcb-render-util0_0.3.10-1_s390x.deb ... 1884s Unpacking libxcb-render-util0:s390x (0.3.10-1) ... 1884s Selecting previously unselected package libxcb-shape0:s390x. 1884s Preparing to unpack .../173-libxcb-shape0_1.17.0-2_s390x.deb ... 1884s Unpacking libxcb-shape0:s390x (1.17.0-2) ... 1884s Selecting previously unselected package libxcb-xinerama0:s390x. 1884s Preparing to unpack .../174-libxcb-xinerama0_1.17.0-2_s390x.deb ... 1884s Unpacking libxcb-xinerama0:s390x (1.17.0-2) ... 1884s Selecting previously unselected package libxcb-xinput0:s390x. 1884s Preparing to unpack .../175-libxcb-xinput0_1.17.0-2_s390x.deb ... 1884s Unpacking libxcb-xinput0:s390x (1.17.0-2) ... 1884s Selecting previously unselected package libxcb-xkb1:s390x. 1884s Preparing to unpack .../176-libxcb-xkb1_1.17.0-2_s390x.deb ... 1884s Unpacking libxcb-xkb1:s390x (1.17.0-2) ... 1884s Selecting previously unselected package libxkbcommon-x11-0:s390x. 1884s Preparing to unpack .../177-libxkbcommon-x11-0_1.7.0-2_s390x.deb ... 1884s Unpacking libxkbcommon-x11-0:s390x (1.7.0-2) ... 1884s Selecting previously unselected package libqt5gui5t64:s390x. 1884s Preparing to unpack .../178-libqt5gui5t64_5.15.15+dfsg-4ubuntu1_s390x.deb ... 1884s Unpacking libqt5gui5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 1884s Selecting previously unselected package libqt5widgets5t64:s390x. 1884s Preparing to unpack .../179-libqt5widgets5t64_5.15.15+dfsg-4ubuntu1_s390x.deb ... 1884s Unpacking libqt5widgets5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 1884s Selecting previously unselected package libqt5xml5t64:s390x. 1884s Preparing to unpack .../180-libqt5xml5t64_5.15.15+dfsg-4ubuntu1_s390x.deb ... 1884s Unpacking libqt5xml5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 1884s Selecting previously unselected package libqt5designer5:s390x. 1884s Preparing to unpack .../181-libqt5designer5_5.15.15-6build1_s390x.deb ... 1884s Unpacking libqt5designer5:s390x (5.15.15-6build1) ... 1884s Selecting previously unselected package libqt5sql5t64:s390x. 1884s Preparing to unpack .../182-libqt5sql5t64_5.15.15+dfsg-4ubuntu1_s390x.deb ... 1884s Unpacking libqt5sql5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 1884s Selecting previously unselected package libqt5help5:s390x. 1884s Preparing to unpack .../183-libqt5help5_5.15.15-6build1_s390x.deb ... 1884s Unpacking libqt5help5:s390x (5.15.15-6build1) ... 1884s Selecting previously unselected package libqt5opengl5t64:s390x. 1884s Preparing to unpack .../184-libqt5opengl5t64_5.15.15+dfsg-4ubuntu1_s390x.deb ... 1884s Unpacking libqt5opengl5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 1884s Selecting previously unselected package libqt5printsupport5t64:s390x. 1884s Preparing to unpack .../185-libqt5printsupport5t64_5.15.15+dfsg-4ubuntu1_s390x.deb ... 1884s Unpacking libqt5printsupport5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 1884s Selecting previously unselected package libqt5test5t64:s390x. 1884s Preparing to unpack .../186-libqt5test5t64_5.15.15+dfsg-4ubuntu1_s390x.deb ... 1884s Unpacking libqt5test5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 1884s Selecting previously unselected package libraqm0:s390x. 1884s Preparing to unpack .../187-libraqm0_0.10.2-1_s390x.deb ... 1884s Unpacking libraqm0:s390x (0.10.2-1) ... 1884s Selecting previously unselected package libssm2:s390x. 1884s Preparing to unpack .../188-libssm2_1.4.0-2build1_s390x.deb ... 1884s Unpacking libssm2:s390x (1.4.0-2build1) ... 1884s Selecting previously unselected package libwebpdemux2:s390x. 1884s Preparing to unpack .../189-libwebpdemux2_1.5.0-0.1_s390x.deb ... 1884s Unpacking libwebpdemux2:s390x (1.5.0-0.1) ... 1884s Selecting previously unselected package libwebpmux3:s390x. 1884s Preparing to unpack .../190-libwebpmux3_1.5.0-0.1_s390x.deb ... 1884s Unpacking libwebpmux3:s390x (1.5.0-0.1) ... 1884s Selecting previously unselected package libwxbase3.2-1t64:s390x. 1884s Preparing to unpack .../191-libwxbase3.2-1t64_3.2.6+dfsg-2ubuntu1_s390x.deb ... 1884s Unpacking libwxbase3.2-1t64:s390x (3.2.6+dfsg-2ubuntu1) ... 1884s Selecting previously unselected package libxtst6:s390x. 1884s Preparing to unpack .../192-libxtst6_2%3a1.2.5-1_s390x.deb ... 1884s Unpacking libxtst6:s390x (2:1.2.5-1) ... 1884s Selecting previously unselected package libwxgtk3.2-1t64:s390x. 1884s Preparing to unpack .../193-libwxgtk3.2-1t64_3.2.6+dfsg-2ubuntu1_s390x.deb ... 1884s Unpacking libwxgtk3.2-1t64:s390x (3.2.6+dfsg-2ubuntu1) ... 1885s Selecting previously unselected package libwxgtk-gl3.2-1t64:s390x. 1885s Preparing to unpack .../194-libwxgtk-gl3.2-1t64_3.2.6+dfsg-2ubuntu1_s390x.deb ... 1885s Unpacking libwxgtk-gl3.2-1t64:s390x (3.2.6+dfsg-2ubuntu1) ... 1885s Selecting previously unselected package libxslt1.1:s390x. 1885s Preparing to unpack .../195-libxslt1.1_1.1.39-0exp1ubuntu4_s390x.deb ... 1885s Unpacking libxslt1.1:s390x (1.1.39-0exp1ubuntu4) ... 1885s Selecting previously unselected package pymol-data. 1885s Preparing to unpack .../196-pymol-data_3.1.0+dfsg-1_all.deb ... 1885s Unpacking pymol-data (3.1.0+dfsg-1) ... 1885s Selecting previously unselected package python-matplotlib-data. 1885s Preparing to unpack .../197-python-matplotlib-data_3.8.3-7build1_all.deb ... 1885s Unpacking python-matplotlib-data (3.8.3-7build1) ... 1885s Selecting previously unselected package python3-all. 1885s Preparing to unpack .../198-python3-all_3.13.2-2_s390x.deb ... 1885s Unpacking python3-all (3.13.2-2) ... 1885s Selecting previously unselected package python3-brotli. 1885s Preparing to unpack .../199-python3-brotli_1.1.0-2build4_s390x.deb ... 1885s Unpacking python3-brotli (1.1.0-2build4) ... 1885s Selecting previously unselected package python3-legacy-cgi. 1885s Preparing to unpack .../200-python3-legacy-cgi_2.6.2-1_all.deb ... 1885s Unpacking python3-legacy-cgi (2.6.2-1) ... 1885s Selecting previously unselected package python3-pycbf. 1885s Preparing to unpack .../201-python3-pycbf_0.9.7+dfsg1-5build1_s390x.deb ... 1885s Unpacking python3-pycbf (0.9.7+dfsg1-5build1) ... 1885s Selecting previously unselected package python3-hdf5plugin. 1885s Preparing to unpack .../202-python3-hdf5plugin_5.0.0-1_all.deb ... 1885s Unpacking python3-hdf5plugin (5.0.0-1) ... 1885s Selecting previously unselected package python3-dateutil. 1885s Preparing to unpack .../203-python3-dateutil_2.9.0-4_all.deb ... 1885s Unpacking python3-dateutil (2.9.0-4) ... 1885s Selecting previously unselected package libopenjp2-7:s390x. 1885s Preparing to unpack .../204-libopenjp2-7_2.5.3-2_s390x.deb ... 1885s Unpacking libopenjp2-7:s390x (2.5.3-2) ... 1885s Selecting previously unselected package python3-pil:s390x. 1885s Preparing to unpack .../205-python3-pil_11.1.0-5build1_s390x.deb ... 1885s Unpacking python3-pil:s390x (11.1.0-5build1) ... 1885s Selecting previously unselected package python3.13-tk. 1885s Preparing to unpack .../206-python3.13-tk_3.13.2-2_s390x.deb ... 1885s Unpacking python3.13-tk (3.13.2-2) ... 1885s Selecting previously unselected package python3-tk:s390x. 1885s Preparing to unpack .../207-python3-tk_3.13.2-1_s390x.deb ... 1885s Unpacking python3-tk:s390x (3.13.2-1) ... 1885s Selecting previously unselected package python3-pil.imagetk:s390x. 1885s Preparing to unpack .../208-python3-pil.imagetk_11.1.0-5build1_s390x.deb ... 1885s Unpacking python3-pil.imagetk:s390x (11.1.0-5build1) ... 1885s Selecting previously unselected package python3-contourpy. 1885s Preparing to unpack .../209-python3-contourpy_1.3.1-1build1_s390x.deb ... 1885s Unpacking python3-contourpy (1.3.1-1build1) ... 1885s Selecting previously unselected package python3-cycler. 1885s Preparing to unpack .../210-python3-cycler_0.12.1-1_all.deb ... 1885s Unpacking python3-cycler (0.12.1-1) ... 1885s Selecting previously unselected package python3-platformdirs. 1885s Preparing to unpack .../211-python3-platformdirs_4.3.6-1_all.deb ... 1885s Unpacking python3-platformdirs (4.3.6-1) ... 1885s Selecting previously unselected package python3-fs. 1885s Preparing to unpack .../212-python3-fs_2.4.16-7_all.deb ... 1885s Unpacking python3-fs (2.4.16-7) ... 1885s Selecting previously unselected package python3-lxml:s390x. 1885s Preparing to unpack .../213-python3-lxml_5.3.1-1build1_s390x.deb ... 1885s Unpacking python3-lxml:s390x (5.3.1-1build1) ... 1885s Selecting previously unselected package python3-lz4. 1885s Preparing to unpack .../214-python3-lz4_4.4.0+dfsg-1build1_s390x.deb ... 1885s Unpacking python3-lz4 (4.4.0+dfsg-1build1) ... 1885s Selecting previously unselected package python3-decorator. 1885s Preparing to unpack .../215-python3-decorator_5.1.1-5_all.deb ... 1885s Unpacking python3-decorator (5.1.1-5) ... 1885s Selecting previously unselected package python3-scipy. 1885s Preparing to unpack .../216-python3-scipy_1.14.1-4ubuntu2_s390x.deb ... 1885s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 1885s Selecting previously unselected package python3-mpmath. 1885s Preparing to unpack .../217-python3-mpmath_1.3.0-1_all.deb ... 1885s Unpacking python3-mpmath (1.3.0-1) ... 1885s Selecting previously unselected package python3-sympy. 1885s Preparing to unpack .../218-python3-sympy_1.13.3-5_all.deb ... 1885s Unpacking python3-sympy (1.13.3-5) ... 1885s Selecting previously unselected package python3-ufolib2. 1885s Preparing to unpack .../219-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 1885s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 1886s Selecting previously unselected package unicode-data. 1886s Preparing to unpack .../220-unicode-data_15.1.0-1_all.deb ... 1886s Unpacking unicode-data (15.1.0-1) ... 1886s Selecting previously unselected package python3-fonttools. 1886s Preparing to unpack .../221-python3-fonttools_4.55.3-2build1_s390x.deb ... 1886s Unpacking python3-fonttools (4.55.3-2build1) ... 1886s Selecting previously unselected package python3-importlib-resources. 1886s Preparing to unpack .../222-python3-importlib-resources_6.5.2-1_all.deb ... 1886s Unpacking python3-importlib-resources (6.5.2-1) ... 1886s Selecting previously unselected package python3-kiwisolver. 1886s Preparing to unpack .../223-python3-kiwisolver_1.4.7-3build1_s390x.deb ... 1886s Unpacking python3-kiwisolver (1.4.7-3build1) ... 1886s Selecting previously unselected package python3-packaging. 1886s Preparing to unpack .../224-python3-packaging_24.2-1_all.deb ... 1886s Unpacking python3-packaging (24.2-1) ... 1886s Selecting previously unselected package python3-matplotlib. 1886s Preparing to unpack .../225-python3-matplotlib_3.8.3-7build1_s390x.deb ... 1886s Unpacking python3-matplotlib (3.8.3-7build1) ... 1886s Selecting previously unselected package sphinx-rtd-theme-common. 1886s Preparing to unpack .../226-sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb ... 1886s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 1886s Selecting previously unselected package python3-mrcfile. 1886s Preparing to unpack .../227-python3-mrcfile_1.5.4-2_all.deb ... 1886s Unpacking python3-mrcfile (1.5.4-2) ... 1886s Selecting previously unselected package python3-natsort. 1886s Preparing to unpack .../228-python3-natsort_8.0.2-2_all.deb ... 1886s Unpacking python3-natsort (8.0.2-2) ... 1886s Selecting previously unselected package python3-flexcache. 1886s Preparing to unpack .../229-python3-flexcache_0.3-2_all.deb ... 1886s Unpacking python3-flexcache (0.3-2) ... 1886s Selecting previously unselected package python3-flexparser. 1886s Preparing to unpack .../230-python3-flexparser_0.4-1_all.deb ... 1886s Unpacking python3-flexparser (0.4-1) ... 1886s Selecting previously unselected package python3-pint. 1886s Preparing to unpack .../231-python3-pint_0.24.4-1_all.deb ... 1886s Unpacking python3-pint (0.24.4-1) ... 1886s Selecting previously unselected package python3-nxmx. 1886s Preparing to unpack .../232-python3-nxmx_0.0.4-1_all.deb ... 1886s Unpacking python3-nxmx (0.0.4-1) ... 1886s Selecting previously unselected package python3-ordered-set. 1886s Preparing to unpack .../233-python3-ordered-set_4.1.0-1_all.deb ... 1886s Unpacking python3-ordered-set (4.1.0-1) ... 1886s Selecting previously unselected package python3-procrunner. 1886s Preparing to unpack .../234-python3-procrunner_2.3.3-2_all.deb ... 1886s Unpacking python3-procrunner (2.3.3-2) ... 1886s Selecting previously unselected package libopengl0:s390x. 1886s Preparing to unpack .../235-libopengl0_1.7.0-1build1_s390x.deb ... 1886s Unpacking libopengl0:s390x (1.7.0-1build1) ... 1886s Selecting previously unselected package libglu1-mesa:s390x. 1886s Preparing to unpack .../236-libglu1-mesa_9.0.2-1.1build1_s390x.deb ... 1886s Unpacking libglu1-mesa:s390x (9.0.2-1.1build1) ... 1886s Selecting previously unselected package python3-opengl. 1886s Preparing to unpack .../237-python3-opengl_3.1.9+dfsg-1syncable1_all.deb ... 1886s Unpacking python3-opengl (3.1.9+dfsg-1syncable1) ... 1886s Selecting previously unselected package python3-pyqt5.sip. 1886s Preparing to unpack .../238-python3-pyqt5.sip_12.17.0-1build1_s390x.deb ... 1886s Unpacking python3-pyqt5.sip (12.17.0-1build1) ... 1886s Selecting previously unselected package python3-pyqt5. 1886s Preparing to unpack .../239-python3-pyqt5_5.15.11+dfsg-2_s390x.deb ... 1886s Unpacking python3-pyqt5 (5.15.11+dfsg-2) ... 1886s Selecting previously unselected package python3-pyqt5.qtopengl. 1886s Preparing to unpack .../240-python3-pyqt5.qtopengl_5.15.11+dfsg-2_s390x.deb ... 1886s Unpacking python3-pyqt5.qtopengl (5.15.11+dfsg-2) ... 1886s Selecting previously unselected package python3-pymol. 1886s Preparing to unpack .../241-python3-pymol_3.1.0+dfsg-1_s390x.deb ... 1886s Unpacking python3-pymol (3.1.0+dfsg-1) ... 1887s Selecting previously unselected package python3-six. 1887s Preparing to unpack .../242-python3-six_1.17.0-1_all.deb ... 1887s Unpacking python3-six (1.17.0-1) ... 1887s Selecting previously unselected package python3-tqdm. 1887s Preparing to unpack .../243-python3-tqdm_4.67.1-2_all.deb ... 1887s Unpacking python3-tqdm (4.67.1-2) ... 1887s Selecting previously unselected package python3-wxgtk4.0. 1887s Preparing to unpack .../244-python3-wxgtk4.0_4.2.2+dfsg-3build1_s390x.deb ... 1887s Unpacking python3-wxgtk4.0 (4.2.2+dfsg-3build1) ... 1887s Selecting previously unselected package python3-cctbx. 1887s Preparing to unpack .../245-python3-cctbx_2024.10+ds2+~3.22.1+ds1-4build2_s390x.deb ... 1887s Unpacking python3-cctbx (2024.10+ds2+~3.22.1+ds1-4build2) ... 1888s Selecting previously unselected package python3-iniconfig. 1888s Preparing to unpack .../246-python3-iniconfig_1.1.1-2_all.deb ... 1888s Unpacking python3-iniconfig (1.1.1-2) ... 1888s Selecting previously unselected package python3-pluggy. 1888s Preparing to unpack .../247-python3-pluggy_1.5.0-1_all.deb ... 1888s Unpacking python3-pluggy (1.5.0-1) ... 1888s Selecting previously unselected package python3-pytest. 1888s Preparing to unpack .../248-python3-pytest_8.3.5-1_all.deb ... 1888s Unpacking python3-pytest (8.3.5-1) ... 1888s Selecting previously unselected package python3-dials-data. 1888s Preparing to unpack .../249-python3-dials-data_2.4.0-2_all.deb ... 1888s Unpacking python3-dials-data (2.4.0-2) ... 1888s Selecting previously unselected package python3-pytest-datadir. 1888s Preparing to unpack .../250-python3-pytest-datadir_1.4.1+ds-1_all.deb ... 1888s Unpacking python3-pytest-datadir (1.4.1+ds-1) ... 1888s Selecting previously unselected package python3-pytest-mock. 1888s Preparing to unpack .../251-python3-pytest-mock_3.14.0-2_all.deb ... 1888s Unpacking python3-pytest-mock (3.14.0-2) ... 1888s Selecting previously unselected package python3-pytest-regressions. 1888s Preparing to unpack .../252-python3-pytest-regressions_2.5.0+ds-2_all.deb ... 1888s Unpacking python3-pytest-regressions (2.5.0+ds-2) ... 1888s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 1888s Setting up libboost-python1.83.0 (1.83.0-4.1ubuntu2) ... 1888s Setting up libxcb-dri3-0:s390x (1.17.0-2) ... 1888s Setting up liblcms2-2:s390x (2.16-2) ... 1888s Setting up python3-iniconfig (1.1.1-2) ... 1888s Setting up libpixman-1-0:s390x (0.44.0-3) ... 1888s Setting up libsharpyuv0:s390x (1.5.0-0.1) ... 1888s Setting up libwayland-server0:s390x (1.23.1-3) ... 1888s Setting up libx11-xcb1:s390x (2:1.8.10-2) ... 1888s Setting up libpciaccess0:s390x (0.17-3build1) ... 1888s Setting up libdouble-conversion3:s390x (3.3.1-1) ... 1888s Setting up fonts-lato (2.015-1) ... 1888s Setting up libxdamage1:s390x (1:1.1.6-1build1) ... 1888s Setting up libxcb-xfixes0:s390x (1.17.0-2) ... 1888s Setting up libantlr3c-3.4-0:s390x (3.4+dfsg-4build2) ... 1888s Setting up hicolor-icon-theme (0.18-2) ... 1888s Setting up libxi6:s390x (2:1.8.2-1) ... 1888s Setting up libxcb-xinput0:s390x (1.17.0-2) ... 1888s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ... 1888s Setting up libdatrie1:s390x (0.2.13-3build1) ... 1888s Setting up python3-importlib-resources (6.5.2-1) ... 1888s Setting up libmmdb2-0:s390x (2.0.22-1) ... 1888s Setting up libboost-timer1.83.0:s390x (1.83.0-4.1ubuntu2) ... 1888s Setting up python3-lz4 (4.4.0+dfsg-1build1) ... 1888s Setting up libxcb-render0:s390x (1.17.0-2) ... 1888s Setting up libevent-pthreads-2.1-7t64:s390x (2.1.12-stable-10) ... 1888s Setting up libglvnd0:s390x (1.7.0-1build1) ... 1888s Setting up fonts-lyx (2.4.3-1) ... 1888s Setting up libxcb-glx0:s390x (1.17.0-2) ... 1888s Setting up python3-tqdm (4.67.1-2) ... 1888s Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... 1888s Setting up libxcb-keysyms1:s390x (0.4.1-1) ... 1888s Setting up libxcb-shape0:s390x (1.17.0-2) ... 1888s Setting up x11-common (1:7.7+23ubuntu3) ... 1888s Setting up libdeflate0:s390x (1.23-1) ... 1888s Setting up libboost-thread1.83.0:s390x (1.83.0-4.1ubuntu2) ... 1888s Setting up libqhull-r8.0:s390x (2020.2-6build1) ... 1888s Setting up libxcb-render-util0:s390x (0.3.10-1) ... 1888s Setting up python3-all (3.13.2-2) ... 1888s Setting up python3-ordered-set (4.1.0-1) ... 1888s Setting up libxcb-shm0:s390x (1.17.0-2) ... 1888s Setting up libxcb-icccm4:s390x (0.4.2-1) ... 1888s Setting up libccp4-data (8.0.0-4) ... 1888s Setting up libgomp1:s390x (15-20250319-1ubuntu1) ... 1888s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 1888s Setting up libpcre2-16-0:s390x (10.45-1) ... 1888s Setting up libaec0:s390x (1.1.3-1) ... 1888s Setting up libcolord2:s390x (1.4.7-3) ... 1888s Setting up python3-platformdirs (4.3.6-1) ... 1889s Setting up libopengl0:s390x (1.7.0-1build1) ... 1889s Setting up python3-natsort (8.0.2-2) ... 1889s Setting up libxcb-util1:s390x (0.4.1-1) ... 1889s Setting up libxxf86vm1:s390x (1:1.1.4-1build4) ... 1889s Setting up libxcb-xkb1:s390x (1.17.0-2) ... 1889s Setting up libxcb-image0:s390x (0.4.0-2build1) ... 1889s Setting up python3-fs (2.4.16-7) ... 1889s Setting up libxnvctrl0:s390x (510.47.03-0ubuntu4) ... 1889s Setting up libxcb-present0:s390x (1.17.0-2) ... 1889s Setting up libdconf1:s390x (0.40.0-5) ... 1889s Setting up unicode-data (15.1.0-1) ... 1889s Setting up python3-six (1.17.0-1) ... 1889s Setting up libqt5core5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 1889s Setting up python3-decorator (5.1.1-5) ... 1889s Setting up libboost-numpy1.83.0 (1.83.0-4.1ubuntu2) ... 1889s Setting up libpcre2-32-0:s390x (10.45-1) ... 1889s Setting up libblas3:s390x (3.12.1-2) ... 1889s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 1889s Setting up python3-packaging (24.2-1) ... 1889s Setting up libxcb-xinerama0:s390x (1.17.0-2) ... 1889s Setting up python3-flexparser (0.4-1) ... 1889s Setting up libmunge2:s390x (0.5.16-1) ... 1889s Setting up libexpat1-dev:s390x (2.6.4-1) ... 1889s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ... 1889s Setting up libann-cctbx0 (1.1.2+doc-9build1) ... 1889s Setting up libepoxy0:s390x (1.5.10-2) ... 1889s Setting up libxfixes3:s390x (1:6.0.0-2build1) ... 1889s Setting up libxcb-sync1:s390x (1.17.0-2) ... 1889s Setting up python3-brotli (1.1.0-2build4) ... 1889s Setting up libavahi-common-data:s390x (0.8-16ubuntu2) ... 1889s Setting up libatspi2.0-0t64:s390x (2.56.0-2) ... 1889s Setting up liblzf1:s390x (3.6-4) ... 1889s Setting up python3-cycler (0.12.1-1) ... 1889s 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(1:1.3.dfsg+really1.3.1-1ubuntu1) ... 1890s Setting up python3-pyqt5.sip (12.17.0-1build1) ... 1890s Setting up libmtdev1t64:s390x (1.1.7-1) ... 1890s Setting up ocl-icd-libopencl1:s390x (2.3.2-1build1) ... 1890s Setting up libxshmfence1:s390x (1.3-1build5) ... 1890s Setting up at-spi2-common (2.56.0-2) ... 1890s Setting up libccp4c0t64:s390x (8.0.0-4) ... 1890s Setting up libxcb-randr0:s390x (1.17.0-2) ... 1890s Setting up libasan8:s390x (15-20250319-1ubuntu1) ... 1890s Setting up libxslt1.1:s390x (1.1.39-0exp1ubuntu4) ... 1890s Setting up libqt5sql5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 1890s Setting up libmd4c0:s390x (0.5.2-2) ... 1890s Setting up librdmacm1t64:s390x (56.0-3ubuntu1) ... 1890s Setting up libopenjp2-7:s390x (2.5.3-2) ... 1890s Setting up libharfbuzz0b:s390x (10.2.0-1) ... 1890s Setting up libthai-data (0.1.29-2build1) ... 1890s Setting up python3-dateutil (2.9.0-4) ... 1890s Setting up python3-flexcache (0.3-2) ... 1890s Setting up libglu1-mesa:s390x (9.0.2-1.1build1) 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... 1890s Setting up libfabric1:s390x (1.17.0-3.1) ... 1890s Setting up python3-sympy (1.13.3-5) ... 1894s Setting up libice6:s390x (2:1.1.1-1) ... 1894s Setting up mesa-libgallium:s390x (25.0.1-2ubuntu2) ... 1894s Setting up liblapack3:s390x (3.12.1-2) ... 1894s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 1894s Setting up libqt5dbus5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 1894s Setting up libssm2:s390x (1.4.0-2build1) ... 1894s Setting up libatk1.0-0t64:s390x (2.56.0-2) ... 1894s Setting up libgbm1:s390x (25.0.1-2ubuntu2) ... 1894s Setting up libwacom9:s390x (2.14.0-1) ... 1894s Setting up fontconfig-config (2.15.0-2.1ubuntu1) ... 1895s Setting up python3-pytest (8.3.5-1) ... 1895s Setting up libxtst6:s390x (2:1.2.5-1) ... 1895s Setting up libwebpdemux2:s390x (1.5.0-0.1) ... 1895s Setting up python3-pytest-datadir (1.4.1+ds-1) ... 1895s Setting up libxcursor1:s390x (1:1.2.3-1) ... 1895s Setting up libgl1-mesa-dri:s390x (25.0.1-2ubuntu2) ... 1895s Setting up libqt5network5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 1895s Setting up libavahi-common3:s390x (0.8-16ubuntu2) ... 1895s Setting up libqt5xml5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 1895s Setting up dconf-service (0.40.0-5) ... 1895s Setting up libqt5test5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 1895s Setting up libhwloc-plugins:s390x (2.12.0-1) ... 1895s Setting up libccp4f0t64:s390x (8.0.0-4) ... 1895s Setting up libinput-bin (1.27.1-1) ... 1895s Setting up python3-pint (0.24.4-1) ... 1895s Setting up libthai0:s390x (0.1.29-2build1) ... 1895s Setting up libegl-mesa0:s390x (25.0.1-2ubuntu2) ... 1895s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 1895s Setting up libraqm0:s390x (0.10.2-1) ... 1895s Setting up libpython3.13-dev:s390x (3.13.2-2) ... 1895s Setting up libpmix2t64:s390x (5.0.6-5) ... 1895s Setting up python3-numpy (1:2.2.3+ds-5) ... 1896s Setting up libjs-sphinxdoc (8.1.3-5) ... 1896s Setting up libhdf5-310:s390x (1.14.5+repack-3) ... 1896s Setting up python3-pytest-mock (3.14.0-2) ... 1896s Setting up python3-lxml:s390x (5.3.1-1build1) ... 1897s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 1897s Setting up libwayland-cursor0:s390x (1.23.1-3) ... 1897s Setting up libegl1:s390x (1.7.0-1build1) ... 1897s Setting up libgdk-pixbuf-2.0-0:s390x (2.42.12+dfsg-2) ... 1897s Setting up python3-contourpy (1.3.1-1build1) ... 1897s Setting up libfontconfig1:s390x (2.15.0-2.1ubuntu1) ... 1897s Setting up libgcc-14-dev:s390x (14.2.0-19ubuntu1) ... 1897s Setting up python3-dials-data (2.4.0-2) ... 1897s Setting up libstdc++-14-dev:s390x (14.2.0-19ubuntu1) ... 1897s Setting up libsm6:s390x (2:1.2.4-1) ... 1897s Setting up libavahi-client3:s390x (0.8-16ubuntu2) ... 1897s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 1897s Setting up python3-mrcfile (1.5.4-2) ... 1897s Setting up libatk-bridge2.0-0t64:s390x (2.56.0-2) ... 1897s Setting up libinput10:s390x (1.27.1-1) ... 1897s Setting up gtk-update-icon-cache (4.18.2+ds-1) ... 1897s Setting up libopenmpi40:s390x (5.0.7-1) ... 1897s Setting up libhdf5-hl-310:s390x (1.14.5+repack-3) ... 1897s Setting up fontconfig (2.15.0-2.1ubuntu1) ... 1899s Regenerating fonts cache... done. 1899s Setting up libxft2:s390x (2.3.6-1build1) ... 1899s Setting up libboost1.83-dev:s390x (1.83.0-4.1ubuntu2) ... 1899s Setting up libglx-mesa0:s390x (25.0.1-2ubuntu2) ... 1899s Setting up python3-scipy (1.14.1-4ubuntu2) ... 1901s Setting up libpython3-dev:s390x (3.13.2-2) ... 1901s Setting up libcbf1t64:s390x (0.9.7+dfsg1-5build1) ... 1901s Setting up libglx0:s390x (1.7.0-1build1) ... 1901s Setting up dconf-gsettings-backend:s390x (0.40.0-5) ... 1901s Setting up libccp4-dev:s390x (8.0.0-4) ... 1901s Setting up python3.13-dev (3.13.2-2) ... 1901s Setting up libtk8.6:s390x (8.6.16-1) ... 1901s Setting up libpango-1.0-0:s390x (1.56.3-1) ... 1901s Setting up libnetcdf22:s390x (1:4.9.3-1) ... 1901s Setting up python3-h5py-serial (3.13.0-1) ... 1901s Setting up libhdf5-openmpi-310:s390x (1.14.5+repack-3) ... 1901s Setting up libcairo2:s390x (1.18.4-1) ... 1901s Setting up python3.13-tk (3.13.2-2) ... 1902s Setting up python3-pil:s390x (11.1.0-5build1) ... 1902s Setting up libgl1:s390x (1.7.0-1build1) ... 1902s Setting up python3-pytest-regressions (2.5.0+ds-2) ... 1902s Setting up adwaita-icon-theme (48.0-1) ... 1902s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 1902s Setting up libglut3.12:s390x (3.4.0-4) ... 1902s Setting up libnotify4:s390x (0.8.4-1) ... 1902s Setting up python3-dev (3.13.2-2) ... 1902s Setting up libboost-python1.83-dev (1.83.0-4.1ubuntu2) ... 1902s Setting up python3-pycbf (0.9.7+dfsg1-5build1) ... 1902s Setting up python3-h5py (3.13.0-1) ... 1902s Setting up libglew2.2:s390x (2.2.0-4build1) ... 1902s Setting up python3-hdf5plugin (5.0.0-1) ... 1902s Setting up libcairo-gobject2:s390x (1.18.4-1) ... 1902s Setting up libpangoft2-1.0-0:s390x (1.56.3-1) ... 1902s Setting up python3-nxmx (0.0.4-1) ... 1902s Setting up libcups2t64:s390x (2.4.11-0ubuntu2) ... 1902s Setting up libgtk-3-common (3.24.49-2ubuntu1) ... 1902s Setting up libpangocairo-1.0-0:s390x (1.56.3-1) ... 1902s Setting up libcctbx0 (2024.10+ds2+~3.22.1+ds1-4build2) ... 1902s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 1902s Setting up bitshuffle (0.5.2-1build2) ... 1902s Setting up blt (2.5.3+dfsg-8) ... 1902s Setting up python3-tk:s390x (3.13.2-1) ... 1902s Setting up python3-opengl (3.1.9+dfsg-1syncable1) ... 1902s /usr/lib/python3/dist-packages/OpenGL/GL/AMD/vertex_shader_tessellator.py:30: SyntaxWarning: invalid escape sequence '\ ' 1902s |\ |\ 1903s Setting up libboost-python-dev (1.83.0.2ubuntu1) ... 1903s Setting up libqt5gui5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 1903s Setting up python3-pil.imagetk:s390x (11.1.0-5build1) ... 1903s Setting up libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4build2) ... 1903s Setting up libqt5widgets5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 1903s Setting up libqt5help5:s390x (5.15.15-6build1) ... 1903s Setting up libqt5opengl5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 1903s Setting up libqt5printsupport5t64:s390x (5.15.15+dfsg-4ubuntu1) ... 1903s Setting up libqt5designer5:s390x (5.15.15-6build1) ... 1903s Setting up python3-pyqt5 (5.15.11+dfsg-2) ... 1903s Setting up python3-pyqt5.qtopengl (5.15.11+dfsg-2) ... 1903s Setting up python3-pymol (3.1.0+dfsg-1) ... 1904s Setting up python3-fonttools (4.55.3-2build1) ... 1905s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 1905s Setting up python3-matplotlib (3.8.3-7build1) ... 1906s Processing triggers for libc-bin (2.41-1ubuntu2) ... 1906s Processing triggers for man-db (2.13.0-1) ... 1906s Processing triggers for libglib2.0-0t64:s390x (2.84.0-1) ... 1906s Setting up libgtk-3-0t64:s390x (3.24.49-2ubuntu1) ... 1906s Processing triggers for udev (257.4-1ubuntu1) ... 1907s Setting up libwxgtk3.2-1t64:s390x (3.2.6+dfsg-2ubuntu1) ... 1907s Setting up libwxgtk-gl3.2-1t64:s390x (3.2.6+dfsg-2ubuntu1) ... 1907s Setting up python3-wxgtk4.0 (4.2.2+dfsg-3build1) ... 1908s Setting up python3-cctbx (2024.10+ds2+~3.22.1+ds1-4build2) ... 1910s /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:18: SyntaxWarning: invalid escape sequence '\{' 1910s []_,.;:"&<>()/\{}'`~!@#$%*|+- 1910s /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:46: SyntaxWarning: invalid escape sequence '\/' 1910s special_characters = """[]_,.;:"&<>()\/\{}'`~!@#$%*|+-""" 1917s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:724: SyntaxWarning: invalid escape sequence '\o' 1917s width=pairwise_differences_db, label='$\omega_{hkl}$' 1917s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:739: SyntaxWarning: invalid escape sequence '\o' 1917s axes[0].set_ylabel('Distribution of $\omega_{hbk}$') 1917s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:740: SyntaxWarning: invalid escape sequence '\o' 1917s axes[0].set_xlabel('Normalized PD ($\omega_{hbk}$)') 1917s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:759: SyntaxWarning: invalid escape sequence '\o' 1917s axes[1].set_xlabel('Sorted Normalized PD ($\omega_{hbk}$)') 1917s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:778: SyntaxWarning: invalid escape sequence '\s' 1917s axes[2].set_ylabel('Standard Deviation of $I_{hbk}/\sigma_{hbk}$') 1917s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:807: SyntaxWarning: invalid escape sequence '\m' 1917s axes_sadd.set_ylabel('$s_{\mathrm{fac}}^2 \\times s_{\mathrm{add}}^2$') 1918s Processing triggers for libc-bin (2.41-1ubuntu2) ... 1948s autopkgtest [13:38:28]: test dxtbx: [----------------------- 1948s Testing dxtbx with python3.13: 1950s Fatal Python error: Segmentation fault 1950s 1950s Current thread 0x000003ffaa0f8120 (most recent call first): 1950s File "/usr/lib/python3/dist-packages/cctbx/sgtbx/__init__.py", line 102 in __init__ 1950s File "/usr/lib/python3/dist-packages/cctbx/crystal/__init__.py", line 75 in __init__ 1950s File "/tmp/autopkgtest.R528VC/autopkgtest_tmp/tests/test_crystal_model_equivalence.py", line 28 in 1950s File "/usr/lib/python3/dist-packages/_pytest/assertion/rewrite.py", line 185 in exec_module 1950s File "", line 935 in _load_unlocked 1950s File "", line 1331 in _find_and_load_unlocked 1950s File "", line 1360 in _find_and_load 1950s File "", line 1387 in _gcd_import 1950s File "/usr/lib/python3.13/importlib/__init__.py", line 88 in import_module 1950s File "/usr/lib/python3/dist-packages/_pytest/pathlib.py", line 587 in import_path 1950s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 493 in importtestmodule 1950s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 546 in _getobj 1950s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 284 in obj 1950s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 562 in _register_setup_module_fixture 1950s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 549 in collect 1950s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389 in collect 1950s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341 in from_call 1950s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 391 in pytest_make_collect_report 1950s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall 1950s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec 1950s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ 1950s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 567 in collect_one_node 1950s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 835 in _collect_one_node 1950s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 970 in genitems 1950s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 975 in genitems 1950s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 975 in genitems 1950s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 809 in perform_collect 1950s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 347 in pytest_collection 1950s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall 1950s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec 1950s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ 1950s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 336 in _main 1950s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 283 in wrap_session 1950s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 330 in pytest_cmdline_main 1950s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall 1950s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec 1950s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ 1950s File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 175 in main 1950s File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 201 in console_main 1950s File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 9 in 1950s File "", line 88 in _run_code 1950s File "", line 198 in _run_module_as_main 1950s 1950s 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) 1954s Segmentation fault (core dumped) 1955s autopkgtest [13:38:35]: test dxtbx: -----------------------] 1956s autopkgtest [13:38:36]: test dxtbx: - - - - - - - - - - results - - - - - - - - - - 1956s dxtbx FAIL non-zero exit status 139 1956s autopkgtest [13:38:36]: @@@@@@@@@@@@@@@@@@@@ summary 1956s cctbx FAIL non-zero exit status 1 1956s dxtbx FAIL non-zero exit status 139 1973s nova [W] Using flock in prodstack6-s390x 1973s flock: timeout while waiting to get lock 1973s Creating nova instance adt-plucky-s390x-cctbx-20250322-130600-juju-7f2275-prod-proposed-migration-environment-20-c0208a91-2f27-4bbf-9999-d7601a55e3e1 from image adt/ubuntu-plucky-s390x-server-20250321.img (UUID 6ae96d8b-e719-4c1b-8809-3b6533761d24)... 1973s nova [W] Timed out waiting for ac476926-ad57-41b6-82d5-a9a11ba5bd71 to get deleted. 1973s nova [W] Using flock in prodstack6-s390x 1973s Creating nova instance adt-plucky-s390x-cctbx-20250322-130600-juju-7f2275-prod-proposed-migration-environment-20-c0208a91-2f27-4bbf-9999-d7601a55e3e1 from image adt/ubuntu-plucky-s390x-server-20250321.img (UUID 6ae96d8b-e719-4c1b-8809-3b6533761d24)... 1973s nova [W] Timed out waiting for f655bb98-b088-4ea9-b123-cda84648dbf0 to get deleted.