0s autopkgtest [10:44:09]: starting date and time: 2025-03-13 10:44:09+0000
  0s autopkgtest [10:44:09]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
  0s autopkgtest [10:44:09]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.tukp_pq6/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:cctbx --apt-upgrade cctbx --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=cctbx/2024.10+ds2+~3.22.1+ds1-4build2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-36.secgroup --name adt-plucky-arm64-cctbx-20250313-104406-juju-7f2275-prod-proposed-migration-environment-2-d8421dd8-b1a3-4f83-8167-0b94862dad3b --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
139s autopkgtest [10:46:28]: testbed dpkg architecture: arm64
139s autopkgtest [10:46:28]: testbed apt version: 2.9.32ubuntu1
139s autopkgtest [10:46:28]: @@@@@@@@@@@@@@@@@@@@ test bed setup
139s autopkgtest [10:46:28]: testbed release detected to be: None
140s autopkgtest [10:46:29]: updating testbed package index (apt update)
141s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB]
141s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
141s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
141s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
141s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [11.5 kB]
141s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [396 kB]
141s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [43.9 kB]
141s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [54.8 kB]
141s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [340 kB]
141s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [3244 B]
142s Fetched 960 kB in 1s (1117 kB/s)
142s Reading package lists...
143s Reading package lists...
143s Building dependency tree...
143s Reading state information...
144s Calculating upgrade...
144s Calculating upgrade...
144s The following packages will be upgraded:
144s   gir1.2-glib-2.0 htop libglib2.0-0t64 libglib2.0-data
145s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
145s Need to get 1982 kB of archives.
145s After this operation, 0 B of additional disk space will be used.
145s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 gir1.2-glib-2.0 arm64 2.84.0-1 [185 kB]
145s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libglib2.0-0t64 arm64 2.84.0-1 [1571 kB]
145s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libglib2.0-data all 2.84.0-1 [53.0 kB]
145s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 htop arm64 3.4.0-2 [173 kB]
146s Fetched 1982 kB in 1s (3175 kB/s)
146s (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 ... 117763 files and directories currently installed.)
146s Preparing to unpack .../gir1.2-glib-2.0_2.84.0-1_arm64.deb ...
146s Unpacking gir1.2-glib-2.0:arm64 (2.84.0-1) over (2.83.5-1) ...
146s Preparing to unpack .../libglib2.0-0t64_2.84.0-1_arm64.deb ...
146s Unpacking libglib2.0-0t64:arm64 (2.84.0-1) over (2.83.5-1) ...
146s Preparing to unpack .../libglib2.0-data_2.84.0-1_all.deb ...
146s Unpacking libglib2.0-data (2.84.0-1) over (2.83.5-1) ...
146s Preparing to unpack .../htop_3.4.0-2_arm64.deb ...
146s Unpacking htop (3.4.0-2) over (3.4.0-1) ...
146s Setting up htop (3.4.0-2) ...
146s Setting up libglib2.0-0t64:arm64 (2.84.0-1) ...
146s No schema files found: doing nothing.
146s Setting up libglib2.0-data (2.84.0-1) ...
146s Setting up gir1.2-glib-2.0:arm64 (2.84.0-1) ...
146s Processing triggers for man-db (2.13.0-1) ...
147s Processing triggers for libc-bin (2.41-1ubuntu1) ...
147s Reading package lists...
147s Building dependency tree...
147s Reading state information...
148s Solving dependencies...
148s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
148s autopkgtest [10:46:37]: upgrading testbed (apt dist-upgrade and autopurge)
149s Reading package lists...
149s Building dependency tree...
149s Reading state information...
150s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
150s Starting 2 pkgProblemResolver with broken count: 0
150s Done
150s Entering ResolveByKeep
151s 
151s Calculating upgrade...
151s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
152s Reading package lists...
152s Building dependency tree...
152s Reading state information...
152s Starting pkgProblemResolver with broken count: 0
153s Starting 2 pkgProblemResolver with broken count: 0
153s Done
153s Solving dependencies...
153s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
156s autopkgtest [10:46:45]: testbed running kernel: Linux 6.14.0-7-generic #7-Ubuntu SMP PREEMPT_DYNAMIC Fri Feb 28 11:47:29 UTC 2025
157s autopkgtest [10:46:46]: @@@@@@@@@@@@@@@@@@@@ apt-source cctbx
161s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe cctbx 2024.10+ds2+~3.22.1+ds1-4build2 (dsc) [4106 B]
161s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe cctbx 2024.10+ds2+~3.22.1+ds1-4build2 (tar) [378 kB]
161s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe cctbx 2024.10+ds2+~3.22.1+ds1-4build2 (tar) [23.9 MB]
161s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe cctbx 2024.10+ds2+~3.22.1+ds1-4build2 (diff) [418 kB]
161s gpgv: Signature made Tue Mar  4 14:45:06 2025 UTC
161s gpgv:                using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2
161s gpgv: Can't check signature: No public key
161s dpkg-source: warning: cannot verify inline signature for ./cctbx_2024.10+ds2+~3.22.1+ds1-4build2.dsc: no acceptable signature found
163s autopkgtest [10:46:52]: testing package cctbx version 2024.10+ds2+~3.22.1+ds1-4build2
164s autopkgtest [10:46:53]: build not needed
170s autopkgtest [10:46:59]: test cctbx: preparing testbed
171s Reading package lists...
171s Building dependency tree...
171s Reading state information...
171s Starting pkgProblemResolver with broken count: 0
171s Starting 2 pkgProblemResolver with broken count: 0
171s Done
172s The following NEW packages will be installed:
172s   adwaita-icon-theme at-spi2-common blt cpp cpp-14 cpp-14-aarch64-linux-gnu
172s   cpp-aarch64-linux-gnu dconf-gsettings-backend dconf-service fontconfig
172s   fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome
172s   fonts-lato fonts-lyx g++ g++-14 g++-14-aarch64-linux-gnu
172s   g++-aarch64-linux-gnu gcc gcc-14 gcc-14-aarch64-linux-gnu
172s   gcc-aarch64-linux-gnu gtk-update-icon-cache hicolor-icon-theme libaec0
172s   libann-cctbx-dev libann-cctbx0 libantlr3c-3.4-0 libasan8
172s   libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 libavahi-client3
172s   libavahi-common-data libavahi-common3 libblas3 libboost-numpy1.83.0
172s   libboost-python-dev libboost-python1.83-dev libboost-python1.83.0
172s   libboost-thread1.83.0 libboost-timer1.83.0 libboost1.83-dev
172s   libcairo-gobject2 libcairo2 libcbf1t64 libcc1-0 libccp4-data libccp4-dev
172s   libccp4c0t64 libccp4f0t64 libcctbx-dev libcctbx0 libcolord2 libcups2t64
172s   libdatrie1 libdconf1 libdeflate0 libdouble-conversion3 libegl-mesa0 libegl1
172s   libepoxy0 libexpat1-dev libfontconfig1 libgbm1 libgcc-14-dev
172s   libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgl1
172s   libgl1-mesa-dri libglew2.2 libglu1-mesa libglvnd0 libglx-mesa0 libglx0
172s   libgomp1 libgraphite2-3 libgtk-3-0t64 libgtk-3-common libharfbuzz0b
172s   libhdf5-310 libhdf5-hl-310 libhwasan0 libice6 libimagequant0 libinput-bin
172s   libinput10 libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery
172s   libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0
172s   liblcms2-2 liblerc4 liblsan0 liblzf1 libmd4c0 libmmdb2-0 libmpc3
172s   libmtdev1t64 libnetcdf22 libnotify4 libopengl0 libopenjp2-7 libpango-1.0-0
172s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpcre2-16-0 libpcre2-32-0
172s   libpixman-1-0 libpython3-dev libpython3.13-dev libqhull-r8.0 libqt5core5t64
172s   libqt5dbus5t64 libqt5designer5 libqt5gui5t64 libqt5help5 libqt5network5t64
172s   libqt5opengl5t64 libqt5printsupport5t64 libqt5sql5t64 libqt5test5t64
172s   libqt5widgets5t64 libqt5xml5t64 libraqm0 libsharpyuv0 libsm6 libssm2
172s   libstdc++-14-dev libsz2 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6
172s   libtsan2 libubsan1 libvulkan1 libwacom-common libwacom9 libwayland-client0
172s   libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2
172s   libwebpmux3 libwxbase3.2-1t64 libwxgtk-gl3.2-1t64 libwxgtk3.2-1t64
172s   libx11-xcb1 libxcb-dri3-0 libxcb-glx0 libxcb-icccm4 libxcb-image0
172s   libxcb-keysyms1 libxcb-present0 libxcb-randr0 libxcb-render-util0
172s   libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-util1
172s   libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxcomposite1
172s   libxcursor1 libxdamage1 libxfixes3 libxft2 libxi6 libxinerama1
172s   libxkbcommon-x11-0 libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1
172s   libxtst6 libxxf86vm1 mesa-libgallium pymol-data python-matplotlib-data
172s   python3-all python3-brotli python3-cctbx python3-contourpy python3-cycler
172s   python3-dateutil python3-decorator python3-dev python3-flexcache
172s   python3-flexparser python3-fonttools python3-fs python3-h5py
172s   python3-h5py-serial python3-hdf5plugin python3-iniconfig python3-kiwisolver
172s   python3-legacy-cgi python3-lxml python3-lz4 python3-matplotlib
172s   python3-mpmath python3-mrcfile python3-natsort python3-numpy
172s   python3-numpy-dev python3-nxmx python3-opengl python3-ordered-set
172s   python3-packaging python3-pil python3-pil.imagetk python3-pint
172s   python3-platformdirs python3-pluggy python3-procrunner python3-pycbf
172s   python3-pymol python3-pyqt5 python3-pyqt5.qtopengl python3-pyqt5.sip
172s   python3-pytest python3-scipy python3-six python3-sympy python3-tk
172s   python3-tqdm python3-ufolib2 python3-wxgtk4.0 python3.12-tk python3.13-dev
172s   python3.13-tk sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data x11-common
172s   zlib1g-dev
172s 0 upgraded, 253 newly installed, 0 to remove and 0 not upgraded.
172s Need to get 244 MB of archives.
172s After this operation, 1172 MB of additional disk space will be used.
172s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-lato all 2.015-1 [2781 kB]
173s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-4 [146 kB]
173s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB]
173s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB]
173s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB]
173s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:2.2.3+ds-4 [3982 kB]
173s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [8004 B]
173s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB]
173s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
173s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB]
173s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB]
173s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB]
174s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB]
174s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB]
174s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB]
174s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-2 [147 kB]
174s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 gtk-update-icon-cache arm64 4.17.5+ds-3ubuntu1 [52.9 kB]
174s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 hicolor-icon-theme all 0.18-2 [13.3 kB]
174s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 adwaita-icon-theme all 48~beta-3 [578 kB]
174s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 at-spi2-common all 2.55.90-1 [9072 B]
174s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB]
174s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
174s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
174s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB]
174s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB]
174s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB]
174s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB]
174s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
174s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B]
174s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB]
174s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-8 [624 kB]
174s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-8 [4824 B]
174s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB]
174s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB]
174s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [10.6 MB]
174s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu3 [1028 B]
174s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B]
174s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB]
174s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libdconf1 arm64 0.40.0-5 [40.0 kB]
174s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 dconf-service arm64 0.40.0-5 [27.1 kB]
174s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 dconf-gsettings-backend arm64 0.40.0-5 [22.3 kB]
174s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB]
174s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB]
174s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.3-1 [171 kB]
174s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250222-0ubuntu1 [44.2 kB]
174s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB]
174s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250222-0ubuntu1 [28.0 kB]
174s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250222-0ubuntu1 [2924 kB]
174s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250222-0ubuntu1 [1319 kB]
174s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250222-0ubuntu1 [2694 kB]
175s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250222-0ubuntu1 [1178 kB]
175s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250222-0ubuntu1 [1642 kB]
175s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu3 [2593 kB]
175s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [20.9 MB]
175s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu3 [526 kB]
175s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B]
175s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B]
175s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu3 [2499 kB]
175s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [12.1 MB]
176s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu3 [21.8 kB]
176s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B]
176s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B]
176s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB]
176s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 libann-cctbx0 arm64 1.1.2+doc-9build1 [32.8 kB]
176s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 libann-cctbx-dev arm64 1.1.2+doc-9build1 [45.1 kB]
176s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 libantlr3c-3.4-0 arm64 3.4+dfsg-4build2 [45.7 kB]
176s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 libatk1.0-0t64 arm64 2.55.90-1 [55.3 kB]
176s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 libxi6 arm64 2:1.8.2-1 [32.4 kB]
176s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libatspi2.0-0t64 arm64 2.55.90-1 [84.4 kB]
176s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libatk-bridge2.0-0t64 arm64 2.55.90-1 [66.7 kB]
176s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-common-data arm64 0.8-16ubuntu1 [30.9 kB]
176s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-common3 arm64 0.8-16ubuntu1 [22.9 kB]
176s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-client3 arm64 0.8-16ubuntu1 [26.9 kB]
176s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-python1.83.0 arm64 1.83.0-4.1ubuntu1 [323 kB]
176s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 libboost-numpy1.83.0 arm64 1.83.0-4.1ubuntu1 [242 kB]
176s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost1.83-dev arm64 1.83.0-4.1ubuntu1 [10.7 MB]
176s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libexpat1-dev arm64 2.6.4-1 [129 kB]
176s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB]
176s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-dev arm64 3.13.2-1 [5399 kB]
176s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-dev arm64 3.13.2-2 [10.7 kB]
176s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-dev arm64 3.13.2-1 [508 kB]
176s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
176s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
176s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 8.1.3-4 [30.9 kB]
176s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dev arm64 3.13.2-2 [26.7 kB]
176s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 libboost-python1.83-dev arm64 1.83.0-4.1ubuntu1 [336 kB]
176s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 libboost-python-dev arm64 1.83.0.2ubuntu1 [4516 B]
176s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-thread1.83.0 arm64 1.83.0-4.1ubuntu1 [276 kB]
176s Get:89 http://ftpmaster.internal/ubuntu plucky/universe arm64 libboost-timer1.83.0 arm64 1.83.0-4.1ubuntu1 [242 kB]
176s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB]
176s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB]
176s Get:92 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B]
176s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB]
176s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo-gobject2 arm64 1.18.2-2 [127 kB]
176s Get:95 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B]
176s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-310 arm64 1.14.5+repack-3 [1331 kB]
177s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcbf1t64 arm64 0.9.7+dfsg1-5build1 [356 kB]
177s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 libccp4-data all 8.0.0-4 [65.2 kB]
177s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 libccp4c0t64 arm64 8.0.0-4 [93.5 kB]
177s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmmdb2-0 arm64 2.0.22-1 [347 kB]
177s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 libccp4f0t64 arm64 8.0.0-4 [202 kB]
177s Get:102 http://ftpmaster.internal/ubuntu plucky/universe arm64 libccp4-dev arm64 8.0.0-4 [42.3 kB]
177s Get:103 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 libcctbx0 arm64 2024.10+ds2+~3.22.1+ds1-4build2 [2016 kB]
177s Get:104 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 libcctbx-dev arm64 2024.10+ds2+~3.22.1+ds1-4build2 [1192 kB]
177s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB]
177s Get:106 http://ftpmaster.internal/ubuntu plucky/main arm64 libcolord2 arm64 1.4.7-3 [151 kB]
177s Get:107 http://ftpmaster.internal/ubuntu plucky/main arm64 libcups2t64 arm64 2.4.11-0ubuntu2 [274 kB]
177s Get:108 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB]
177s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 libdouble-conversion3 arm64 3.3.1-1 [38.8 kB]
177s Get:110 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-server0 arm64 1.23.1-3 [36.1 kB]
177s Get:111 http://ftpmaster.internal/ubuntu plucky/main arm64 libx11-xcb1 arm64 2:1.8.10-2 [8020 B]
177s Get:112 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-dri3-0 arm64 1.17.0-2 [7606 B]
177s Get:113 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-present0 arm64 1.17.0-2 [6224 B]
178s Get:114 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-randr0 arm64 1.17.0-2 [18.5 kB]
178s Get:115 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-sync1 arm64 1.17.0-2 [9688 B]
178s Get:116 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-xfixes0 arm64 1.17.0-2 [10.6 kB]
178s Get:117 http://ftpmaster.internal/ubuntu plucky/main arm64 libxshmfence1 arm64 1.3-1build5 [4938 B]
178s Get:118 http://ftpmaster.internal/ubuntu plucky/main arm64 mesa-libgallium arm64 25.0.1-2ubuntu1 [9450 kB]
178s Get:119 http://ftpmaster.internal/ubuntu plucky/main arm64 libgbm1 arm64 25.0.1-2ubuntu1 [33.7 kB]
178s Get:120 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-client0 arm64 1.23.1-3 [27.0 kB]
178s Get:121 http://ftpmaster.internal/ubuntu plucky/main arm64 libegl-mesa0 arm64 25.0.1-2ubuntu1 [122 kB]
178s Get:122 http://ftpmaster.internal/ubuntu plucky/main arm64 libepoxy0 arm64 1.5.10-2 [236 kB]
178s Get:123 http://ftpmaster.internal/ubuntu plucky/main arm64 libvulkan1 arm64 1.4.304.0-1 [158 kB]
178s Get:124 http://ftpmaster.internal/ubuntu plucky/main arm64 libgl1-mesa-dri arm64 25.0.1-2ubuntu1 [34.5 kB]
178s Get:125 http://ftpmaster.internal/ubuntu plucky/main arm64 libglvnd0 arm64 1.7.0-1build1 [60.6 kB]
178s Get:126 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-glx0 arm64 1.17.0-2 [25.5 kB]
178s Get:127 http://ftpmaster.internal/ubuntu plucky/main arm64 libxxf86vm1 arm64 1:1.1.4-1build4 [9130 B]
178s Get:128 http://ftpmaster.internal/ubuntu plucky/main arm64 libglx-mesa0 arm64 25.0.1-2ubuntu1 [151 kB]
178s Get:129 http://ftpmaster.internal/ubuntu plucky/main arm64 libglx0 arm64 1.7.0-1build1 [33.2 kB]
178s Get:130 http://ftpmaster.internal/ubuntu plucky/main arm64 libgl1 arm64 1.7.0-1build1 [106 kB]
178s Get:131 http://ftpmaster.internal/ubuntu plucky/universe arm64 libglew2.2 arm64 2.2.0-4build1 [191 kB]
178s Get:132 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB]
178s Get:133 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB]
178s Get:134 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB]
178s Get:135 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB]
178s Get:136 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.1-1 [238 kB]
178s Get:137 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.1-1 [49.6 kB]
178s Get:138 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.1-1 [27.6 kB]
178s Get:139 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-cursor0 arm64 1.23.1-3 [10.8 kB]
178s Get:140 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-egl1 arm64 1.23.1-3 [6180 B]
178s Get:141 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcomposite1 arm64 1:0.4.6-1 [6626 B]
178s Get:142 http://ftpmaster.internal/ubuntu plucky/main arm64 libxfixes3 arm64 1:6.0.0-2build1 [11.2 kB]
178s Get:143 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcursor1 arm64 1:1.2.3-1 [22.2 kB]
178s Get:144 http://ftpmaster.internal/ubuntu plucky/main arm64 libxdamage1 arm64 1:1.1.6-1build1 [6236 B]
178s Get:145 http://ftpmaster.internal/ubuntu plucky/main arm64 libxinerama1 arm64 2:1.1.4-3build1 [6394 B]
178s Get:146 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrandr2 arm64 2:1.5.4-1 [19.6 kB]
178s Get:147 http://ftpmaster.internal/ubuntu plucky/main arm64 libgtk-3-common all 3.24.48-3ubuntu1 [1424 kB]
178s Get:148 http://ftpmaster.internal/ubuntu plucky/main arm64 libgtk-3-0t64 arm64 3.24.48-3ubuntu1 [2916 kB]
178s Get:149 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [59.8 kB]
178s Get:150 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB]
178s Get:151 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB]
178s Get:152 http://ftpmaster.internal/ubuntu plucky/main arm64 libwacom-common all 2.14.0-1 [103 kB]
178s Get:153 http://ftpmaster.internal/ubuntu plucky/main arm64 libwacom9 arm64 2.14.0-1 [26.7 kB]
178s Get:154 http://ftpmaster.internal/ubuntu plucky/main arm64 libinput-bin arm64 1.27.1-1 [23.5 kB]
178s Get:155 http://ftpmaster.internal/ubuntu plucky/main arm64 libmtdev1t64 arm64 1.1.7-1 [14.6 kB]
178s Get:156 http://ftpmaster.internal/ubuntu plucky/main arm64 libinput10 arm64 1.27.1-1 [136 kB]
178s Get:157 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
178s Get:158 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB]
178s Get:159 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B]
178s Get:160 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmd4c0 arm64 0.5.2-2 [42.4 kB]
178s Get:161 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnetcdf22 arm64 1:4.9.3-1 [504 kB]
178s Get:162 http://ftpmaster.internal/ubuntu plucky/main arm64 libnotify4 arm64 0.8.4-1 [26.5 kB]
178s Get:163 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-16-0 arm64 10.45-1 [222 kB]
179s Get:164 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-32-0 arm64 10.45-1 [210 kB]
179s Get:165 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB]
179s Get:166 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5core5t64 arm64 5.15.15+dfsg-4ubuntu1 [1999 kB]
179s Get:167 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5dbus5t64 arm64 5.15.15+dfsg-4ubuntu1 [222 kB]
179s Get:168 http://ftpmaster.internal/ubuntu plucky/main arm64 libegl1 arm64 1.7.0-1build1 [29.5 kB]
179s Get:169 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5network5t64 arm64 5.15.15+dfsg-4ubuntu1 [735 kB]
179s Get:170 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB]
179s Get:171 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-icccm4 arm64 0.4.2-1 [10.9 kB]
179s Get:172 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-util1 arm64 0.4.1-1 [10.9 kB]
179s Get:173 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-image0 arm64 0.4.0-2build1 [10.8 kB]
179s Get:174 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-keysyms1 arm64 0.4.1-1 [8802 B]
179s Get:175 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render-util0 arm64 0.3.10-1 [10.5 kB]
179s Get:176 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shape0 arm64 1.17.0-2 [6246 B]
179s Get:177 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-xinerama0 arm64 1.17.0-2 [5590 B]
179s Get:178 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-xinput0 arm64 1.17.0-2 [34.2 kB]
179s Get:179 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-xkb1 arm64 1.17.0-2 [32.5 kB]
179s Get:180 http://ftpmaster.internal/ubuntu plucky/main arm64 libxkbcommon-x11-0 arm64 1.7.0-2 [13.8 kB]
179s Get:181 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5gui5t64 arm64 5.15.15+dfsg-4ubuntu1 [3680 kB]
179s Get:182 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5widgets5t64 arm64 5.15.15+dfsg-4ubuntu1 [2568 kB]
179s Get:183 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5xml5t64 arm64 5.15.15+dfsg-4ubuntu1 [124 kB]
179s Get:184 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5designer5 arm64 5.15.15-6build1 [2840 kB]
179s Get:185 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5sql5t64 arm64 5.15.15+dfsg-4ubuntu1 [123 kB]
179s Get:186 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5help5 arm64 5.15.15-6build1 [165 kB]
179s Get:187 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5opengl5t64 arm64 5.15.15+dfsg-4ubuntu1 [149 kB]
179s Get:188 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5printsupport5t64 arm64 5.15.15+dfsg-4ubuntu1 [209 kB]
179s Get:189 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5test5t64 arm64 5.15.15+dfsg-4ubuntu1 [144 kB]
179s Get:190 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB]
179s Get:191 http://ftpmaster.internal/ubuntu plucky/universe arm64 libssm2 arm64 1.4.0-2build1 [83.8 kB]
179s Get:192 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB]
179s Get:193 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB]
179s Get:194 http://ftpmaster.internal/ubuntu plucky/universe arm64 libwxbase3.2-1t64 arm64 3.2.6+dfsg-2ubuntu1 [870 kB]
179s Get:195 http://ftpmaster.internal/ubuntu plucky/main arm64 libxtst6 arm64 2:1.2.5-1 [13.2 kB]
179s Get:196 http://ftpmaster.internal/ubuntu plucky/universe arm64 libwxgtk3.2-1t64 arm64 3.2.6+dfsg-2ubuntu1 [4426 kB]
179s Get:197 http://ftpmaster.internal/ubuntu plucky/universe arm64 libwxgtk-gl3.2-1t64 arm64 3.2.6+dfsg-2ubuntu1 [52.8 kB]
179s Get:198 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu2 [168 kB]
179s Get:199 http://ftpmaster.internal/ubuntu plucky/universe arm64 pymol-data all 3.0.0+dfsg-3build2 [1394 kB]
180s Get:200 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-7build1 [2934 kB]
180s Get:201 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.13.2-2 [886 B]
180s Get:202 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build4 [342 kB]
180s Get:203 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-legacy-cgi all 2.6.2-1 [16.6 kB]
180s Get:204 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pycbf arm64 0.9.7+dfsg1-5build1 [152 kB]
180s Get:205 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.13.0-1 [1126 kB]
180s Get:206 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.13.0-1 [7978 B]
180s Get:207 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-hdf5plugin all 5.0.0-1 [23.1 kB]
180s Get:208 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB]
180s Get:209 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu3 [182 kB]
180s Get:210 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 11.1.0-5build1 [463 kB]
180s Get:211 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.9-1 [115 kB]
180s Get:212 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.2-1 [106 kB]
180s Get:213 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.13.1-1 [9770 B]
180s Get:214 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 11.1.0-5build1 [9892 B]
180s Get:215 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.1-1build1 [182 kB]
180s Get:216 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B]
180s Get:217 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB]
180s Get:218 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-7 [90.8 kB]
180s Get:219 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.1-1build1 [1258 kB]
180s Get:220 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.4.0+dfsg-1build1 [27.1 kB]
180s Get:221 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB]
180s Get:222 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu2 [16.7 MB]
182s Get:223 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB]
182s Get:224 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-5 [4229 kB]
182s Get:225 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB]
182s Get:226 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB]
183s Get:227 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.55.3-2build1 [1466 kB]
183s Get:228 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-3build1 [50.7 kB]
183s Get:229 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB]
183s Get:230 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-7build1 [17.3 MB]
184s Get:231 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB]
184s Get:232 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mrcfile all 1.5.4-2 [116 kB]
184s Get:233 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-natsort all 8.0.2-2 [33.8 kB]
184s Get:234 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-flexcache all 0.3-2 [13.4 kB]
184s Get:235 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-flexparser all 0.4-1 [43.8 kB]
184s Get:236 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pint all 0.24.4-1 [203 kB]
184s Get:237 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-nxmx all 0.0.4-1 [16.4 kB]
184s Get:238 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ordered-set all 4.1.0-1 [9778 B]
184s Get:239 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-procrunner all 2.3.3-2 [12.0 kB]
184s Get:240 http://ftpmaster.internal/ubuntu plucky/main arm64 libopengl0 arm64 1.7.0-1build1 [35.1 kB]
184s Get:241 http://ftpmaster.internal/ubuntu plucky/main arm64 libglu1-mesa arm64 9.0.2-1.1build1 [139 kB]
184s Get:242 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-opengl all 3.1.7+dfsg-1 [612 kB]
184s Get:243 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyqt5.sip arm64 12.17.0-1build1 [67.6 kB]
184s Get:244 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyqt5 arm64 5.15.11+dfsg-2 [2580 kB]
184s Get:245 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyqt5.qtopengl arm64 5.15.11+dfsg-2 [119 kB]
185s Get:246 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pymol arm64 3.0.0+dfsg-3build2 [3961 kB]
185s Get:247 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.17.0-1 [13.2 kB]
185s Get:248 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tqdm all 4.67.1-2 [92.5 kB]
185s Get:249 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-wxgtk4.0 arm64 4.2.2+dfsg-3build1 [7689 kB]
185s Get:250 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-cctbx arm64 2024.10+ds2+~3.22.1+ds1-4build2 [28.3 MB]
188s Get:251 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B]
188s Get:252 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB]
188s Get:253 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.4-1 [252 kB]
189s Fetched 244 MB in 16s (15.7 MB/s)
189s Selecting previously unselected package fonts-lato.
189s (Reading database ... 
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189s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ...
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189s Selecting previously unselected package python3-numpy-dev:arm64.
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189s Selecting previously unselected package libblas3:arm64.
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189s Selecting previously unselected package libgfortran5:arm64.
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189s Selecting previously unselected package liblapack3:arm64.
189s Preparing to unpack .../004-liblapack3_3.12.1-2_arm64.deb ...
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189s Selecting previously unselected package python3-numpy.
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189s Selecting previously unselected package libgdk-pixbuf2.0-common.
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189s Selecting previously unselected package libjpeg-turbo8:arm64.
189s Preparing to unpack .../007-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ...
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189s Selecting previously unselected package libjpeg8:arm64.
189s Preparing to unpack .../008-libjpeg8_8c-2ubuntu11_arm64.deb ...
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189s Selecting previously unselected package libdeflate0:arm64.
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190s Selecting previously unselected package libjbig0:arm64.
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190s Selecting previously unselected package liblerc4:arm64.
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190s Selecting previously unselected package libsharpyuv0:arm64.
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190s Selecting previously unselected package libwebp7:arm64.
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190s Selecting previously unselected package libtiff6:arm64.
190s Preparing to unpack .../014-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ...
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190s Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64.
190s Preparing to unpack .../015-libgdk-pixbuf-2.0-0_2.42.12+dfsg-2_arm64.deb ...
190s Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-2) ...
190s Selecting previously unselected package gtk-update-icon-cache.
190s Preparing to unpack .../016-gtk-update-icon-cache_4.17.5+ds-3ubuntu1_arm64.deb ...
190s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed.
190s 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.
190s Unpacking gtk-update-icon-cache (4.17.5+ds-3ubuntu1) ...
190s Selecting previously unselected package hicolor-icon-theme.
190s Preparing to unpack .../017-hicolor-icon-theme_0.18-2_all.deb ...
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190s Selecting previously unselected package adwaita-icon-theme.
190s Preparing to unpack .../018-adwaita-icon-theme_48~beta-3_all.deb ...
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190s Selecting previously unselected package at-spi2-common.
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190s Selecting previously unselected package libtcl8.6:arm64.
190s Preparing to unpack .../020-libtcl8.6_8.6.16+dfsg-1_arm64.deb ...
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190s Selecting previously unselected package fonts-dejavu-mono.
190s Preparing to unpack .../021-fonts-dejavu-mono_2.37-8_all.deb ...
190s Unpacking fonts-dejavu-mono (2.37-8) ...
190s Selecting previously unselected package fonts-dejavu-core.
190s Preparing to unpack .../022-fonts-dejavu-core_2.37-8_all.deb ...
190s Unpacking fonts-dejavu-core (2.37-8) ...
190s Selecting previously unselected package fontconfig-config.
190s Preparing to unpack .../023-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ...
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191s Selecting previously unselected package libfontconfig1:arm64.
191s Preparing to unpack .../024-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ...
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191s Selecting previously unselected package libxrender1:arm64.
191s Preparing to unpack .../025-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ...
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191s Selecting previously unselected package libxft2:arm64.
191s Preparing to unpack .../026-libxft2_2.3.6-1build1_arm64.deb ...
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191s Selecting previously unselected package x11-common.
191s Preparing to unpack .../027-x11-common_1%3a7.7+23ubuntu3_all.deb ...
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191s Selecting previously unselected package libxss1:arm64.
191s Preparing to unpack .../028-libxss1_1%3a1.2.3-1build3_arm64.deb ...
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191s Selecting previously unselected package libtk8.6:arm64.
191s Preparing to unpack .../029-libtk8.6_8.6.16-1_arm64.deb ...
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191s Selecting previously unselected package tk8.6-blt2.5.
191s Preparing to unpack .../030-tk8.6-blt2.5_2.5.3+dfsg-8_arm64.deb ...
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191s Selecting previously unselected package blt.
191s Preparing to unpack .../031-blt_2.5.3+dfsg-8_arm64.deb ...
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191s Selecting previously unselected package libisl23:arm64.
191s Preparing to unpack .../032-libisl23_0.27-1_arm64.deb ...
191s Unpacking libisl23:arm64 (0.27-1) ...
191s Selecting previously unselected package libmpc3:arm64.
191s Preparing to unpack .../033-libmpc3_1.3.1-1build2_arm64.deb ...
191s Unpacking libmpc3:arm64 (1.3.1-1build2) ...
191s Selecting previously unselected package cpp-14-aarch64-linux-gnu.
191s Preparing to unpack .../034-cpp-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ...
191s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
192s Selecting previously unselected package cpp-14.
192s Preparing to unpack .../035-cpp-14_14.2.0-17ubuntu3_arm64.deb ...
192s Unpacking cpp-14 (14.2.0-17ubuntu3) ...
192s Selecting previously unselected package cpp-aarch64-linux-gnu.
192s Preparing to unpack .../036-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ...
192s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
192s Selecting previously unselected package cpp.
192s Preparing to unpack .../037-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ...
192s Unpacking cpp (4:14.2.0-1ubuntu1) ...
192s Selecting previously unselected package libdconf1:arm64.
192s Preparing to unpack .../038-libdconf1_0.40.0-5_arm64.deb ...
192s Unpacking libdconf1:arm64 (0.40.0-5) ...
192s Selecting previously unselected package dconf-service.
192s Preparing to unpack .../039-dconf-service_0.40.0-5_arm64.deb ...
192s Unpacking dconf-service (0.40.0-5) ...
192s Selecting previously unselected package dconf-gsettings-backend:arm64.
192s Preparing to unpack .../040-dconf-gsettings-backend_0.40.0-5_arm64.deb ...
192s Unpacking dconf-gsettings-backend:arm64 (0.40.0-5) ...
192s Selecting previously unselected package fontconfig.
192s Preparing to unpack .../041-fontconfig_2.15.0-2ubuntu1_arm64.deb ...
192s Unpacking fontconfig (2.15.0-2ubuntu1) ...
192s Selecting previously unselected package fonts-font-awesome.
192s Preparing to unpack .../042-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ...
192s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
192s Selecting previously unselected package fonts-lyx.
192s Preparing to unpack .../043-fonts-lyx_2.4.3-1_all.deb ...
192s Unpacking fonts-lyx (2.4.3-1) ...
192s Selecting previously unselected package libcc1-0:arm64.
192s Preparing to unpack .../044-libcc1-0_15-20250222-0ubuntu1_arm64.deb ...
192s Unpacking libcc1-0:arm64 (15-20250222-0ubuntu1) ...
192s Selecting previously unselected package libgomp1:arm64.
192s Preparing to unpack .../045-libgomp1_15-20250222-0ubuntu1_arm64.deb ...
192s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ...
192s Selecting previously unselected package libitm1:arm64.
192s Preparing to unpack .../046-libitm1_15-20250222-0ubuntu1_arm64.deb ...
192s Unpacking libitm1:arm64 (15-20250222-0ubuntu1) ...
192s Selecting previously unselected package libasan8:arm64.
192s Preparing to unpack .../047-libasan8_15-20250222-0ubuntu1_arm64.deb ...
192s Unpacking libasan8:arm64 (15-20250222-0ubuntu1) ...
192s Selecting previously unselected package liblsan0:arm64.
192s Preparing to unpack .../048-liblsan0_15-20250222-0ubuntu1_arm64.deb ...
192s Unpacking liblsan0:arm64 (15-20250222-0ubuntu1) ...
192s Selecting previously unselected package libtsan2:arm64.
192s Preparing to unpack .../049-libtsan2_15-20250222-0ubuntu1_arm64.deb ...
192s Unpacking libtsan2:arm64 (15-20250222-0ubuntu1) ...
193s Selecting previously unselected package libubsan1:arm64.
193s Preparing to unpack .../050-libubsan1_15-20250222-0ubuntu1_arm64.deb ...
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193s Selecting previously unselected package libhwasan0:arm64.
193s Preparing to unpack .../051-libhwasan0_15-20250222-0ubuntu1_arm64.deb ...
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193s Selecting previously unselected package libgcc-14-dev:arm64.
193s Preparing to unpack .../052-libgcc-14-dev_14.2.0-17ubuntu3_arm64.deb ...
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193s Selecting previously unselected package gcc-14-aarch64-linux-gnu.
193s Preparing to unpack .../053-gcc-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ...
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193s Selecting previously unselected package gcc-14.
193s Preparing to unpack .../054-gcc-14_14.2.0-17ubuntu3_arm64.deb ...
193s Unpacking gcc-14 (14.2.0-17ubuntu3) ...
193s Selecting previously unselected package gcc-aarch64-linux-gnu.
193s Preparing to unpack .../055-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ...
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193s Selecting previously unselected package gcc.
193s Preparing to unpack .../056-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ...
193s Unpacking gcc (4:14.2.0-1ubuntu1) ...
193s Selecting previously unselected package libstdc++-14-dev:arm64.
194s Preparing to unpack .../057-libstdc++-14-dev_14.2.0-17ubuntu3_arm64.deb ...
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194s Selecting previously unselected package g++-14-aarch64-linux-gnu.
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194s Selecting previously unselected package g++-14.
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194s Selecting previously unselected package g++-aarch64-linux-gnu.
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194s Unpacking g++ (4:14.2.0-1ubuntu1) ...
194s Selecting previously unselected package libaec0:arm64.
194s Preparing to unpack .../062-libaec0_1.1.3-1_arm64.deb ...
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194s Selecting previously unselected package libann-cctbx0.
194s Preparing to unpack .../063-libann-cctbx0_1.1.2+doc-9build1_arm64.deb ...
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194s Selecting previously unselected package libantlr3c-3.4-0:arm64.
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194s Selecting previously unselected package libatk1.0-0t64:arm64.
195s Preparing to unpack .../066-libatk1.0-0t64_2.55.90-1_arm64.deb ...
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195s Selecting previously unselected package libxi6:arm64.
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195s Selecting previously unselected package libatspi2.0-0t64:arm64.
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195s Selecting previously unselected package libatk-bridge2.0-0t64:arm64.
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195s Selecting previously unselected package libavahi-common-data:arm64.
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195s Selecting previously unselected package libavahi-common3:arm64.
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195s Selecting previously unselected package libavahi-client3:arm64.
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195s Selecting previously unselected package libboost-python1.83.0.
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195s Selecting previously unselected package libboost-numpy1.83.0.
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195s Selecting previously unselected package libboost1.83-dev:arm64.
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197s Selecting previously unselected package libexpat1-dev:arm64.
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197s Selecting previously unselected package zlib1g-dev:arm64.
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197s Selecting previously unselected package libpython3.13-dev:arm64.
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197s Selecting previously unselected package libjs-jquery.
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197s Selecting previously unselected package libjs-underscore.
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197s Selecting previously unselected package libjs-sphinxdoc.
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197s Selecting previously unselected package python3-dev.
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197s Selecting previously unselected package libboost-python1.83-dev.
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198s Selecting previously unselected package libboost-thread1.83.0:arm64.
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198s Selecting previously unselected package libboost-timer1.83.0:arm64.
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198s Selecting previously unselected package libpixman-1-0:arm64.
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198s Selecting previously unselected package libxcb-render0:arm64.
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198s Selecting previously unselected package libxcb-shm0:arm64.
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198s Selecting previously unselected package libcairo2:arm64.
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198s Selecting previously unselected package libcairo-gobject2:arm64.
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198s Selecting previously unselected package libcbf1t64:arm64.
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198s Selecting previously unselected package libccp4-data.
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198s Selecting previously unselected package libccp4c0t64:arm64.
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198s Unpacking libccp4c0t64:arm64 (8.0.0-4) ...
198s Selecting previously unselected package libmmdb2-0:arm64.
198s Preparing to unpack .../099-libmmdb2-0_2.0.22-1_arm64.deb ...
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198s Selecting previously unselected package libccp4f0t64:arm64.
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199s Selecting previously unselected package libcctbx0.
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199s Selecting previously unselected package liblcms2-2:arm64.
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199s Selecting previously unselected package libcolord2:arm64.
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199s Selecting previously unselected package libcups2t64:arm64.
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199s Selecting previously unselected package libdatrie1:arm64.
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199s Selecting previously unselected package libwayland-server0:arm64.
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199s Selecting previously unselected package libx11-xcb1:arm64.
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201s Selecting previously unselected package libgl1-mesa-dri:arm64.
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201s Selecting previously unselected package libxcb-glx0:arm64.
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201s Selecting previously unselected package libglew2.2:arm64.
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201s Selecting previously unselected package libgraphite2-3:arm64.
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201s Selecting previously unselected package libharfbuzz0b:arm64.
201s Preparing to unpack .../132-libharfbuzz0b_10.2.0-1_arm64.deb ...
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201s Selecting previously unselected package libthai-data.
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201s Selecting previously unselected package libthai0:arm64.
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201s Selecting previously unselected package libpango-1.0-0:arm64.
201s Preparing to unpack .../135-libpango-1.0-0_1.56.1-1_arm64.deb ...
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201s Selecting previously unselected package libpangoft2-1.0-0:arm64.
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201s Selecting previously unselected package libpangocairo-1.0-0:arm64.
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202s Selecting previously unselected package libwayland-cursor0:arm64.
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202s Selecting previously unselected package libwayland-egl1:arm64.
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202s Selecting previously unselected package libxcomposite1:arm64.
202s Preparing to unpack .../140-libxcomposite1_1%3a0.4.6-1_arm64.deb ...
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202s Selecting previously unselected package libxfixes3:arm64.
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202s Selecting previously unselected package libxcursor1:arm64.
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202s Unpacking libxcursor1:arm64 (1:1.2.3-1) ...
202s Selecting previously unselected package libxdamage1:arm64.
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202s Selecting previously unselected package libxinerama1:arm64.
202s Preparing to unpack .../144-libxinerama1_2%3a1.1.4-3build1_arm64.deb ...
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202s Selecting previously unselected package libxrandr2:arm64.
202s Preparing to unpack .../145-libxrandr2_2%3a1.5.4-1_arm64.deb ...
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202s Selecting previously unselected package libgtk-3-common.
202s Preparing to unpack .../146-libgtk-3-common_3.24.48-3ubuntu1_all.deb ...
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202s Selecting previously unselected package libgtk-3-0t64:arm64.
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202s Selecting previously unselected package libhdf5-hl-310:arm64.
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202s Selecting previously unselected package libice6:arm64.
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202s Selecting previously unselected package libimagequant0:arm64.
203s Preparing to unpack .../150-libimagequant0_2.18.0-1build1_arm64.deb ...
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203s Selecting previously unselected package libwacom-common.
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203s Selecting previously unselected package libwacom9:arm64.
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203s Selecting previously unselected package libinput-bin.
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203s Selecting previously unselected package libmtdev1t64:arm64.
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203s Selecting previously unselected package libinput10:arm64.
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203s Selecting previously unselected package libjs-jquery-ui.
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203s Selecting previously unselected package libmd4c0:arm64.
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203s Selecting previously unselected package libnotify4:arm64.
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203s Selecting previously unselected package libpcre2-16-0:arm64.
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203s Selecting previously unselected package libqhull-r8.0:arm64.
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204s Selecting previously unselected package libegl1:arm64.
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204s Selecting previously unselected package libxcb-icccm4:arm64.
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204s Selecting previously unselected package libxcb-image0:arm64.
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204s Selecting previously unselected package libxcb-keysyms1:arm64.
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204s Selecting previously unselected package libxcb-render-util0:arm64.
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204s Selecting previously unselected package libxcb-xinerama0:arm64.
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204s Selecting previously unselected package libxcb-xinput0:arm64.
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204s Selecting previously unselected package libxcb-xkb1:arm64.
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204s Selecting previously unselected package libxkbcommon-x11-0:arm64.
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204s Selecting previously unselected package libqt5gui5t64:arm64.
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205s Selecting previously unselected package libqt5xml5t64:arm64.
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205s Selecting previously unselected package libqt5designer5:arm64.
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205s Selecting previously unselected package libqt5sql5t64:arm64.
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205s Selecting previously unselected package libqt5help5:arm64.
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205s Selecting previously unselected package libqt5printsupport5t64:arm64.
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205s Selecting previously unselected package libraqm0:arm64.
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205s Selecting previously unselected package libssm2:arm64.
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205s Selecting previously unselected package libwebpdemux2:arm64.
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205s Selecting previously unselected package libwebpmux3:arm64.
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205s Selecting previously unselected package libwxbase3.2-1t64:arm64.
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206s Selecting previously unselected package libxtst6:arm64.
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206s Selecting previously unselected package libwxgtk3.2-1t64:arm64.
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206s Selecting previously unselected package libwxgtk-gl3.2-1t64:arm64.
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206s Unpacking libwxgtk-gl3.2-1t64:arm64 (3.2.6+dfsg-2ubuntu1) ...
206s Selecting previously unselected package libxslt1.1:arm64.
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206s Selecting previously unselected package pymol-data.
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206s Unpacking pymol-data (3.0.0+dfsg-3build2) ...
206s Selecting previously unselected package python-matplotlib-data.
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206s Selecting previously unselected package python3-all.
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206s Selecting previously unselected package python3-brotli.
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206s Selecting previously unselected package python3-legacy-cgi.
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206s Selecting previously unselected package python3-pycbf.
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206s Selecting previously unselected package python3-hdf5plugin.
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207s Selecting previously unselected package python3-dateutil.
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207s Selecting previously unselected package libopenjp2-7:arm64.
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207s Selecting previously unselected package python3-pil:arm64.
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207s Selecting previously unselected package python3.12-tk.
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207s Selecting previously unselected package python3-tk:arm64.
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207s Selecting previously unselected package python3-pil.imagetk:arm64.
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207s Selecting previously unselected package python3-contourpy.
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207s Selecting previously unselected package python3-cycler.
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207s Selecting previously unselected package python3-platformdirs.
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207s Selecting previously unselected package python3-fs.
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207s Selecting previously unselected package python3-lxml:arm64.
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207s Selecting previously unselected package python3-lz4.
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207s Selecting previously unselected package python3-decorator.
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207s Selecting previously unselected package python3-scipy.
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208s Selecting previously unselected package python3-mpmath.
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208s Selecting previously unselected package python3-ufolib2.
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209s Selecting previously unselected package sphinx-rtd-theme-common.
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210s Selecting previously unselected package python3-nxmx.
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210s Selecting previously unselected package libopengl0:arm64.
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213s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
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213s Setting up python3-iniconfig (1.1.1-2) ...
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214s Setting up x11-common (1:7.7+23ubuntu3) ...
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214s Setting up libxcb-render-util0:arm64 (0.3.10-1) ...
214s Setting up python3-all (3.13.2-2) ...
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214s Setting up libxcb-shm0:arm64 (1.17.0-2) ...
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214s Setting up libccp4-data (8.0.0-4) ...
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214s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ...
214s Setting up libpcre2-16-0:arm64 (10.45-1) ...
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214s Setting up libcolord2:arm64 (1.4.7-3) ...
214s Setting up python3-platformdirs (4.3.6-1) ...
214s Setting up libopengl0:arm64 (1.7.0-1build1) ...
214s Setting up python3-natsort (8.0.2-2) ...
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214s Setting up libxxf86vm1:arm64 (1:1.1.4-1build4) ...
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214s Setting up libxcb-image0:arm64 (0.4.0-2build1) ...
214s Setting up python3-fs (2.4.16-7) ...
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215s Setting up libdconf1:arm64 (0.40.0-5) ...
215s Setting up unicode-data (15.1.0-1) ...
215s Setting up python3-six (1.17.0-1) ...
215s Setting up libqt5core5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
215s Setting up python3-decorator (5.1.1-5) ...
215s Setting up libboost-numpy1.83.0 (1.83.0-4.1ubuntu1) ...
215s Setting up libpcre2-32-0:arm64 (10.45-1) ...
215s Setting up libblas3:arm64 (3.12.1-2) ...
215s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
215s Setting up python3-packaging (24.2-1) ...
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215s Setting up python3-flexparser (0.4-1) ...
215s Setting up libexpat1-dev:arm64 (2.6.4-1) ...
215s Setting up libann-cctbx0 (1.1.2+doc-9build1) ...
215s Setting up libepoxy0:arm64 (1.5.10-2) ...
215s Setting up libxfixes3:arm64 (1:6.0.0-2build1) ...
215s Setting up libxcb-sync1:arm64 (1.17.0-2) ...
215s Setting up python3-brotli (1.1.0-2build4) ...
215s Setting up libavahi-common-data:arm64 (0.8-16ubuntu1) ...
215s Setting up libatspi2.0-0t64:arm64 (2.55.90-1) ...
215s Setting up liblzf1:arm64 (3.6-4) ...
215s Setting up python3-cycler (0.12.1-1) ...
216s Setting up libxinerama1:arm64 (2:1.1.4-3build1) ...
216s Setting up libimagequant0:arm64 (2.18.0-1build1) ...
216s Setting up pymol-data (3.0.0+dfsg-3build2) ...
216s Setting up libxkbcommon-x11-0:arm64 (1.7.0-2) ...
216s Setting up fonts-dejavu-mono (2.37-8) ...
216s Setting up python3-kiwisolver (1.4.7-3build1) ...
216s Setting up libmpc3:arm64 (1.3.1-1build2) ...
216s Setting up python3-numpy-dev:arm64 (1:2.2.3+ds-4) ...
216s Setting up libxrandr2:arm64 (2:1.5.4-1) ...
216s Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ...
216s Setting up fonts-dejavu-core (2.37-8) ...
216s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ...
216s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ...
216s Setting up libvulkan1:arm64 (1.4.304.0-1) ...
216s Setting up python3-pluggy (1.5.0-1) ...
216s Setting up libwebp7:arm64 (1.5.0-0.1) ...
216s Setting up libubsan1:arm64 (15-20250222-0ubuntu1) ...
216s Setting up python3-legacy-cgi (2.6.2-1) ...
216s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
216s Setting up python3-pyqt5.sip (12.17.0-1build1) ...
216s Setting up libmtdev1t64:arm64 (1.1.7-1) ...
216s Setting up libxshmfence1:arm64 (1.3-1build5) ...
216s Setting up libhwasan0:arm64 (15-20250222-0ubuntu1) ...
216s Setting up at-spi2-common (2.55.90-1) ...
216s Setting up libccp4c0t64:arm64 (8.0.0-4) ...
216s Setting up libxcb-randr0:arm64 (1.17.0-2) ...
216s Setting up libasan8:arm64 (15-20250222-0ubuntu1) ...
216s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ...
216s Setting up libqt5sql5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
216s Setting up libmd4c0:arm64 (0.5.2-2) ...
216s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu3) ...
216s Setting up libharfbuzz0b:arm64 (10.2.0-1) ...
216s Setting up libthai-data (0.1.29-2build1) ...
216s Setting up python3-dateutil (2.9.0-3) ...
216s Setting up python3-flexcache (0.3-2) ...
216s Setting up libglu1-mesa:arm64 (9.0.2-1.1build1) ...
216s Setting up libwayland-egl1:arm64 (1.23.1-3) ...
216s Setting up libxss1:arm64 (1:1.2.3-1build3) ...
216s Setting up libtsan2:arm64 (15-20250222-0ubuntu1) ...
216s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
216s Setting up libwxbase3.2-1t64:arm64 (3.2.6+dfsg-2ubuntu1) ...
216s Setting up python3-mpmath (1.3.0-1) ...
217s Setting up libisl23:arm64 (0.27-1) ...
217s Setting up python-matplotlib-data (3.8.3-7build1) ...
217s Setting up libwebpmux3:arm64 (1.5.0-0.1) ...
217s Setting up libxcomposite1:arm64 (1:0.4.6-1) ...
217s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
217s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-2) ...
217s Setting up libcc1-0:arm64 (15-20250222-0ubuntu1) ...
217s Setting up python3-procrunner (2.3.3-2) ...
217s Setting up liblsan0:arm64 (15-20250222-0ubuntu1) ...
217s Setting up libsz2:arm64 (1.1.3-1) ...
217s Setting up libitm1:arm64 (15-20250222-0ubuntu1) ...
217s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
217s Setting up libann-cctbx-dev (1.1.2+doc-9build1) ...
217s Setting up libwacom-common (2.14.0-1) ...
217s Setting up libwayland-client0:arm64 (1.23.1-3) ...
217s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
217s Setting up python3-sympy (1.13.3-5) ...
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224s Setting up mesa-libgallium:arm64 (25.0.1-2ubuntu1) ...
224s Setting up liblapack3:arm64 (3.12.1-2) ...
224s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
224s Setting up libqt5dbus5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
224s Setting up libssm2:arm64 (1.4.0-2build1) ...
224s Setting up libatk1.0-0t64:arm64 (2.55.90-1) ...
224s Setting up libgbm1:arm64 (25.0.1-2ubuntu1) ...
224s Setting up libwacom9:arm64 (2.14.0-1) ...
224s Setting up fontconfig-config (2.15.0-2ubuntu1) ...
224s Setting up python3-pytest (8.3.4-1) ...
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224s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ...
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224s Setting up libavahi-common3:arm64 (0.8-16ubuntu1) ...
224s Setting up libqt5xml5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
224s Setting up dconf-service (0.40.0-5) ...
224s Setting up libqt5test5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
224s Setting up libccp4f0t64:arm64 (8.0.0-4) ...
224s Setting up libinput-bin (1.27.1-1) ...
224s Setting up python3-pint (0.24.4-1) ...
225s Setting up libthai0:arm64 (0.1.29-2build1) ...
225s Setting up libegl-mesa0:arm64 (25.0.1-2ubuntu1) ...
225s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
225s Setting up libraqm0:arm64 (0.10.2-1) ...
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225s Setting up python3-numpy (1:2.2.3+ds-4) ...
227s Setting up libjs-sphinxdoc (8.1.3-4) ...
227s Setting up libhdf5-310:arm64 (1.14.5+repack-3) ...
227s Setting up cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
227s Setting up python3-lxml:arm64 (5.3.1-1build1) ...
227s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ...
227s Setting up libwayland-cursor0:arm64 (1.23.1-3) ...
227s Setting up libegl1:arm64 (1.7.0-1build1) ...
227s Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-2) ...
227s Setting up python3-contourpy (1.3.1-1build1) ...
227s Setting up libfontconfig1:arm64 (2.15.0-2ubuntu1) ...
227s Setting up libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ...
227s Setting up libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ...
227s Setting up libsm6:arm64 (2:1.2.4-1) ...
227s Setting up libavahi-client3:arm64 (0.8-16ubuntu1) ...
227s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ...
227s Setting up python3-mrcfile (1.5.4-2) ...
227s Setting up libatk-bridge2.0-0t64:arm64 (2.55.90-1) ...
227s Setting up libinput10:arm64 (1.27.1-1) ...
227s Setting up gtk-update-icon-cache (4.17.5+ds-3ubuntu1) ...
227s Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3) ...
227s Setting up fontconfig (2.15.0-2ubuntu1) ...
229s Regenerating fonts cache... done.
229s Setting up libxft2:arm64 (2.3.6-1build1) ...
229s Setting up libboost1.83-dev:arm64 (1.83.0-4.1ubuntu1) ...
229s Setting up libglx-mesa0:arm64 (25.0.1-2ubuntu1) ...
229s Setting up python3-scipy (1.14.1-4ubuntu2) ...
233s Setting up libpython3-dev:arm64 (3.13.2-2) ...
233s Setting up libcbf1t64:arm64 (0.9.7+dfsg1-5build1) ...
233s Setting up libglx0:arm64 (1.7.0-1build1) ...
233s Setting up dconf-gsettings-backend:arm64 (0.40.0-5) ...
233s Setting up libccp4-dev:arm64 (8.0.0-4) ...
233s Setting up python3.13-dev (3.13.2-1) ...
233s Setting up libtk8.6:arm64 (8.6.16-1) ...
233s Setting up libpango-1.0-0:arm64 (1.56.1-1) ...
233s Setting up python3.12-tk (3.12.9-1) ...
233s Setting up libnetcdf22:arm64 (1:4.9.3-1) ...
233s Setting up python3-h5py-serial (3.13.0-1) ...
233s Setting up libcairo2:arm64 (1.18.2-2) ...
233s Setting up python3.13-tk (3.13.2-1) ...
233s Setting up python3-pil:arm64 (11.1.0-5build1) ...
233s Setting up cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
233s Setting up libgl1:arm64 (1.7.0-1build1) ...
233s Setting up adwaita-icon-theme (48~beta-3) ...
233s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
233s Setting up libnotify4:arm64 (0.8.4-1) ...
233s Setting up python3-dev (3.13.2-2) ...
233s Setting up libboost-python1.83-dev (1.83.0-4.1ubuntu1) ...
233s Setting up python3-pycbf (0.9.7+dfsg1-5build1) ...
233s Setting up python3-h5py (3.13.0-1) ...
234s Setting up libglew2.2:arm64 (2.2.0-4build1) ...
234s Setting up python3-hdf5plugin (5.0.0-1) ...
234s Setting up cpp-14 (14.2.0-17ubuntu3) ...
234s Setting up cpp (4:14.2.0-1ubuntu1) ...
234s Setting up libcairo-gobject2:arm64 (1.18.2-2) ...
234s Setting up gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
234s Setting up libpangoft2-1.0-0:arm64 (1.56.1-1) ...
234s Setting up python3-nxmx (0.0.4-1) ...
234s Setting up libcups2t64:arm64 (2.4.11-0ubuntu2) ...
234s Setting up libgtk-3-common (3.24.48-3ubuntu1) ...
234s Setting up libpangocairo-1.0-0:arm64 (1.56.1-1) ...
234s Setting up libcctbx0 (2024.10+ds2+~3.22.1+ds1-4build2) ...
234s Setting up gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
234s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ...
234s Setting up g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
234s Setting up blt (2.5.3+dfsg-8) ...
234s Setting up python3-tk:arm64 (3.13.1-1) ...
234s Setting up python3-opengl (3.1.7+dfsg-1) ...
234s /usr/lib/python3/dist-packages/OpenGL/GL/AMD/vertex_shader_tessellator.py:1: SyntaxWarning: invalid escape sequence '\ '
234s   '''OpenGL extension AMD.vertex_shader_tessellator
235s Setting up gcc-14 (14.2.0-17ubuntu3) ...
235s Setting up libboost-python-dev (1.83.0.2ubuntu1) ...
235s Setting up libqt5gui5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
235s Setting up python3-pil.imagetk:arm64 (11.1.0-5build1) ...
236s Setting up g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
236s Setting up g++-14 (14.2.0-17ubuntu3) ...
236s Setting up libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4build2) ...
236s Setting up libqt5widgets5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
236s Setting up libqt5help5:arm64 (5.15.15-6build1) ...
236s Setting up gcc (4:14.2.0-1ubuntu1) ...
236s Setting up g++ (4:14.2.0-1ubuntu1) ...
236s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
236s Setting up libqt5opengl5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
236s Setting up libqt5printsupport5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
236s Setting up libqt5designer5:arm64 (5.15.15-6build1) ...
236s Setting up python3-pyqt5 (5.15.11+dfsg-2) ...
236s Setting up python3-pyqt5.qtopengl (5.15.11+dfsg-2) ...
236s Setting up python3-pymol (3.0.0+dfsg-3build2) ...
236s Setting up python3-fonttools (4.55.3-2build1) ...
237s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ...
238s Setting up python3-matplotlib (3.8.3-7build1) ...
239s Processing triggers for libc-bin (2.41-1ubuntu1) ...
239s Processing triggers for man-db (2.13.0-1) ...
240s Processing triggers for libglib2.0-0t64:arm64 (2.84.0-1) ...
240s Setting up libgtk-3-0t64:arm64 (3.24.48-3ubuntu1) ...
240s Processing triggers for udev (257.3-1ubuntu3) ...
241s Setting up libwxgtk3.2-1t64:arm64 (3.2.6+dfsg-2ubuntu1) ...
241s Setting up libwxgtk-gl3.2-1t64:arm64 (3.2.6+dfsg-2ubuntu1) ...
241s Setting up python3-wxgtk4.0 (4.2.2+dfsg-3build1) ...
242s Setting up python3-cctbx (2024.10+ds2+~3.22.1+ds1-4build2) ...
245s /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:8: SyntaxWarning: invalid escape sequence '\{'
245s   """ Iterator to generate strings of length n_chars, using upper-case,
245s /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:46: SyntaxWarning: invalid escape sequence '\/'
245s   special_characters = """[]_,.;:"&<>()\/\{}'`~!@#$%*|+-"""
255s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:724: SyntaxWarning: invalid escape sequence '\o'
255s   width=pairwise_differences_db, label='$\omega_{hkl}$'
255s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:739: SyntaxWarning: invalid escape sequence '\o'
255s   axes[0].set_ylabel('Distribution of $\omega_{hbk}$')
255s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:740: SyntaxWarning: invalid escape sequence '\o'
255s   axes[0].set_xlabel('Normalized PD ($\omega_{hbk}$)')
255s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:759: SyntaxWarning: invalid escape sequence '\o'
255s   axes[1].set_xlabel('Sorted Normalized PD ($\omega_{hbk}$)')
255s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:778: SyntaxWarning: invalid escape sequence '\s'
255s   axes[2].set_ylabel('Standard Deviation of $I_{hbk}/\sigma_{hbk}$')
255s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:807: SyntaxWarning: invalid escape sequence '\m'
255s   axes_sadd.set_ylabel('$s_{\mathrm{fac}}^2 \\times s_{\mathrm{add}}^2$')
256s Processing triggers for libc-bin (2.41-1ubuntu1) ...
257s autopkgtest [10:48:26]: test cctbx: [-----------------------
257s Testing cctbx with python3.13:
258s Running 546 tests on 2 processors:
258s   libtbx.python "/usr/lib/python3/dist-packages/annlib_adaptbx/annlib_adaptbx/sample.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/annlib_adaptbx/annlib_adaptbx/self_match.py"
258s   "/usr/lib/cctbx/python3.13/boost_adaptbx/tests/tst_optional_copy"
258s   libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_libc_backtrace.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_rational.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_optional.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_std_pair.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_tuple.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_stdout.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_stderr_stdout.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_deprecation_tools.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_python_streambuf.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sf_low_res_accuracy.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_double_step_filtration.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_is_periodic.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_reindexing.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_map_to_asu_isym.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_data_manipulation.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_bfgs.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_dev.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry/tests/tst_geometry.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/covariance/tests/tst_covariance.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_goodness_of_symmetry.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_from_map.py" P312
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_aniso_restraints.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/math/boost_python/tst_math.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_targets_fd.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_xray.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray.py" I41/acd
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_r1.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_shelxl_wght_ls.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_f_model.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/array_family/boost_python/tst_flex.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_uctbx.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_crystal_orientation.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_sgtbx.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_N_fold_rot.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_ext.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_distance_based_connectivity.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_super_cell.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/adptbx/boost_python/tst_adptbx.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/boost_python/tst_miller.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_chemical_elements.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_xray_scattering.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_henke.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_icsd_radii.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_covalent_radii.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_neutron.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_sasaki.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_tiny_pse.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_wavelengths.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_formula.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_attenuation_coefficient.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/boost_python/tst_maptbx.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_bcr.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_loft.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/dmtbx/boost_python/tst_dmtbx.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/translation_search/boost_python/tst_translation_search.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_ext.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_proxy_registry.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_nonbonded_overlaps.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_process_nonbonded_proxies.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_angle_derivs.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_motif.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/adp_restraints/tst_ext.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_math_module.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_krivy_gruber.py" --Quick
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_itvb_2001_table_a1427_hall_symbols.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_space_group_type_tidy_cb_op_t.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_denominators.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_subgroups.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_lattice_symmetry.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints.py" P3
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints_cartesian.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_site_constraints.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reflection_statistics.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_harker.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_special_op_simplifier.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_twin_target.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/symbol_confidence.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/bravais_types.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_lookup_utils.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal.py" I41/acd
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_direct_space_asu.py" I41/acd
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pair_asu_table.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_asu_clusters.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_coordination_sequences.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_close_packing.py" R-3mr
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fourier_transform_real_part_at_x.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem_2.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reciprocal_space_asu.py" P312
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_triplet_generator.py" P41
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_emma.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_expand_to_p1.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_change_basis.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wilson_plot.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_derivatives.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_fast_gradients.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F_sq P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_structure_factors.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_weights_for_symmetry_summation.py" Pmmm
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_real_space_refinement_simple.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation_2.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_loc_res.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_target_and_gradients.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_merge_equivalents.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grouped_data.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_fft_map.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sampled_model_density.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fast_nv1995.py" F222
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_lbfgs.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_2.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grm_pickling.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_french_wilson.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/make_cns_input.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/tst_cns_epsilon.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/tst_cns_hl.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/run_shelx76.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pointgroup_tools.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/sub_lattice_tools.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/rational_matrices_point_groups.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/cosets.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_pg_tools.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_twin_laws.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_find_best_cell.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_amplitude_normalisation.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_statistics_graphs.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_web_change_basis.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/direct_space_asu/proto/tst_asu.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_tidy_pickling.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/masks/tests/tst_flood_fill.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_r_free_utils.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/observations/tst_observations.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_ccp.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_mask.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_map_peak_3d_as_2d.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_asymmetric_map.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_peak_volume_estimate.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_resolution_from_map_and_model.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_curves.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_radius_as_central_peak_width.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_get_percentile_cutoffs.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_box.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_create_models_or_maps.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sphericity.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_statistics.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/merging/brehm_diederichs.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/multipolar/regression/tst_multipolar.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity_allsym.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grm_modifications.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_prepare_map_for_docking.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wavelength_units.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fcalc_fft_stability.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/cma_es/tst_cma_es.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/fable/tst_ext.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/fable/tst_equivalence.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/fable/tst_read.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/fable/tst_cout.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_show_calls.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_command_line.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_separate_files.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/fable/tst_cout_compile.py" stop
258s   libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_io.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/gltbx/tst_ellipsoids.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mrc_io.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_wildcard.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/gui_tools/tst.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_parser.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phil.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_cif_inputs.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_manager.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager_wrapping.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_2.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_3.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_4.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_model_sharpening_5.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_model_sharpening_5_cif.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_call_consistency.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_external_sharpening_7.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_half_map_sharpening_6.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_tls_from_map_8.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_cif.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry_cif.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_local_resolution_10.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_tools.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_patterson.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_restraints_merge.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_atom_selections_10k.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/ranges.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_crystal_symmetry_from_any.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_poscar.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/kriber/tst_strudat.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_geometry.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_lex_parse_build.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_restraints.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_parser.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_citations.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model_builder.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_lex_parse_build.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_hklf.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_writer.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_fvar_encoding.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_pdb.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy_2.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_tls.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/hybrid_36.py" exercise
258s   "/usr/lib/cctbx/python3.13/iotbx/pdb/hybrid_36_fem"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy_atom_sort.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy_flip_symmetric.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_selected_hierarchy_flip.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_ext.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_rna_dna_atom_names.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_name_interpretation.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_extract_rfactors_resolutions_sigma.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/modified_aa_names.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/modified_rna_dna_names.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_sheet.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation_long.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/secondary_structure.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection_string.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_secondary_structure.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_utils.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_secondary_structure_2.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/remediation/tst_remediator.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_to_map_simple.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_truncate_to_ala/tst.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_tardy_conf_sampling_simple.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_examples.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/space_group_symbols.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/tst_cns.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_merge.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/no_merge_original_index.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/ccp4_map/tst.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_ext.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_extract_from_symmetry_lib.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_dano.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_miller_dict.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_unmerged.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/tst_mtz_free_flipper.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_utils.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_adsc.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_detectors.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/xplor/tst_xplormap.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phases.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdbx_mmcif_tutorial.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_statistics.py" Fdd2 P31m
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_plots.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_csv_utils.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_file_reader.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_bioinformatics.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_segids.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_input.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_forward_compatible_pdb.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_multimodel.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_add_conformations.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_symmetry.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reindex.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_editor.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_as_fasta.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_link_records.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_merging_statistics.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_map_coefficients.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_xparm.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_xds_inp.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_integrate_hkl.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_spots_xds.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_as_cif.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_no_merge_original_index.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_export_scalepack_unmerged.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/dsn6/tst.py" P31
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_mtrix_biomt_cmdl.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_mmcif_biomt_reduction_output.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_ligs.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_broken_chain.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_shortcut_1.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_groups_preprocessing.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_input.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_user_selections.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_without_validation.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_read_mtrix_records_from_cif.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_show_systematic_absences.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_miller_sort_asu.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_reader.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_xray_scale.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_alignment_as_hsearch.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_ebi_wu_blast_xml.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_ncbi_blast_xml.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/pdb_info.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_as_pdb_1atom.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_1.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_all_chain_ids.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_extract_xtal_data.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cli_parser.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mtz_as_cif.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_group_rounding.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_occupancies_rounding.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_merge_atoms_at_end_to_residues.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_chain_ids_1.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_1.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_2.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_3.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_4.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_copy_select.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_id_str.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_altlocs.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_fetch.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_debug_write.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_reordered_chains.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_to_from_hierarchy.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/metric_prefixes.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_utils.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/test_utils/__init__.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/queuing_system_utils/pbs_utils.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/queuing_system_utils/sge_utils.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/introspection.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_thread_utils.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp_state.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_pickle.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_fully_buffered_timeout.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_scheduling.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/easy_run.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_containers.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_path.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_math_utils.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/assert_utils.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_str_utils.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/table_utils.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_dlite.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_tokenizer.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_experimental.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_interface.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_object_oriented_patterns.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/find_reference_cycles.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_binary_search.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_topological_sort.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/clusterTests.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_citations.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_python_code_parsing.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_representation.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_find_unused_imports.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_program_template.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_version.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp_multicore.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_runtime_utils.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_xmlrpc_utils.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_smoothing.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_genetic_algorithm_with_mp.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_basic.py"
258s   "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_1"
258s   "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_2"
258s   "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_3"
258s   "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_4"
258s   "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_5"
258s   "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_vec3"
258s   "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_unsigned_float_arithmetic"
258s   "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_mat3"
258s   "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_sym_mat3"
258s   "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_ref_matrix_facet"
258s   "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_accessors"
258s   "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_optional_copy"
258s   "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_rectangular_full_packed"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex_argument_passing.py"
258s   "/usr/lib/cctbx/python3.13/scitbx/serialization/tst_base_256"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_minimum_covering_ellipsoid.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian_fit_1d_analytical.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_cubic_equation.py"
258s   "/usr/lib/cctbx/python3.13/scitbx/math/tests/tst"
258s   "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_givens"
258s   "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_householder"
258s   "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_svd"
258s   "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_cholesky"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/tests/tst_row_echelon.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/tests/tst_householder.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_matrix.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_cholesky.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_svd.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_eigensystem.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_svd.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_dsyev.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/error/tst_error.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_map.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_set.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_vector.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/regression_test.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_numpy_bridge.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_smart_selection.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_shared.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_integer_offsets_vs_pointers.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_cost_of_m_handle_in_af_shared.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_cubicle_neighbors.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_r3_utils.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_regular_grid_on_unit_sphere.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/__init__.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_random_transform.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_graph.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_robust.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/superpose.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/spe.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/incremental_SO3_sampling.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_curve_fitting.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_weighted_correlation.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_similarity_indices.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_exp_functions.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_fit_quadratic_function.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gcd.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_math.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_r3_rotation.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_resample.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_line_search.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_quadrature.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_bessel.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_halton.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_euler_angles.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_superpose.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_uniform_rotation_matrix.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike_mom.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/sieve_of_eratosthenes.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/besselk.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/scale_curves.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_fit_peak.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_clustering.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_orthonormal_basis.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_g_function.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_angle_derivative.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_periodogram.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_error_propagation_matrix_inverse.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_tetrahedron.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_undirected_graph.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_so3_lie_algebra.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/minpack/tst.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_ext.py" 
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_curvatures.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_func_free_line_search.py"
258s   "/usr/lib/cctbx/python3.13/scitbx/lbfgs/tst_lbfgs"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgsb/boost_python/tst_lbfgsb.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/fftpack/boost_python/tst_fftpack.py" 
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_grid.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_array_loops.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/principal_axes_of_inertia.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_recipe.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_linear_least_squares_fit.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/chebyshev_lsq_example.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/immoptibox_ports.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/rigid_body_refinement_core.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/integrating_a_weighted_sinc_function.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/minimizer_comparisons.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_utils.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/rigidity.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_rigidity.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/rigidity_matrix_symbolic.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree_find_paths.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/test_cases_tardy_pdb.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_basic.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_tardy.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_energy_plots.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/tst.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/free_motion_reference_impl.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_featherstone.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion_hard.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_joint_lib.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_singular.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_spherical_refinement.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_molecules.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_sparse.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_lu_factorization.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/iso_surface/tst_iso_surface.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/simplex.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/differential_evolution.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/golden_section_search.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/direct_search_simulated_annealing.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/random/tests/tst_random.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/tst_normal_equations.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/test_problems.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/glmtbx/tests/tst.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_basic.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_booth.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_twisted.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/suffixtree/test/tst_single.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/absolute_structure/tests/tst_absolute_structure.py" --fix_random_seeds
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/ab_initio/tests/tst_ab_initio_ext.py"
258s   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"
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/masks/tests/tst_masks.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/structure_factors/direct/tests/tst_standard_xray.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_weighting_schemes.py" --fix_random_seeds
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_lbfgs.py"
258s   "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_reparametrisation"
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_occupancies.py"
258s   "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens"
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_same_group.py"
258s   "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_special_position"
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_reparametrisation.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=naive
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_disorder.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=levenberg-marquardt
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_rigid.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_direction.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_adp_restraints.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_manager.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_restraints.py" --verbose --scatterers=5 --resolution=0.2
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_refine.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/tests/tst_utils.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_least_squares.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/rstbx/dps_core/tst_iotbx_converter.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_predict.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_ewald_sphere.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_partial_derivatives.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/fastbragg/tst_bragg_minimal.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/rstbx/sublattice_support/tst_sublattice.py"
258s   libtbx.python -c "from rstbx.run_tests import run; run()"
258s   libtbx.python "/usr/lib/python3/dist-packages/spotfinder/core_toolbox/boost_python/tst_small_image.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/spotfinder/diffraction/geometry.py"
258s   libtbx.python "/usr/lib/python3/dist-packages/spotfinder/math_support/sphere_formulae.py"
258s 
258s libtbx.python "/usr/lib/python3/dist-packages/annlib_adaptbx/annlib_adaptbx/self_match.py" [OK] 0.3s
258s   Time:  0.30
258s   Return code: 0
258s   OKs: 1
258s   Standard out:
258s     OK
258s "/usr/lib/cctbx/python3.13/boost_adaptbx/tests/tst_optional_copy" [OK] 0.0s
258s   Time:  0.01
258s   Return code: 0
258s   OKs: 1
258s   Standard out:
258s     OK
258s   Standard error:
258s     show_stack(1): /usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_libc_backtrace.py(9) run
258s     show_stack(2): /usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_libc_backtrace.py(15) <module>
258s     libc backtrace (20 frames, most recent call last):
258s       /usr/bin/python3.13(_start+0x30) [0x5c08b0]
258s       /lib/aarch64-linux-gnu/libc.so.6(__libc_start_main+0x9c) [0xe077777823bc]
258s       /lib/aarch64-linux-gnu/libc.so.6(+0x222dc) [0xe077777822dc]
258s       /usr/bin/python3.13(Py_BytesMain+0x28) [0x5c1d28]
258s       /usr/bin/python3.13(Py_RunMain+0x2b8) [0x628eb8]
258s       /usr/bin/python3.13() [0x62b36c]
258s       /usr/bin/python3.13() [0x62b5d4]
258s       /usr/bin/python3.13() [0x62c234]
258s       /usr/bin/python3.13() [0x5fdd90]
258s       /usr/bin/python3.13() [0x603c7c]
258s       /usr/bin/python3.13(PyEval_EvalCode+0xc0) [0x5d808c]
258s       /usr/bin/python3.13(_PyEval_EvalFrameDefault+0x2a80) [0x4c56e0]
258s       /usr/bin/python3.13(_PyObject_MakeTpCall+0x274) [0x4a761c]
258s       /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0(+0x219c0) [0xe07776ed19c0]
258s       /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0(boost::python::handle_exception_impl(boost::function0<void>)+0xa8) [0xe07776ed16c8]
258s       /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0(+0x26140) [0xe07776ed6140]
258s       /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0(boost::python::objects::function::call(_object*, _object*) const+0x108) [0xe07776ecbc14]
258s       /usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-313-aarch64-linux-gnu.so(+0x18c04) [0xe07776f28c04]
258s       /usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-313-aarch64-linux-gnu.so(+0x23794) [0xe07776f33794]
258s       /usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-313-aarch64-linux-gnu.so(+0x232ac) [0xe07776f332ac]
258s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_libc_backtrace.py" [OK] 0.1s
258s   Time:  0.08
258s   Return code: 0
258s   OKs: 1
258s   Standard out:
258s     OK
258s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_rational.py" [OK] 0.2s
258s   Time:  0.18
258s   Return code: 0
258s   OKs: 1
258s   Standard out:
258s     OK
258s libtbx.python "/usr/lib/python3/dist-packages/annlib_adaptbx/annlib_adaptbx/sample.py" [OK] 0.6s
258s   Time:  0.62
258s   Return code: 0
258s   OKs: 1
258s   Standard out:
258s     OK
258s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_optional.py" [OK] 0.1s
258s   Time:  0.14
258s   Return code: 0
258s   OKs: 1
258s   Standard out:
258s     exercise_wstring: <Boost.Python.function object at 0x19d14020>
258s     OK
258s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_std_pair.py" [OK] 0.1s
258s   Time:  0.13
258s   Return code: 0
258s   OKs: 1
258s   Standard out:
258s     OK
258s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_tuple.py" [OK] 0.1s
258s   Time:  0.08
258s   Return code: 0
258s   OKs: 1
258s   Standard out:
258s     OK
258s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_stderr_stdout.py" [OK] 0.1s
258s   Time:  0.08
258s   Return code: 0
258s   OKs: 1
258s   Standard out:
258s     OK
259s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_stdout.py" [OK] 0.2s
259s   Time:  0.16
259s   Return code: 0
259s   OKs: 1
259s   Standard out:
259s     OK
259s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_deprecation_tools.py" [OK] 0.1s
259s   Time:  0.08
259s   Return code: 0
259s   OKs: 1
259s   Standard out:
259s     OK
263s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
263s 1
263s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
263s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_python_streambuf.py" [EXPECTED FAIL] 4.6s
263s   Time:  4.59
263s   Return code: 1
263s   OKs: 0
263s   Standard error:
263s     Traceback (most recent call last):
263s       File "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_python_streambuf.py", line 7, in <module>
263s         import StringIO
263s     ModuleNotFoundError: No module named 'StringIO'
264s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
264s 139
264s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
264s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sf_low_res_accuracy.py" [FAIL] 5.5s
264s   Time:  5.48
264s   Return code: 139
264s   OKs: 0
264s   Standard error:
264s     Segmentation fault (core dumped)
268s   Standard error:
268s     Segmentation fault (core dumped)
268s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
268s 139
268s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
268s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_double_step_filtration.py" [FAIL] 5.3s
268s   Time:  5.26
268s   Return code: 139
268s   OKs: 0
272s   Standard error:
272s     Segmentation fault (core dumped)
272s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
272s 139
272s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
272s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_is_periodic.py" [FAIL] 8.3s
272s   Time:  8.26
272s   Return code: 139
272s   OKs: 0
273s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_map_to_asu_isym.py" [OK] 0.5s
273s   Time:  0.46
273s   Return code: 0
273s   OKs: 1
273s   Standard out:
273s     OK
276s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
276s 139
276s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
276s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_reindexing.py" [FAIL] 7.7s
276s   Time:  7.73
276s   Return code: 139
276s   OKs: 0
276s   Standard error:
276s     Segmentation fault (core dumped)
280s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
280s 139
280s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
280s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_data_manipulation.py" [FAIL] 7.3s
280s   Time:  7.27
280s   Return code: 139
280s   OKs: 0
280s   Standard error:
280s     Segmentation fault (core dumped)
284s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
284s 139
284s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
284s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_bfgs.py" [FAIL] 7.5s
284s   Standard error:
284s     Segmentation fault (core dumped)
284s   Time:  7.45
284s   Return code: 139
284s   OKs: 0
288s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
288s 139
288s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
288s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_dev.py" P31 [FAIL] 7.5s
288s   Time:  7.46
288s   Return code: 139
288s   OKs: 0
288s   Standard error:
288s     Segmentation fault (core dumped)
291s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
291s 139
291s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
291s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry/tests/tst_geometry.py" [FAIL] 7.9s
291s   Time:  7.88
291s   Return code: 139
291s   OKs: 0
291s   Standard error:
291s     Segmentation fault (core dumped)
295s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
295s 139
295s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
295s libtbx.python "/usr/lib/python3/dist-packages/cctbx/covariance/tests/tst_covariance.py" [FAIL] 7.7s
295s   Time:  7.69
295s   Return code: 139
295s   OKs: 0
295s   Standard error:
295s     Segmentation fault (core dumped)
299s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
299s 139
299s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
299s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_goodness_of_symmetry.py" [FAIL] 7.6s
299s   Time:  7.63
299s   Return code: 139
299s   OKs: 0
299s   Standard error:
299s     Segmentation fault (core dumped)
299s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_aniso_restraints.py" [OK] 0.3s
299s   Time:  0.33
299s   Return code: 0
299s   OKs: 1
299s   Standard out:
299s     Skipping exercise(): chem_data directory not available
299s     OK
300s libtbx.python "/usr/lib/python3/dist-packages/cctbx/math/boost_python/tst_math.py" [OK] 0.1s
300s   Time:  0.13
300s   Return code: 0
300s   OKs: 1
300s   Standard out:
300s     OK
300s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_targets_fd.py" [OK] 0.5s
300s   Time:  0.48
300s   Return code: 0
300s   OKs: 1
300s   Standard out:
300s     OK
303s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
303s 139
303s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
303s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_from_map.py" P312 [FAIL] 7.7s
303s   Time:  7.70
303s   Return code: 139
303s   OKs: 0
303s   Standard error:
303s     Segmentation fault (core dumped)
307s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
307s 139
307s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
307s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_xray.py" [FAIL] 7.0s
307s   Time:  7.01
307s   Return code: 139
307s   OKs: 0
307s   Standard error:
307s     Segmentation fault (core dumped)
311s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
311s 139
311s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
311s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray.py" I41/acd [FAIL] 8.3s
311s   Time:  8.33
311s   Return code: 139
311s   OKs: 0
311s   Standard error:
311s     Segmentation fault (core dumped)
315s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
315s 139
315s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
315s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_r1.py" [FAIL] 8.0s
315s   Time:  7.97
315s   Return code: 139
315s   OKs: 0
315s   Standard error:
315s     Segmentation fault (core dumped)
319s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
319s 139
319s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
319s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_shelxl_wght_ls.py" [FAIL] 8.1s
319s   Standard error:
319s     Segmentation fault (core dumped)
319s   Time:  8.10
319s   Return code: 139
319s   OKs: 0
323s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
323s 139
323s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_f_model.py" [FAIL] 8.3s
323s   Time:  8.30
323s   Return code: 139
323s   OKs: 0
323s   Standard error:
323s     Segmentation fault (core dumped)
327s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
327s 139
327s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
327s libtbx.python "/usr/lib/python3/dist-packages/cctbx/array_family/boost_python/tst_flex.py" [FAIL] 7.5s
327s   Time:  7.51
327s   Return code: 139
327s   OKs: 0
327s   Standard error:
327s     Segmentation fault (core dumped)
330s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
330s 139
330s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
330s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_uctbx.py" [FAIL] 7.1s
330s   Time:  7.06
330s   Return code: 139
330s   OKs: 0
330s   Standard error:
330s     Segmentation fault (core dumped)
334s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
334s 139
334s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
334s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_crystal_orientation.py" [FAIL] 6.8s
334s   Time:  6.76
334s   Return code: 139
334s   OKs: 0
334s   Standard error:
334s     Segmentation fault (core dumped)
334s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_N_fold_rot.py" [OK] 0.2s
334s   Time:  0.24
334s   Return code: 0
334s   OKs: 1
334s   Standard out:
334s     OK
338s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
338s 139
338s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
338s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_sgtbx.py" [FAIL] 7.3s
338s   Time:  7.28
338s   Return code: 139
338s   OKs: 0
338s   Standard error:
338s     Segmentation fault (core dumped)
341s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
341s 139
341s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
341s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_ext.py" [FAIL] 7.6s
341s   Time:  7.61
341s   Return code: 139
341s   OKs: 0
341s   Standard error:
341s     Segmentation fault (core dumped)
345s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
345s 139
345s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
345s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_distance_based_connectivity.py" [FAIL] 7.5s
345s   Time:  7.51
345s   Return code: 139
345s   OKs: 0
345s   Standard error:
345s     Segmentation fault (core dumped)
350s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
350s 139
350s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
350s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_super_cell.py" [FAIL] 8.1s
350s   Time:  8.14
350s   Return code: 139
350s   OKs: 0
350s   Standard error:
350s     Segmentation fault (core dumped)
354s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
354s 139
354s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
354s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adptbx/boost_python/tst_adptbx.py" [FAIL] 8.3s
354s   Time:  8.34
354s   Return code: 139
354s   OKs: 0
354s   Standard error:
354s     Segmentation fault (core dumped)
354s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_chemical_elements.py" [OK] 0.1s
354s   Time:  0.11
354s   Return code: 0
354s   OKs: 1
354s   Standard out:
354s     OK
357s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
357s 139
357s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
357s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/boost_python/tst_miller.py" [FAIL] 7.9s
357s   Time:  7.87
357s   Return code: 139
357s   OKs: 0
357s   Standard error:
357s     Segmentation fault (core dumped)
358s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_henke.py" [OK] 0.1s
358s   Time:  0.12
358s   Return code: 0
358s   OKs: 1
358s   Standard out:
358s     OK
358s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_icsd_radii.py" [OK] 0.1s
358s   Time:  0.11
358s   Return code: 0
358s   OKs: 1
358s   Standard out:
358s     OK
358s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_covalent_radii.py" [OK] 0.1s
358s   Time:  0.12
358s   Return code: 0
358s   OKs: 1
358s   Standard out:
358s     OK
358s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_neutron.py" [OK] 0.1s
358s   Time:  0.12
358s   Return code: 0
358s   OKs: 1
358s   Standard out:
358s     OK
358s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_sasaki.py" [OK] 0.1s
358s   Time:  0.11
358s   Return code: 0
358s   OKs: 1
358s   Standard out:
358s     OK
358s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_tiny_pse.py" [OK] 0.1s
358s   Time:  0.12
358s   Return code: 0
358s   OKs: 1
358s   Standard out:
358s     OK
358s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_wavelengths.py" [OK] 0.1s
358s   Time:  0.12
358s   Return code: 0
358s   OKs: 1
358s   Standard out:
358s     OK
361s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
361s 139
361s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
361s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_xray_scattering.py" [FAIL] 7.4s
361s   Time:  7.43
361s   Return code: 139
361s   OKs: 0
361s   Standard error:
361s     Segmentation fault (core dumped)
364s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
364s 139
364s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
364s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_formula.py" [FAIL] 6.2s
364s   Time:  6.17
364s   Return code: 139
364s   OKs: 0
364s   Standard error:
364s     Segmentation fault (core dumped)
368s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
368s 139
368s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
368s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_attenuation_coefficient.py" [FAIL] 7.2s
368s   Time:  7.19
368s   Return code: 139
368s   OKs: 0
368s   Standard error:
368s     Segmentation fault (core dumped)
372s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
372s 139
372s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
372s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/boost_python/tst_maptbx.py" [FAIL] 7.3s
372s   Time:  7.26
372s   Return code: 139
372s   OKs: 0
372s   Standard error:
372s     Segmentation fault (core dumped)
376s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
376s 139
376s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
376s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_bcr.py" [FAIL] 8.0s
376s   Time:  7.97
376s   Return code: 139
376s   OKs: 0
376s   Standard error:
376s     Segmentation fault (core dumped)
380s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
380s 139
380s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
380s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_loft.py" [FAIL] 8.7s
380s   Time:  8.71
380s   Return code: 139
380s   OKs: 0
380s   Standard error:
380s     Segmentation fault (core dumped)
384s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
384s 139
384s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
384s libtbx.python "/usr/lib/python3/dist-packages/cctbx/dmtbx/boost_python/tst_dmtbx.py" [FAIL] 8.2s
384s   Time:  8.17
384s   Return code: 139
384s   OKs: 0
384s   Standard error:
384s     Segmentation fault (core dumped)
388s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
388s 139
388s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
388s libtbx.python "/usr/lib/python3/dist-packages/cctbx/translation_search/boost_python/tst_translation_search.py" [FAIL] 7.8s
388s   Time:  7.84
388s   Return code: 139
388s   OKs: 0
388s   Standard error:
388s     Segmentation fault (core dumped)
389s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_proxy_registry.py" [OK] 0.3s
389s   Time:  0.29
389s   Return code: 0
389s   OKs: 1
389s   Standard out:
389s     OK
389s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_nonbonded_overlaps.py" [OK] 0.8s
389s   Time:  0.83
389s   Return code: 0
389s   OKs: 0
389s   Standard out:
389s     chem_data not present, skipping
390s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_process_nonbonded_proxies.py" [OK] 0.8s
390s   Time:  0.83
390s   Return code: 0
390s   OKs: 0
390s   Standard out:
390s     Test skipped, need monomer library
392s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
392s 139
392s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
392s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_ext.py" [FAIL] 7.9s
392s   Time:  7.94
392s   Return code: 139
392s   OKs: 0
392s   Standard error:
392s     Segmentation fault (core dumped)
393s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_motif.py" [OK] 0.3s
393s   Time:  0.30
393s   Return code: 0
393s   OKs: 0
393s   Standard out:
393s     u+s,u,s: 0.22 0.19 0.03
396s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
396s 139
396s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
396s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_angle_derivs.py" [FAIL] 5.7s
396s   Time:  5.69
396s   Return code: 139
396s   OKs: 0
396s   Standard error:
396s     Segmentation fault (core dumped)
396s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_math_module.py" [OK] 0.1s
396s   Time:  0.13
396s   Return code: 0
396s   OKs: 1
396s   Standard out:
396s     OK
400s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
400s 139
400s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
400s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adp_restraints/tst_ext.py" [FAIL] 7.5s
400s   Time:  7.50
400s   Return code: 139
400s   OKs: 0
400s   Standard error:
400s     Segmentation fault (core dumped)
404s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
404s 139
404s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
404s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_krivy_gruber.py" --Quick [FAIL] 7.5s
404s   Time:  7.54
404s   Return code: 139
404s   OKs: 0
404s   Standard error:
404s     Segmentation fault (core dumped)
404s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_itvb_2001_table_a1427_hall_symbols.py" [OK] 0.3s
404s   Time:  0.26
404s   Return code: 0
404s   OKs: 1
404s   Standard out:
404s     Skipping exercise(): input file not available
404s     OK
407s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
407s 139
407s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
407s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx.py" [FAIL] 7.2s
407s   Time:  7.22
407s   Return code: 139
407s   OKs: 0
407s   Standard error:
407s     Segmentation fault (core dumped)
411s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
411s 139
411s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
411s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_space_group_type_tidy_cb_op_t.py" [FAIL] 7.3s
411s   Standard error:
411s     Segmentation fault (core dumped)
411s   Time:  7.32
411s   Return code: 139
411s   OKs: 0
415s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
415s 139
415s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
415s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_denominators.py" P31 [FAIL] 7.3s
415s   Time:  7.30
415s   Return code: 139
415s   OKs: 0
415s   Standard error:
415s     Segmentation fault (core dumped)
418s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
418s 139
418s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
418s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_subgroups.py" [FAIL] 7.1s
418s   Time:  7.12
418s   Return code: 139
418s   OKs: 0
418s   Standard error:
418s     Segmentation fault (core dumped)
422s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
422s 139
422s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
422s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_lattice_symmetry.py" [FAIL] 7.1s
422s   Time:  7.09
422s   Return code: 139
422s   OKs: 0
422s   Standard error:
422s     Segmentation fault (core dumped)
425s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
425s 139
425s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
425s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints.py" P3 [FAIL] 6.9s
425s   Time:  6.94
425s   Return code: 139
425s   OKs: 0
425s   Standard error:
425s     Segmentation fault (core dumped)
426s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_site_constraints.py" [OK] 0.4s
426s   Time:  0.43
426s   Return code: 0
426s   OKs: 0
426s   Standard out:
426s     Skipping process_zeolite_atlas(): input file not available
426s     u+s,u,s: 0.33 0.27 0.06
428s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
428s 139
428s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
428s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints_cartesian.py" [FAIL] 6.7s
428s   Time:  6.67
428s   Return code: 139
428s   OKs: 0
428s   Standard error:
428s     Segmentation fault (core dumped)
432s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
432s 139
432s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
432s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reflection_statistics.py" [FAIL] 6.0s
432s   Time:  6.05
432s   Return code: 139
432s   OKs: 0
432s   Standard error:
432s     Segmentation fault (core dumped)
435s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
435s 139
435s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
435s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_harker.py" [FAIL] 6.5s
435s   Time:  6.51
435s   Return code: 139
435s   OKs: 0
435s   Standard error:
435s     Segmentation fault (core dumped)
439s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
439s 139
439s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
439s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_special_op_simplifier.py" [FAIL] 7.0s
439s   Time:  6.97
439s   Return code: 139
439s   OKs: 0
439s   Standard error:
439s     Segmentation fault (core dumped)
442s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
442s 139
442s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
442s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_twin_target.py" [FAIL] 7.4s
442s   Time:  7.40
442s   Return code: 139
442s   OKs: 0
442s   Standard error:
442s     Segmentation fault (core dumped)
446s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
446s 139
446s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
446s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/symbol_confidence.py" [FAIL] 7.0s
446s   Time:  7.03
446s   Return code: 139
446s   OKs: 0
446s   Standard error:
446s     Segmentation fault (core dumped)
449s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
449s 139
449s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
449s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/bravais_types.py" [FAIL] 6.6s
449s   Time:  6.60
449s   Return code: 139
449s   OKs: 0
449s   Standard error:
449s     Segmentation fault (core dumped)
453s   Standard error:
453s     Segmentation fault (core dumped)
453s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
453s 139
453s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
453s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_lookup_utils.py" [FAIL] 6.9s
453s   Time:  6.92
453s   Return code: 139
453s   OKs: 0
456s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
456s 139
456s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
456s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal.py" I41/acd [FAIL] 7.4s
456s   Time:  7.35
456s   Return code: 139
456s   OKs: 0
456s   Standard error:
456s     Segmentation fault (core dumped)
460s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
460s 139
460s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
460s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_direct_space_asu.py" I41/acd [FAIL] 7.0s
460s   Time:  7.05
460s   Return code: 139
460s   OKs: 0
460s   Standard error:
460s     Segmentation fault (core dumped)
463s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
463s 139
463s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
463s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pair_asu_table.py" [FAIL] 6.8s
463s   Time:  6.80
463s   Return code: 139
463s   OKs: 0
463s   Standard error:
463s     Segmentation fault (core dumped)
464s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_coordination_sequences.py" [OK] 0.4s
464s   Time:  0.42
464s   Return code: 0
464s   OKs: 1
464s   Standard out:
464s     Skipping exercise(): input file not available
464s     OK
466s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
466s 139
466s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
466s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_asu_clusters.py" [FAIL] 6.7s
466s   Time:  6.67
466s   Return code: 139
466s   OKs: 0
466s   Standard error:
466s     Segmentation fault (core dumped)
470s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
470s 139
470s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
470s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_close_packing.py" R-3mr [FAIL] 6.4s
470s   Time:  6.43
470s   Return code: 139
470s   OKs: 0
470s   Standard error:
470s     Segmentation fault (core dumped)
474s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
474s 139
474s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
474s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fourier_transform_real_part_at_x.py" P31 [FAIL] 7.2s
474s   Time:  7.17
474s   Return code: 139
474s   OKs: 0
474s   Standard error:
474s     Segmentation fault (core dumped)
478s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
478s 139
478s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
478s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller.py" P31 [FAIL] 7.7s
478s   Time:  7.73
478s   Return code: 139
478s   OKs: 0
478s   Standard error:
478s     Segmentation fault (core dumped)
478s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem_2.py" [OK] 0.4s
478s   Time:  0.36
478s   Return code: 0
478s   OKs: 0
478s   Standard out:
478s     Skipping test: phenix not available
482s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
482s 139
482s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
482s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem.py" [FAIL] 8.4s
482s   Time:  8.40
482s   Return code: 139
482s   OKs: 0
482s   Standard error:
482s     Segmentation fault (core dumped)
485s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
485s 139
485s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
485s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reciprocal_space_asu.py" P312 [FAIL] 7.3s
485s   Time:  7.33
485s   Return code: 139
485s   OKs: 0
485s   Standard error:
485s     Segmentation fault (core dumped)
489s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
489s 139
489s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
489s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_triplet_generator.py" P41 [FAIL] 7.1s
489s   Time:  7.13
489s   Return code: 139
489s   OKs: 0
489s   Standard error:
489s     Segmentation fault (core dumped)
493s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
493s 139
493s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
493s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_emma.py" P31 [FAIL] 7.8s
493s   Time:  7.81
493s   Return code: 139
493s   OKs: 0
493s   Standard error:
493s     Segmentation fault (core dumped)
497s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
497s 139
497s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
497s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_expand_to_p1.py" P31 [FAIL] 7.9s
497s   Time:  7.88
497s   Return code: 139
497s   OKs: 0
497s   Standard error:
497s     Segmentation fault (core dumped)
500s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
500s 139
500s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
500s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_change_basis.py" P31 [FAIL] 7.2s
500s   Time:  7.19
500s   Return code: 139
500s   OKs: 0
500s   Standard error:
500s     Segmentation fault (core dumped)
504s   Standard error:
504s     Segmentation fault (core dumped)
504s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
504s 139
504s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
504s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wilson_plot.py" P31 [FAIL] 6.9s
504s   Time:  6.88
504s   Return code: 139
504s   OKs: 0
507s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
507s 139
507s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
507s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_derivatives.py" P31 [FAIL] 6.9s
507s   Time:  6.93
507s   Return code: 139
507s   OKs: 0
507s   Standard error:
507s     Segmentation fault (core dumped)
511s   Standard error:
511s     Segmentation fault (core dumped)
511s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
511s 139
511s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
511s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_fast_gradients.py" P31 [FAIL] 7.0s
511s   Time:  7.01
511s   Return code: 139
511s   OKs: 0
514s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
514s 139
514s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
514s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F P31 [FAIL] 7.1s
514s   Time:  7.06
514s   Return code: 139
514s   OKs: 0
514s   Standard error:
514s     Segmentation fault (core dumped)
514s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
514s 139
514s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
514s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F_sq P31 [FAIL] 3.6s
514s   Time:  3.56
514s   Return code: 139
514s   OKs: 0
514s   Standard error:
514s     Segmentation fault (core dumped)
519s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
519s 139
519s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
519s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_structure_factors.py" P31 [FAIL] 4.7s
519s   Time:  4.68
519s   Return code: 139
519s   OKs: 0
519s   Standard error:
519s     Segmentation fault (core dumped)
524s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
524s 139
524s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
524s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_weights_for_symmetry_summation.py" Pmmm [FAIL] 9.1s
524s   Time:  9.11
524s   Return code: 139
524s   OKs: 0
524s   Standard error:
524s     Segmentation fault (core dumped)
528s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
528s 139
528s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
528s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_real_space_refinement_simple.py" [FAIL] 8.5s
528s   Time:  8.53
528s   Return code: 139
528s   OKs: 0
528s   Standard error:
528s     Segmentation fault (core dumped)
531s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
531s 139
531s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
531s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation.py" [FAIL] 7.9s
531s   Time:  7.86
531s   Return code: 139
531s   OKs: 0
531s   Standard error:
531s     Segmentation fault (core dumped)
535s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
535s 139
535s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
535s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation_2.py" [FAIL] 7.8s
535s   Time:  7.84
535s   Return code: 139
535s   OKs: 0
535s   Standard error:
535s     Segmentation fault (core dumped)
540s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
540s 139
540s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
540s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_loc_res.py" [FAIL] 8.6s
540s   Time:  8.58
540s   Return code: 139
540s   OKs: 0
540s   Standard error:
540s     Segmentation fault (core dumped)
544s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
544s 139
544s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
544s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_target_and_gradients.py" [FAIL] 8.2s
544s   Time:  8.19
544s   Return code: 139
544s   OKs: 0
544s   Standard error:
544s     Segmentation fault (core dumped)
547s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
547s 139
547s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
547s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_merge_equivalents.py" P31 [FAIL] 7.2s
547s   Time:  7.15
547s   Return code: 139
547s   OKs: 0
547s   Standard error:
547s     Segmentation fault (core dumped)
551s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
551s 139
551s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
551s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grouped_data.py" P31 [FAIL] 7.4s
551s   Time:  7.42
551s   Return code: 139
551s   OKs: 0
551s   Standard error:
551s     Segmentation fault (core dumped)
555s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
555s 139
555s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
555s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_fft_map.py" P31 [FAIL] 7.8s
555s   Time:  7.81
555s   Return code: 139
555s   OKs: 0
555s   Standard error:
555s     Segmentation fault (core dumped)
559s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
559s 139
559s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
559s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sampled_model_density.py" P31 [FAIL] 8.1s
559s   Time:  8.08
559s   Return code: 139
559s   OKs: 0
559s   Standard error:
559s     Segmentation fault (core dumped)
560s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints.py" [OK] 0.8s
560s   Time:  0.79
560s   Return code: 0
560s   OKs: 1
560s   Standard out:
560s     OK
563s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
563s 139
563s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
563s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fast_nv1995.py" F222 [FAIL] 8.5s
563s   Time:  8.49
563s   Return code: 139
563s   OKs: 0
563s   Standard error:
563s     Segmentation fault (core dumped)
567s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
567s 139
567s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
567s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_lbfgs.py" [FAIL] 7.5s
567s   Time:  7.51
567s   Return code: 139
567s   OKs: 0
567s   Standard error:
567s     Segmentation fault (core dumped)
568s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grm_pickling.py" [OK] 0.5s
568s   Time:  0.51
568s   Return code: 0
568s   OKs: 0
568s   Standard out:
568s     Can not initialize monomer_library, skipping test.
572s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
572s 139
572s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
572s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_2.py" [FAIL] 8.2s
572s   Time:  8.19
572s   Return code: 139
572s   OKs: 0
572s   Standard error:
572s     Segmentation fault (core dumped)
575s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
575s 139
575s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
575s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_french_wilson.py" [FAIL] 7.3s
575s   Time:  7.31
575s   Return code: 139
575s   OKs: 0
575s   Standard error:
575s     Segmentation fault (core dumped)
576s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/tst_cns_epsilon.py" P31 [OK] 0.3s
576s   Time:  0.32
576s   Return code: 0
576s   OKs: 0
576s   Standard out:
576s     Skipping tests: cns not available.
576s     u+s,u,s: 0.23 0.20 0.03
576s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/tst_cns_hl.py" P31 [OK] 0.3s
576s   Time:  0.32
576s   Return code: 0
576s   OKs: 0
576s   Standard out:
576s     Skipping tests: cns not available.
576s     u+s,u,s: 0.24 0.21 0.03
576s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/run_shelx76.py" P31 [OK] 0.3s
576s   Time:  0.34
576s   Return code: 0
576s   OKs: 0
576s   Standard out:
576s     shelx76 not available.
579s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
579s 139
579s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
579s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/make_cns_input.py" P31 [FAIL] 7.3s
579s   Time:  7.28
579s   Return code: 139
579s   OKs: 0
579s   Standard error:
579s     Segmentation fault (core dumped)
582s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
582s 139
582s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
582s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pointgroup_tools.py" [FAIL] 6.2s
582s   Time:  6.25
582s   Return code: 139
582s   OKs: 0
582s   Standard error:
582s     Segmentation fault (core dumped)
586s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
586s 139
586s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
586s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/sub_lattice_tools.py" [FAIL] 7.3s
586s   Time:  7.28
586s   Return code: 139
586s   OKs: 0
586s   Standard error:
586s     Segmentation fault (core dumped)
590s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
590s 139
590s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
590s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/rational_matrices_point_groups.py" [FAIL] 7.8s
590s   Time:  7.85
590s   Return code: 139
590s   OKs: 0
590s   Standard error:
590s     Segmentation fault (core dumped)
594s   Standard error:
594s     Segmentation fault (core dumped)
594s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
594s 139
594s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
594s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/cosets.py" [FAIL] 7.7s
594s   Time:  7.73
594s   Return code: 139
594s   OKs: 0
598s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
598s 139
598s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
598s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_pg_tools.py" [FAIL] 7.4s
598s   Time:  7.43
598s   Return code: 139
598s   OKs: 0
598s   Standard error:
598s     Segmentation fault (core dumped)
601s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
601s 139
601s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
601s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_twin_laws.py" [FAIL] 7.3s
601s   Time:  7.30
601s   Return code: 139
601s   OKs: 0
601s   Standard error:
601s     Segmentation fault (core dumped)
605s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
605s 139
605s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
605s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_find_best_cell.py" [FAIL] 7.1s
605s   Time:  7.11
605s   Return code: 139
605s   OKs: 0
605s   Standard error:
605s     Segmentation fault (core dumped)
609s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
609s 139
609s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
609s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_amplitude_normalisation.py" [FAIL] 7.3s
609s   Time:  7.34
609s   Return code: 139
609s   OKs: 0
609s   Standard error:
609s     Segmentation fault (core dumped)
613s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
613s 139
613s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
613s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_statistics_graphs.py" [FAIL] 7.6s
613s   Time:  7.63
613s   Return code: 139
613s   OKs: 0
613s   Standard error:
613s     Segmentation fault (core dumped)
617s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
617s 139
617s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
617s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_web_change_basis.py" [FAIL] 8.1s
617s   Time:  8.11
617s   Return code: 139
617s   OKs: 0
617s   Standard error:
617s     Segmentation fault (core dumped)
620s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
620s 139
620s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
620s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/direct_space_asu/proto/tst_asu.py" [FAIL] 7.7s
620s   Time:  7.67
620s   Return code: 139
620s   OKs: 0
620s   Standard error:
620s     Segmentation fault (core dumped)
624s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
624s 139
624s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
624s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_tidy_pickling.py" [FAIL] 7.7s
624s   Time:  7.68
624s   Return code: 139
624s   OKs: 0
624s   Standard error:
624s     Segmentation fault (core dumped)
628s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
628s 139
628s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
628s libtbx.python "/usr/lib/python3/dist-packages/cctbx/masks/tests/tst_flood_fill.py" [FAIL] 8.1s
628s   Time:  8.13
628s   Return code: 139
628s   OKs: 0
628s   Standard error:
628s     Segmentation fault (core dumped)
629s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/observations/tst_observations.py" [OK] 0.3s
629s   Time:  0.34
629s   Return code: 0
629s   OKs: 1
629s   Standard out:
629s     OK
632s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
632s 139
632s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
632s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_r_free_utils.py" [FAIL] 8.0s
632s   Time:  8.01
632s   Return code: 139
632s   OKs: 0
632s   Standard error:
632s     Segmentation fault (core dumped)
636s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
636s 139
636s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
636s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_ccp.py" [FAIL] 7.4s
636s   Time:  7.43
636s   Return code: 139
636s   OKs: 0
636s   Standard error:
636s     Segmentation fault (core dumped)
640s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
640s 139
640s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
640s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_mask.py" [FAIL] 7.3s
640s   Time:  7.32
640s   Return code: 139
640s   OKs: 0
640s   Standard error:
640s     Segmentation fault (core dumped)
644s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
644s 139
644s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
644s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_map_peak_3d_as_2d.py" [FAIL] 7.5s
644s   Time:  7.55
644s   Return code: 139
644s   OKs: 0
644s   Standard error:
644s     Segmentation fault (core dumped)
648s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
648s 139
648s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
648s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_asymmetric_map.py" [FAIL] 7.9s
648s   Time:  7.87
648s   Return code: 139
648s   OKs: 0
648s   Standard error:
648s     Segmentation fault (core dumped)
651s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
651s 139
651s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
651s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_peak_volume_estimate.py" [FAIL] 7.5s
651s   Time:  7.48
651s   Return code: 139
651s   OKs: 0
651s   Standard error:
651s     Segmentation fault (core dumped)
655s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
655s 139
655s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
655s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_resolution_from_map_and_model.py" [FAIL] 7.2s
655s   Time:  7.15
655s   Return code: 139
655s   OKs: 0
655s   Standard error:
655s     Segmentation fault (core dumped)
658s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
658s 139
658s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
658s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_curves.py" [FAIL] 7.0s
658s   Time:  7.03
658s   Return code: 139
658s   OKs: 0
658s   Standard error:
658s     Segmentation fault (core dumped)
662s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
662s 139
662s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
662s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_radius_as_central_peak_width.py" [FAIL] 7.0s
662s   Time:  6.98
662s   Return code: 139
662s   OKs: 0
662s   Standard error:
662s     Segmentation fault (core dumped)
663s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_box.py" [OK] 0.8s
663s   Time:  0.81
663s   Return code: 0
663s   OKs: 0
663s   Standard out:
663s     phenix is not available, skipping test
663s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_create_models_or_maps.py" [OK] 0.9s
663s   Time:  0.88
663s   Return code: 0
663s   OKs: 1
663s   Standard out:
663s     Skipping exercise(): chem_data directory not available
663s     OK
665s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
665s 139
665s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
665s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_get_percentile_cutoffs.py" [FAIL] 7.3s
665s   Time:  7.29
665s   Return code: 139
665s   OKs: 0
665s   Standard error:
665s     Segmentation fault (core dumped)
669s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
669s 139
669s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
669s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sphericity.py" [FAIL] 5.6s
669s   Time:  5.59
669s   Return code: 139
669s   OKs: 0
669s   Standard error:
669s     Segmentation fault (core dumped)
669s libtbx.python "/usr/lib/python3/dist-packages/cctbx/merging/brehm_diederichs.py" [OK] 0.3s
669s   Time:  0.30
669s   Return code: 0
669s   OKs: 1
669s   Standard out:
669s     OK
669s libtbx.python "/usr/lib/python3/dist-packages/cctbx/multipolar/regression/tst_multipolar.py" [OK] 0.2s
669s   Time:  0.21
669s   Return code: 0
669s   OKs: 3
669s   Standard out:
669s     OK
669s     0
669s     1
669s     2
669s     OK
669s     Skipping exercise(): chem_data directory not available
669s     OK
672s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
672s 139
672s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
672s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_statistics.py" [FAIL] 7.0s
672s   Time:  7.03
672s   Return code: 139
672s   OKs: 0
672s   Standard error:
672s     Segmentation fault (core dumped)
676s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
676s 139
676s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
676s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity.py" [FAIL] 6.5s
676s   Time:  6.49
676s   Return code: 139
676s   OKs: 0
676s   Standard error:
676s     Segmentation fault (core dumped)
679s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
679s 139
679s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
679s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity_allsym.py" [FAIL] 7.0s
679s   Time:  6.97
679s   Return code: 139
679s   OKs: 0
679s   Standard error:
679s     Segmentation fault (core dumped)
680s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grm_modifications.py" [OK] 0.8s
680s   Time:  0.83
680s   Return code: 0
680s   OKs: 1
680s   Standard out:
680s     Can not initialize monomer_library, skipping test.
680s     OK
687s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
687s 1
687s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
687s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py" [FAIL] 10.8s
687s   Time: 10.82
687s   Return code: 1
687s   OKs: 0
687s   Standard error:
687s     Segmentation fault (core dumped)
687s     Traceback (most recent call last):
687s       File "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py", line 140, in <module>
687s         exercise()
687s         ~~~~~~~~^^
687s       File "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py", line 126, in exercise
687s         assert not easy_run.call(cmd)
687s                ^^^^^^^^^^^^^^^^^^^^^^
687s     AssertionError
688s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
688s 139
688s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
688s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_prepare_map_for_docking.py" [FAIL] 8.1s
688s   Time:  8.06
688s   Return code: 139
688s   OKs: 0
688s   Standard error:
688s     Segmentation fault (core dumped)
690s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wavelength_units.py" [OK] 3.5s
690s   Time:  3.50
690s   Return code: 0
690s   OKs: 1
690s   Standard out:
690s     OK
692s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
692s 139
692s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
692s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fcalc_fft_stability.py" [EXPECTED UNSTABLE] 4.1s
692s   Time:  4.08
692s   Return code: 139
692s   OKs: 0
692s   Standard error:
692s     Segmentation fault (core dumped)
693s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_ext.py" [OK] 0.1s
693s   Time:  0.12
693s   Return code: 0
693s   OKs: 1
693s   Standard out:
693s     OK
693s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_equivalence.py" [OK] 0.1s
693s   Time:  0.12
693s   Return code: 0
693s   OKs: 1
693s   Standard out:
693s     OK
693s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_read.py" [OK] 0.6s
693s   Time:  0.60
693s   Return code: 0
693s   OKs: 1
693s   Standard out:
693s     OK
694s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_cout.py" [OK] 0.5s
694s   Time:  0.48
694s   Return code: 0
694s   OKs: 1
694s   Standard out:
694s     OK
694s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_show_calls.py" [OK] 0.4s
694s   Time:  0.36
694s   Return code: 0
694s   OKs: 1
694s   Standard out:
694s     OK
696s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
696s 139
696s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
696s libtbx.python "/usr/lib/python3/dist-packages/cma_es/tst_cma_es.py" [FAIL] 5.9s
696s   Time:  5.91
696s   Return code: 139
696s   OKs: 0
696s   Standard error:
696s     Segmentation fault (core dumped)
702s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_command_line.py" [OK] 8.2s
702s   Time:  8.19
702s   Return code: 0
702s   OKs: 1
702s   Standard out:
702s     fable.split "/usr/lib/python3/dist-packages/fable/test/valid/subroutine_1.f"
702s     fable.read --each "/usr/lib/python3/dist-packages/fable/test/valid/write_star.f"
702s     fable.read --warnings "/usr/lib/python3/dist-packages/fable/test/valid/equivalence_mixed.f"
702s     fable.show_calls --write-graphviz-dot=tmp.dot --top-procedure=sub "/usr/lib/python3/dist-packages/fable/test/valid/external_arg_layers.f"
702s     fable.show_calls "/usr/lib/python3/dist-packages/fable/test/valid/dependency_cycle.f"
702s     fable.fem_include_search_paths --with-quotes
702s     fable.cout --each "/usr/lib/python3/dist-packages/fable/test/valid/write_star.f"
702s     fable.cout "/usr/lib/python3/dist-packages/fable/test/valid/common_variants.f"
702s     fable.cout "/usr/lib/python3/dist-packages/fable/test/valid/subroutine_3.f" --top-procedure=sub3 --fortran-file-comments
702s     fable.cout --compile "/usr/lib/python3/dist-packages/fable/test/valid/write_star.f"
702s     fable.cout --namespace=test --run "/usr/lib/python3/dist-packages/fable/test/valid/write_star.f"
702s     fable.cout --example
702s     fable.cout /usr/lib/python3/dist-packages/fable/test/valid/sf.f --namespace example --run
702s     fable.cout "/usr/lib/python3/dist-packages/fable/test/valid/dynamic_parameters_1.f" --dynamic-parameter="int root_size=1"
702s     OK
707s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_cout_compile.py" stop [OK] 4.7s
707s   Time:  4.71
707s   Return code: 0
707s   OKs: 1
707s   Standard out:
707s     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"
707s     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"
707s     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"
707s     OK
707s     usr+sys time: 0.15 seconds
707s     wall clock time: 4.65 seconds
711s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_separate_files.py" [OK] 14.5s
711s   Time: 14.54
711s   Return code: 0
711s   OKs: 1
711s   Standard out:
711s     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"
711s     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"
711s     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"
711s     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"
711s     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"
711s     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"
711s     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"
711s     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"
711s     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"
711s     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"
711s     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"
711s     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"
711s     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"
711s     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"
711s     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"
711s     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"
711s     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"
711s     OK
711s     usr+sys time: 0.32 seconds
711s     wall clock time: 14.48 seconds
711s libtbx.python "/usr/lib/python3/dist-packages/gltbx/tst_ellipsoids.py" [OK] 0.4s
711s   Time:  0.39
711s   Return code: 0
711s   OKs: 1
711s   Standard out:
711s     OK
715s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
715s 139
715s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
715s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mrc_io.py" [FAIL] 4.0s
715s   Time:  3.99
715s   Return code: 139
715s   OKs: 0
715s   Standard error:
715s     Segmentation fault (core dumped)
715s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_wildcard.py" [OK] 0.1s
715s   Time:  0.10
715s   Return code: 0
715s   OKs: 1
715s   Standard out:
715s     OK
717s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_io.py" [OK] 10.3s
717s   Time: 10.29
717s   Return code: 0
717s   OKs: 1
717s   Standard out:
717s     OK
717s     usr+sys time: 0.24 seconds
717s     wall clock time: 10.22 seconds
717s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_parser.py" [OK] 0.1s
717s   Time:  0.10
717s   Return code: 0
717s   OKs: 1
717s   Standard out:
717s     OK
719s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
719s 139
719s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
719s libtbx.python "/usr/lib/python3/dist-packages/iotbx/gui_tools/tst.py" [FAIL] 4.2s
719s   Time:  4.17
719s   Return code: 139
719s   OKs: 0
719s   Standard error:
719s     Segmentation fault (core dumped)
720s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_cif_inputs.py" [OK] 0.4s
720s   Time:  0.36
720s   Return code: 0
720s   OKs: 1
720s   Standard out:
720s     OK
723s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
723s 139
723s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
723s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phil.py" [FAIL] 5.7s
723s   Time:  5.73
723s   Return code: 139
723s   OKs: 0
723s   Standard error:
723s     Segmentation fault (core dumped)
727s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
727s 139
727s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
727s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_manager.py" [FAIL] 7.6s
727s   Time:  7.65
727s   Return code: 139
727s   OKs: 0
727s   Standard error:
727s     Segmentation fault (core dumped)
731s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
731s 139
731s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
731s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager_wrapping.py" [FAIL] 8.0s
731s   Time:  8.02
731s   Return code: 139
731s   OKs: 0
731s   Standard error:
731s     Segmentation fault (core dumped)
732s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager.py" [OK] 0.8s
732s   Time:  0.85
732s   Return code: 0
732s   OKs: 1
732s   Standard out:
732s     Skip test_01, chem_data not available
732s     OK
733s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_2.py" [OK] 0.9s
733s   Time:  0.90
733s   Return code: 0
733s   OKs: 0
733s   Standard out:
733s     chem_data is not available, skipping
734s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_3.py" [OK] 0.8s
734s   Time:  0.84
734s   Return code: 0
734s   OKs: 1
734s   Standard out:
734s     Skipped: Requires phenix module
734s     OK
734s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_4.py" [OK] 0.2s
734s   Time:  0.24
734s   Return code: 0
734s   OKs: 1
734s   Standard out:
734s     Skipping tst_map_model_manager_4 tests becuase Phenix is not available.
734s     OK
735s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_model_sharpening_5.py" [OK] 0.8s
735s   Time:  0.84
735s   Return code: 0
735s   OKs: 1
735s   Standard out:
735s     Skip test_01, chem_data not available
735s     OK
735s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
735s 139
735s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
735s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager.py" [FAIL] 7.9s
735s   Time:  7.87
735s   Return code: 139
735s   OKs: 0
735s   Standard error:
735s     Segmentation fault (core dumped)
736s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_model_sharpening_5_cif.py" [OK] 0.8s
736s   Time:  0.84
736s   Return code: 0
736s   OKs: 1
736s   Standard out:
736s     Skip test_01, chem_data not available
736s     OK
736s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_call_consistency.py" [OK] 0.8s
736s   Time:  0.80
736s   Return code: 0
736s   OKs: 1
736s   Standard out:
736s     
736s     Expected and actual args in calls for with_bounds
736s     
736s     box.with_bounds.__init__ :
736s     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'] 
736s     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']
736s     
736s     box_all_maps_with_bounds_and_shift_origin :
736s     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'] 
736s     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']
736s     
736s     extract_all_maps_with_bounds :
736s     Expected :['lower_bounds', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'upper_bounds', 'use_cubic_boxing'] 
736s     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']
736s     
736s     Expected and actual args in calls for around_model
736s     
736s     box.around_model.__init__ :
736s     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'] 
736s     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']
736s     
736s     box_all_maps_around_model_and_shift_origin :
736s     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'] 
736s     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']
736s     
736s     extract_all_maps_around_model :
736s     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'] 
736s     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']
736s     
736s     Expected and actual args in calls for around_density
736s     
736s     box.around_density.__init__ :
736s     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'] 
736s     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']
736s     
736s     box_all_maps_around_density_and_shift_origin :
736s     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'] 
736s     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']
736s     
736s     extract_all_maps_around_density :
736s     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'] 
736s     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']
736s     
736s     Expected and actual args in calls for around_mask
736s     
736s     box.around_mask.__init__ :
736s     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'] 
736s     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']
736s     
736s     box_all_maps_around_mask_and_shift_origin :
736s     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'] 
736s     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']
736s     
736s     extract_all_maps_around_mask :
736s     Expected :['box_cushion', 'mask_id', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'use_cubic_boxing'] 
736s     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']
736s     
736s     Expected and actual args in calls for around_unique
736s     
736s     box.around_unique.__init__ :
736s     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'] 
736s     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']
736s     
736s     box_all_maps_around_unique_and_shift_origin :
736s     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'] 
736s     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']
736s     
736s     extract_all_maps_around_unique :
736s     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'] 
736s     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']
736s     
736s     Expected and actual args in calls for around_atoms
736s     
736s     cctbx.maptbx.mask.create_mask_around_atoms.__init__ :
736s     Expected :['invert_mask', 'map_manager', 'mask_atoms_atom_radius', 'model', 'n_real', 'self', 'wrapping', 'xray_structure'] 
736s     Found   : ['invert_mask', 'map_manager', 'mask_atoms_atom_radius', 'model', 'n_real', 'self', 'wrapping', 'xray_structure']
736s     
736s     map_model_manager.create_mask_around_atoms :
736s     Expected :['invert_mask', 'mask_atoms_atom_radius', 'mask_id', 'model', 'self', 'soft_mask', 'soft_mask_radius'] 
736s     Found   : ['invert_mask', 'mask_atoms_atom_radius', 'mask_id', 'model', 'self', 'soft_mask', 'soft_mask_radius']
736s     
736s     Expected and actual args in calls for around_edges
736s     
736s     cctbx.maptbx.mask.create_mask_around_edges.__init__ :
736s     Expected :['boundary_radius', 'map_manager', 'self'] 
736s     Found   : ['boundary_radius', 'map_manager', 'self']
736s     
736s     map_model_manager.create_mask_around_edges :
736s     Expected :['boundary_radius', 'mask_id', 'self'] 
736s     Found   : ['boundary_radius', 'boundary_to_smoothing_ratio', 'mask_id', 'self', 'soft_mask_radius']
736s     
736s     Expected and actual args in calls for around_density
736s     
736s     cctbx.maptbx.mask.create_mask_around_density.__init__ :
736s     Expected :['map_manager', 'molecular_mass', 'resolution', 'self', 'sequence', 'solvent_content'] 
736s     Found   : ['map_manager', 'molecular_mass', 'resolution', 'self', 'sequence', 'solvent_content']
736s     
736s     map_model_manager.create_mask_around_density :
736s     Expected :['map_id', 'mask_id', 'resolution', 'self', 'soft_mask', 'soft_mask_radius', 'solvent_content'] 
736s     Found   : ['map_id', 'mask_id', 'resolution', 'self', 'soft_mask', 'soft_mask_radius', 'solvent_content']
736s     OK
736s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_external_sharpening_7.py" [OK] 0.8s
736s   Time:  0.84
736s   Return code: 0
736s   OKs: 1
736s   Standard out:
736s     Skip test_01, chem_data not available
736s     OK
737s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_half_map_sharpening_6.py" [OK] 0.8s
737s   Time:  0.80
737s   Return code: 0
737s   OKs: 1
737s   Standard out:
737s     Skip test_01, chem_data not available
737s     OK
737s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_tls_from_map_8.py" [OK] 0.9s
737s   Time:  0.86
737s   Return code: 0
737s   OKs: 1
737s   Standard out:
737s     Skip test_01, chem_data not available
737s     OK
738s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_cif.py" [OK] 0.8s
738s   Time:  0.83
738s   Return code: 0
738s   OKs: 1
738s   Standard out:
738s     Skip test_01, chem_data not available
738s     OK
743s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
743s 139
743s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
743s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry.py" [FAIL] 5.4s
743s   Time:  5.41
743s   Return code: 139
743s   OKs: 0
743s   Standard error:
743s     Segmentation fault (core dumped)
744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_local_resolution_10.py" [OK] 0.8s
744s   Time:  0.82
744s   Return code: 0
744s   OKs: 1
744s   Standard out:
744s     Skip test_01, chem_data not available
744s     OK
748s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
748s 139
748s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
748s 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] 9.8s
748s   Time:  9.80
748s   Return code: 139
748s   OKs: 0
748s   Standard error:
748s     Segmentation fault (core dumped)
748s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_patterson.py" [OK] 0.1s
748s   Time:  0.10
748s   Return code: 0
748s   OKs: 1
748s   Standard out:
748s     phenix_regression not available, skipping
748s     OK
748s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_restraints_merge.py" [OK] 0.4s
748s   Time:  0.37
748s   Return code: 0
748s   OKs: 0
751s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
751s 139
751s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
751s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_tools.py" [FAIL] 7.7s
751s   Time:  7.73
751s   Return code: 139
751s   OKs: 0
751s   Standard error:
751s     Segmentation fault (core dumped)
751s libtbx.python "/usr/lib/python3/dist-packages/iotbx/ranges.py" [OK] 0.0s
751s   Time:  0.04
751s   Return code: 0
751s   OKs: 1
751s   Standard out:
751s     OK
755s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
755s 139
755s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
755s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_atom_selections_10k.py" [FAIL] 7.2s
755s   Time:  7.25
755s   Return code: 139
755s   OKs: 0
755s   Standard error:
755s     Segmentation fault (core dumped)
755s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_poscar.py" [OK] 0.1s
755s   Time:  0.10
755s   Return code: 0
755s   OKs: 1
755s   Standard out:
755s     Skipping POSCAR tests: input files not available
755s     OK
759s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
759s 139
759s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
759s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_crystal_symmetry_from_any.py" [FAIL] 7.7s
759s   Time:  7.72
759s   Return code: 139
759s   OKs: 0
759s   Standard error:
759s     Segmentation fault (core dumped)
763s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
763s 139
763s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
763s libtbx.python "/usr/lib/python3/dist-packages/iotbx/kriber/tst_strudat.py" [FAIL] 7.4s
763s   Time:  7.41
763s   Return code: 139
763s   OKs: 0
763s   Standard error:
763s     Segmentation fault (core dumped)
766s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
766s 139
766s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
766s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_geometry.py" [FAIL] 7.3s
766s   Time:  7.25
766s   Return code: 139
766s   OKs: 0
766s   Standard error:
766s     Segmentation fault (core dumped)
770s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
770s 139
770s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
770s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_lex_parse_build.py" [FAIL] 7.7s
770s   Time:  7.68
770s   Return code: 139
770s   OKs: 0
770s   Standard error:
770s     Segmentation fault (core dumped)
774s   Standard error:
774s     Segmentation fault (core dumped)
774s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
774s 139
774s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
774s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model.py" [FAIL] 7.8s
774s   Time:  7.83
774s   Return code: 139
774s   OKs: 0
778s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
778s 1
778s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
778s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py" [FAIL] 3.6s
778s   Time:  3.57
778s   Return code: 1
778s   OKs: 0
778s   Standard out:
778s     Skipping tst_validation.exercise_smart_load() because of URLError.
778s   Standard error:
778s     Traceback (most recent call last):
778s       File "/usr/lib/python3.13/urllib/request.py", line 1541, in ftp_open
778s         fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout)
778s       File "/usr/lib/python3.13/urllib/request.py", line 1561, in connect_ftp
778s         return ftpwrapper(user, passwd, host, port, dirs, timeout,
778s                           persistent=False)
778s       File "/usr/lib/python3.13/urllib/request.py", line 2409, in __init__
778s         self.init()
778s         ~~~~~~~~~^^
778s       File "/usr/lib/python3.13/urllib/request.py", line 2418, in init
778s         self.ftp.connect(self.host, self.port, self.timeout)
778s         ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
778s       File "/usr/lib/python3.13/ftplib.py", line 158, in connect
778s         self.sock = socket.create_connection((self.host, self.port), self.timeout,
778s                     ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
778s                                              source_address=self.source_address)
778s                                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
778s       File "/usr/lib/python3.13/socket.py", line 864, in create_connection
778s         raise exceptions[0]
778s       File "/usr/lib/python3.13/socket.py", line 849, in create_connection
778s         sock.connect(sa)
778s         ~~~~~~~~~~~~^^^^
778s     ConnectionRefusedError: [Errno 111] Connection refused
778s     
778s     The above exception was the direct cause of the following exception:
778s     
778s     Traceback (most recent call last):
778s       File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 327, in <module>
778s         exercise(sys.argv[1:])
778s         ~~~~~~~~^^^^^^^^^^^^^^
778s       File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 26, in exercise
778s         exercise_validation()
778s         ~~~~~~~~~~~~~~~~~~~^^
778s       File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 29, in exercise_validation
778s         cd = validation.smart_load_dictionary(name="cif_core.dic")
778s       File "/usr/lib/python3/dist-packages/iotbx/cif/validation.py", line 111, in smart_load_dictionary
778s         url = locate_dictionary(name, registry_location=registry_location)
778s       File "/usr/lib/python3/dist-packages/iotbx/cif/validation.py", line 129, in locate_dictionary
778s         cm = cif.reader(file_object=urlopen(registry_location)).model()
778s                                     ~~~~~~~^^^^^^^^^^^^^^^^^^^
778s       File "/usr/lib/python3.13/urllib/request.py", line 189, in urlopen
778s         return opener.open(url, data, timeout)
778s                ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^
778s       File "/usr/lib/python3.13/urllib/request.py", line 489, in open
778s         response = self._open(req, data)
778s       File "/usr/lib/python3.13/urllib/request.py", line 506, in _open
778s         result = self._call_chain(self.handle_open, protocol, protocol +
778s                                   '_open', req)
778s       File "/usr/lib/python3.13/urllib/request.py", line 466, in _call_chain
778s         result = func(*args)
778s       File "/usr/lib/python3.13/urllib/request.py", line 1558, in ftp_open
778s         raise URLError(exp) from exp
778s     urllib.error.URLError: <urlopen error [Errno 111] Connection refused>
778s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_parser.py" [OK] 0.3s
778s   Time:  0.31
778s   Return code: 0
778s   OKs: 0
778s   Standard out:
778s     1 0 0
778s     1 0 0
778s     1 0 0
778s     1 0 0
778s     1 0 0
778s     1 0 0
778s     1 0 0
778s     1 0 0
778s     1 0 0
778s     0 0 0
778s     0 0 0
778s     1 0 0
778s     0 0 0
778s     0 0 0
778s     1 0 0
778s     1 0 0
778s     1 0 0
778s     1 0 0
778s     1 0 0
778s     1 0 0
778s     1 0 0
778s     1 0 0
778s     1 0 0
778s     1 0 0
778s     1 0 0
778s     1 0 0
778s     0 0 0
778s     1 0 0
778s     1 0 0
778s     1 0 0
778s     1 0 0
778s     1 0 0
778s     0 0 0
778s     0 1 0
778s     0 1 0
778s     0 0 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     0 1 0
778s     1 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s     2 0 0
778s   Standard error:
778s     Segmentation fault (core dumped)
778s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
778s 139
778s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
778s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_restraints.py" [FAIL] 7.9s
778s   Time:  7.93
778s   Return code: 139
778s   OKs: 0
779s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_citations.py" [OK] 0.5s
779s   Time:  0.49
779s   Return code: 0
779s   OKs: 1
779s   Standard out:
779s     OK
779s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model_builder.py" [OK] 0.3s
779s   Time:  0.34
779s   Return code: 0
779s   OKs: 0
783s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
783s 139
783s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
783s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_lex_parse_build.py" [FAIL] 4.2s
783s   Time:  4.16
783s   Return code: 139
783s   OKs: 0
783s   Standard error:
783s     Segmentation fault (core dumped)
786s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
786s 139
786s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
786s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_hklf.py" [FAIL] 7.7s
786s   Time:  7.65
786s   Return code: 139
786s   OKs: 0
786s   Standard error:
786s     Segmentation fault (core dumped)
790s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
790s 139
790s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
790s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_writer.py" [FAIL] 7.5s
790s   Time:  7.50
790s   Return code: 139
790s   OKs: 0
790s   Standard error:
790s     Segmentation fault (core dumped)
794s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
794s 139
794s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
794s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_fvar_encoding.py" [FAIL] 7.4s
794s   Time:  7.39
794s   Return code: 139
794s   OKs: 0
794s   Standard error:
794s     Segmentation fault (core dumped)
794s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif.py" [OK] 0.3s
794s   Time:  0.32
794s   Return code: 0
794s   OKs: 1
794s   Standard out:
794s     OK
797s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
797s 134
797s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
797s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_pdb.py" [FAIL] 7.1s
797s   Time:  7.15
797s   Return code: 134
797s   OKs: 0
797s   Standard error:
797s     *** buffer overflow detected ***: terminated
797s     Aborted (core dumped)
800s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy_2.py" [OK] 2.3s
800s   Time:  2.28
800s   Return code: 0
800s   OKs: 1
800s   Standard out:
800s     OK
800s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_tls.py" [OK] 0.8s
800s   Time:  0.79
800s   Return code: 0
800s   OKs: 1
800s   Standard out:
800s     Skipping exercise_mmcif_tls(): missing phenix_regression directory.
800s     OK
801s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/hybrid_36.py" exercise [OK] 0.1s
801s   Time:  0.10
801s   Return code: 0
801s   OKs: 1
801s   Standard out:
801s     OK
802s "/usr/lib/cctbx/python3.13/iotbx/pdb/hybrid_36_fem" [OK] 1.2s
802s   Time:  1.22
802s   Return code: 0
802s   OKs: 0
802s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
802s 134
802s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
802s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy.py" [FAIL] 8.0s
802s   Time:  8.02
802s   Return code: 134
802s   OKs: 0
802s   Standard error:
802s     *** buffer overflow detected ***: terminated
802s     Aborted (core dumped)
802s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy_atom_sort.py" [OK] 0.4s
802s   Time:  0.38
802s   Return code: 0
802s   OKs: 1
802s   Standard out:
802s     OK
803s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy_flip_symmetric.py" [OK] 0.3s
803s   Time:  0.34
803s   Return code: 0
803s   OKs: 0
803s   Standard out:
803s     chem_data is missing, skipping test
803s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_selected_hierarchy_flip.py" [OK] 0.4s
803s   Time:  0.38
803s   Return code: 0
803s   OKs: 0
806s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
806s 139
806s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
806s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy.py" [FAIL] 4.5s
806s   Time:  4.52
806s   Return code: 139
806s   OKs: 0
806s   Standard error:
806s     Segmentation fault (core dumped)
810s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
810s 139
810s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
810s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_ext.py" [FAIL] 6.7s
810s   Time:  6.75
810s   Return code: 139
810s   OKs: 0
810s   Standard error:
810s     Segmentation fault (core dumped)
810s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_rna_dna_atom_names.py" [OK] 0.3s
810s   Time:  0.34
810s   Return code: 0
810s   OKs: 1
810s   Standard out:
810s     OK
811s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_name_interpretation.py" [OK] 0.3s
811s   Time:  0.34
811s   Return code: 0
811s   OKs: 1
811s   Standard out:
811s     OK
811s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_extract_rfactors_resolutions_sigma.py" [OK] 0.3s
811s   Time:  0.34
811s   Return code: 0
811s   OKs: 1
811s   Standard out:
811s     OK
811s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/modified_aa_names.py" [OK] 0.0s
811s   Time:  0.04
811s   Return code: 0
811s   OKs: 0
811s   Standard out:
811s     2141
811s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/modified_rna_dna_names.py" [OK] 0.0s
811s   Time:  0.04
811s   Return code: 0
811s   OKs: 0
811s   Standard out:
811s     792
811s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_sheet.py" [OK] 0.3s
811s   Time:  0.35
811s   Return code: 0
811s   OKs: 1
811s   Standard out:
811s     OK
811s     u+s,u,s: 0.25 0.22 0.03
814s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
814s 139
814s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
814s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection.py" [FAIL] 7.5s
814s   Time:  7.48
814s   Return code: 139
814s   OKs: 0
814s   Standard error:
814s     Segmentation fault (core dumped)
814s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation_long.py" [OK] 0.4s
814s   Time:  0.36
814s   Return code: 0
814s   OKs: 1
814s   Standard out:
814s     OK time =   0.014
814s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/secondary_structure.py" [OK] 0.4s
814s   Time:  0.37
814s   Return code: 0
814s   OKs: 0
818s   Standard error:
818s     Segmentation fault (core dumped)
818s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
818s 139
818s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
818s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation.py" [FAIL] 6.3s
818s   Time:  6.28
818s   Return code: 139
818s   OKs: 0
818s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_secondary_structure.py" [OK] 0.8s
818s   Time:  0.76
818s   Return code: 0
818s   OKs: 5
818s   Standard out:
818s     OK
818s     OK
818s     OK
818s     OK
818s     OK
822s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
822s 139
822s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
822s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection_string.py" [FAIL] 7.5s
822s   Time:  7.47
822s   Return code: 139
822s   OKs: 0
822s   Standard error:
822s     Segmentation fault (core dumped)
823s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_secondary_structure_2.py" [OK] 1.5s
823s   Time:  1.54
823s   Return code: 0
823s   OKs: 2
823s   Standard out:
823s     OK
823s     OK
824s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/remediation/tst_remediator.py" [OK] 0.9s
824s   Time:  0.89
824s   Return code: 0
824s   OKs: 0
824s   Standard out:
824s     chem_data is not available for remediator tests, skipping
825s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_to_map_simple.py" [OK] 0.4s
825s   Time:  0.38
825s   Return code: 0
825s   OKs: 0
825s   Standard out:
825s     Usage: iotbx.python pdb_to_map_simple.py [options] pdb_file...
825s     
825s     Options:
825s       -h, --help     show this help message and exit
825s       --d_min=FLOAT  high-resolution limit for structure-factor calculation
826s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
826s 139
826s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
826s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_utils.py" [FAIL] 7.8s
826s   Time:  7.79
826s   Return code: 139
826s   OKs: 0
826s   Standard error:
826s     Segmentation fault (core dumped)
827s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_tardy_conf_sampling_simple.py" [OK] 0.3s
827s   Time:  0.34
827s   Return code: 0
827s   OKs: 0
827s   Standard out:
827s     Time importing extensions: 0.24
827s     skipping test: phenix_regression not available.
830s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
830s 134
830s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
830s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_truncate_to_ala/tst.py" [FAIL] 5.5s
830s   Time:  5.47
830s   Return code: 134
830s   OKs: 0
830s   Standard error:
830s     *** buffer overflow detected ***: terminated
830s     Aborted (core dumped)
835s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
835s 139
835s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
835s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_examples.py" [FAIL] 8.1s
835s   Time:  8.11
835s   Return code: 139
835s   OKs: 0
835s   Standard error:
835s     Segmentation fault (core dumped)
839s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
839s 139
839s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
839s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/space_group_symbols.py" [FAIL] 8.3s
839s   Time:  8.35
839s   Return code: 139
839s   OKs: 0
839s   Standard error:
839s     Segmentation fault (core dumped)
843s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
843s 139
843s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
843s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/tst_cns.py" [FAIL] 8.3s
843s   Time:  8.35
843s   Return code: 139
843s   OKs: 0
843s   Standard error:
843s     Segmentation fault (core dumped)
847s   Standard error:
847s     Segmentation fault (core dumped)
847s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
847s 139
847s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
847s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_merge.py" P31 [FAIL] 7.9s
847s   Time:  7.93
847s   Return code: 139
847s   OKs: 0
850s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
850s 139
850s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
850s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/no_merge_original_index.py" [FAIL] 6.9s
850s   Time:  6.88
850s   Return code: 139
850s   OKs: 0
850s   Standard error:
850s     Segmentation fault (core dumped)
854s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
854s 139
854s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
854s libtbx.python "/usr/lib/python3/dist-packages/iotbx/ccp4_map/tst.py" [FAIL] 7.1s
854s   Time:  7.08
854s   Return code: 139
854s   OKs: 0
854s   Standard error:
854s     Segmentation fault (core dumped)
858s   Standard error:
858s     Segmentation fault (core dumped)
858s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
858s 139
858s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
858s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_ext.py" [FAIL] 7.8s
858s   Time:  7.84
858s   Return code: 139
858s   OKs: 0
861s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
861s 139
861s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
861s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_extract_from_symmetry_lib.py" [FAIL] 7.7s
861s   Time:  7.73
861s   Return code: 139
861s   OKs: 0
861s   Standard error:
861s     /usr/lib/python3/dist-packages/ccp4io_adaptbx/__init__.py:25: UserWarning: ccp4io_adaptbx: cannot locate syminfo.lib
861s       warnings.warn("ccp4io_adaptbx: cannot locate syminfo.lib")
861s     Segmentation fault (core dumped)
862s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_miller_dict.py" [OK] 0.3s
862s   Time:  0.31
862s   Return code: 0
862s   OKs: 0
862s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_unmerged.py" [OK] 0.3s
862s   Time:  0.30
862s   Return code: 0
862s   OKs: 0
862s   Standard out:
862s     Title: .
862s     Space group symbol from file: I23
862s     Space group number from file: 197
862s     Space group from matrices: I 2 3 (No. 197)
862s     Point group symbol from file: PG23
862s     Number of batches: 45
862s     Number of crystals: 2
862s     Number of Miller indices: 13
862s     Resolution range: 39.0022 31.8451
862s     History:
862s       From MTZUTILS 21/11/2017 16:26:11 after history:
862s       From MOSFLM run on  1/ 7/08
862s       From MOSFLM run on  1/ 7/08
862s     Crystal 1:
862s       Name: HKL_base
862s       Project: HKL_base
862s       Id: 1
862s       Unit cell: (78.0043, 78.0043, 78.0043, 90, 90, 90)
862s       Number of datasets: 1
862s       Dataset 1:
862s         Name: HKL_base
862s         Id: 0
862s         Wavelength: 0
862s         Number of columns: 18
862s         label        #valid  %valid     min      max type
862s         H                13 100.00%    0.00     1.00 H: index h,k,l
862s         K                13 100.00%    2.00     2.00 H: index h,k,l
862s         L                13 100.00%    0.00     1.00 H: index h,k,l
862s         M_ISYM           13 100.00%    6.00   272.00 Y: M/ISYM, packed partial/reject flag and symmetry number
862s         BATCH            13 100.00%   16.00    43.00 B: BATCH number
862s         I                13 100.00%  -19.71     7.39 J: intensity
862s         SIGI             13 100.00%    0.41     3.05 Q: standard deviation
862s         IPR              13 100.00%  -10.84     4.99 J: intensity
862s         SIGIPR           13 100.00%    0.41     3.05 Q: standard deviation
862s         FRACTIONCALC     13 100.00%    0.07     1.15 R: real
862s         XDET             13 100.00% 1099.43  1215.80 R: real
862s         YDET             13 100.00% 1110.92  1201.06 R: real
862s         ROT              13 100.00%   15.33    41.55 R: real
862s         WIDTH            13 100.00%    0.37     2.19 R: real
862s         LP               13 100.00%    0.00     0.03 R: real
862s         MPART            13 100.00%    0.00   303.00 I: integer
862s         FLAG             13 100.00%    0.00    40.00 I: integer
862s         BGPKRATIOS       13 100.00%    8.04 10610.05 R: real
862s     Crystal 2:
862s       Name: DEFAULT
862s       Project: AUTOMATIC
862s       Id: 2
862s       Unit cell: (78.0043, 78.0043, 78.0043, 90, 90, 90)
862s       Number of datasets: 1
862s       Dataset 1:
862s         Name: NATIVE_SWEEP1
862s         Id: 1
862s         Wavelength: 0.979
862s         Number of columns: 0
862s     asu:        (1, 2, 1)    orig:      (-1, 1, -2)    M/ISYM:  15
862s     asu:        (1, 2, 1)    orig:       (1, -1, 2)    M/ISYM: 272
862s     asu:        (1, 2, 1)    orig:       (1, -1, 2)    M/ISYM: 272
862s     asu:        (1, 2, 1)    orig:       (-1, 2, 1)    M/ISYM:   6
862s     asu:        (1, 2, 1)    orig:      (1, -2, -1)    M/ISYM: 261
862s     asu:        (1, 2, 1)    orig:      (-1, 2, -1)    M/ISYM: 263
862s     asu:        (1, 2, 1)    orig:      (1, -2, -1)    M/ISYM: 261
862s     asu:        (1, 2, 1)    orig:      (-1, 2, -1)    M/ISYM: 263
862s     asu:        (1, 2, 1)    orig:       (1, -2, 1)    M/ISYM: 264
862s     asu:        (1, 2, 1)    orig:       (1, -2, 1)    M/ISYM: 264
862s     asu:        (0, 2, 0)    orig:       (0, 0, -2)    M/ISYM: 266
862s     asu:        (0, 2, 0)    orig:       (0, 0, -2)    M/ISYM: 266
862s     asu:        (0, 2, 0)    orig:       (0, 0, -2)    M/ISYM: 266
865s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
865s 139
865s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
865s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_dano.py" [FAIL] 7.0s
865s   Time:  7.03
865s   Return code: 139
865s   OKs: 0
865s   Standard error:
865s     Segmentation fault (core dumped)
865s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/tst_mtz_free_flipper.py" [OK] 0.3s
865s   Time:  0.35
865s   Return code: 0
865s   OKs: 0
865s   Standard out:
865s     Skipping exercise(): input file not available
865s     u+s,u,s: 0.27 0.22 0.05
868s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
868s 139
868s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
868s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst.py" P31 [FAIL] 6.5s
868s   Time:  6.47
868s   Return code: 139
868s   OKs: 0
868s   Standard error:
868s     Segmentation fault (core dumped)
869s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_adsc.py" [OK] 0.3s
869s   Time:  0.28
869s   Return code: 0
869s   OKs: 1
869s   Standard out:
869s     Skipping exercise_adscread(): input file not available
869s     OK
869s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_detectors.py" [OK] 0.1s
869s   Time:  0.09
869s   Return code: 0
869s   OKs: 0
869s   Standard out:
869s     bpcx_regression not configured, skipping test
872s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
872s 139
872s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
872s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_utils.py" [FAIL] 6.9s
872s   Time:  6.92
872s   Return code: 139
872s   OKs: 0
872s   Standard error:
872s     Segmentation fault (core dumped)
875s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
875s 139
875s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
875s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xplor/tst_xplormap.py" [FAIL] 6.5s
875s   Time:  6.47
875s   Return code: 139
875s   OKs: 0
875s   Standard error:
875s     Segmentation fault (core dumped)
875s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdbx_mmcif_tutorial.py" [OK] 0.1s
875s   Time:  0.09
875s   Return code: 0
875s   OKs: 1
875s   Standard out:
875s     phenix_regression not configured, skipping tst_pdbx_mmcif_tutorial.py
875s     OK
879s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
879s 139
879s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
879s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phases.py" P31 [FAIL] 6.6s
879s   Time:  6.60
879s   Return code: 139
879s   OKs: 0
879s   Standard error:
879s     Segmentation fault (core dumped)
885s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
885s 1
885s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
885s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py" [FAIL] 9.9s
885s   Time:  9.90
885s   Return code: 1
885s   OKs: 0
885s   Standard error:
885s     Traceback (most recent call last):
885s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 477, in <module>
885s         exercise(sys.argv[1:])
885s         ~~~~~~~~^^^^^^^^^^^^^^
885s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 22, in exercise
885s           run_and_compare(
885s           ~~~~~~~~~~~~~~~^
885s             ['iotbx.lattice_symmetry'
885s             ^^^^^^^^^^^^^^^^^^^^^^^^^
885s         ...<31 lines>...
885s         
885s         
885s         """)
885s         ^^^^
885s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 17, in run_and_compare
885s         command=command).raise_if_errors().stdout_lines
885s                          ~~~~~~~~~~~~~~~^^
885s       File "/usr/lib/python3/dist-packages/libtbx/easy_run.py", line 46, in raise_if_errors
885s         raise Error(msg)
885s     RuntimeError: child process stderr output:
885s       command: 'iotbx.lattice_symmetry --unit_cell="12.7923,12.8923,29.4356,102.846,103.846,22.7475"'
885s       Segmentation fault (core dumped)
885s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_plots.py" [OK] 0.1s
885s   Time:  0.09
885s   Return code: 0
885s   OKs: 1
885s   Standard out:
885s     OK
886s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_csv_utils.py" [OK] 0.2s
886s   Time:  0.20
886s   Return code: 0
886s   OKs: 1
886s   Standard out:
886s     OK
886s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
886s 139
886s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
886s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_statistics.py" Fdd2 P31m [FAIL] 7.6s
886s   Time:  7.64
886s   Return code: 139
886s   OKs: 0
886s   Standard error:
886s     Segmentation fault (core dumped)
886s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_bioinformatics.py" [OK] 0.1s
886s   Time:  0.14
886s   Return code: 0
886s   OKs: 3
886s   Standard out:
886s     Testing guess_chain_types ... OK
886s     Testing merge_sequences ... OK
886s     testEquality (__main__.test_sequence.testEquality) ... ok
886s     testNonEquality (__main__.test_sequence.testNonEquality) ... ok
886s     testFormat (__main__.test_fasta_sequence.testFormat) ... ok
886s     testStr (__main__.test_fasta_sequence.testStr) ... ok
886s     testFormat (__main__.test_pir_sequence.testFormat) ... ok
886s     testStr (__main__.test_pir_sequence.testStr) ... ok
886s     testConservationCode (__main__.test_midline.testConservationCode) ... ok
886s     testMidline (__main__.test_midline.testMidline) ... ok
886s     test__str__ (__main__.test_alignment.test__str__) ... ok
886s     test_copy (__main__.test_alignment.test_copy) ... ok
886s     test_error (__main__.test_alignment.test_error) ... ok
886s     test_extend (__main__.test_alignment.test_extend) ... ok
886s     test_identity_count (__main__.test_alignment.test_identity_count) ... ok
886s     test_identity_fraction (__main__.test_alignment.test_identity_fraction) ... ok
886s     test_length (__main__.test_alignment.test_length) ... ok
886s     test_multiplicity (__main__.test_alignment.test_multiplicity) ... ok
886s     test__str__ (__main__.test_fasta_alignment.test__str__) ... ok
886s     test_copy (__main__.test_fasta_alignment.test_copy) ... ok
886s     test_error (__main__.test_fasta_alignment.test_error) ... ok
886s     test_format (__main__.test_fasta_alignment.test_format) ... ok
886s     test__str__ (__main__.test_pir_alignment.test__str__) ... ok
886s     test_copy (__main__.test_pir_alignment.test_copy) ... ok
886s     test_error (__main__.test_pir_alignment.test_error) ... ok
886s     test_format (__main__.test_pir_alignment.test_format) ... ok
886s     test__str__ (__main__.test_clustal_alignment.test__str__) ... ok
886s     test_copy (__main__.test_clustal_alignment.test_copy) ... ok
886s     test_format (__main__.test_clustal_alignment.test_format) ... ok
886s     testFasta (__main__.test_sequence_parse.testFasta) ... ok
886s     testPir (__main__.test_sequence_parse.testPir) ... ok
886s     testSequence (__main__.test_sequence_parse.testSequence) ... ok
886s     testTolerantPir (__main__.test_sequence_parse.testTolerantPir) ... ok
886s     test_dbfetch_parse (__main__.test_sequence_parse.test_dbfetch_parse) ... ok
886s     test_filename_selection (__main__.test_sequence_parse.test_filename_selection) ... ok
886s     test_known_formats (__main__.test_sequence_parse.test_known_formats) ... ok
886s     test_ls_parse (__main__.test_sequence_parse.test_ls_parse) ... ok
886s     test_tf_parse (__main__.test_sequence_parse.test_tf_parse) ... ok
886s     testAli (__main__.test_alignment_parse.testAli) ... ok
886s     testClustal (__main__.test_alignment_parse.testClustal) ... ok
886s     testFasta (__main__.test_alignment_parse.testFasta) ... ok
886s     testPir (__main__.test_alignment_parse.testPir) ... ok
886s     test_filename_selection (__main__.test_alignment_parse.test_filename_selection) ... ok
886s     test_known_formats (__main__.test_alignment_parse.test_known_formats) ... ok
886s     test_process_header (__main__.test_hhsearch_parser.test_process_header) ... ok
886s     test_process_hits (__main__.test_hhsearch_parser.test_process_hits) ... ok
886s     test_process_header (__main__.test_hhalign_parser.test_process_header) ... ok
886s     test_process_hits (__main__.test_hhalign_parser.test_process_hits) ... ok
886s     
886s     ----------------------------------------------------------------------
886s     Ran 46 tests in 0.007s
886s     
886s     OK
890s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
890s 139
890s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
890s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_file_reader.py" [FAIL] 4.4s
890s   Time:  4.37
890s   Return code: 139
890s   OKs: 0
890s   Standard error:
890s     Segmentation fault (core dumped)
898s   Standard error:
898s     *** buffer overflow detected ***: terminated
898s     Aborted (core dumped)
898s     Traceback (most recent call last):
898s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py", line 138, in <module>
898s         exercise()
898s         ~~~~~~~~^^
898s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py", line 48, in exercise
898s         assert not easy_run.call("iotbx.pdb.box_around_molecule %s.pdb" % (
898s                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
898s             prefix))
898s             ^^^^^^^^
898s     AssertionError
898s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
898s 1
898s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
898s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py" [FAIL] 11.0s
898s   Time: 11.04
898s   Return code: 1
898s   OKs: 0
898s   Standard out:
898s     Starting iotbx.pdb.box_around_molecule
898s     on Thu Mar 13 10:58:56 2025 by ubuntu
898s     ===============================================================================
898s     
898s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_input.py" [OK] 0.3s
898s   Time:  0.32
898s   Return code: 0
898s   OKs: 0
898s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
898s 134
898s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
898s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_segids.py" [FAIL] 8.4s
898s   Time:  8.37
898s   Return code: 134
898s   OKs: 0
898s   Standard error:
898s     *** buffer overflow detected ***: terminated
898s     Aborted (core dumped)
899s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_multimodel.py" [OK] 0.6s
899s   Time:  0.65
899s   Return code: 0
899s   OKs: 0
899s   Standard out:
899s     ['_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']
899s     ['_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']
899s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_add_conformations.py" [OK] 0.3s
899s   Time:  0.32
899s   Return code: 0
899s   OKs: 0
899s   Standard out:
899s     phenix_regression not available, skipping test.
902s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
902s 134
902s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
902s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_forward_compatible_pdb.py" [FAIL] 4.0s
902s   Time:  3.97
902s   Return code: 134
902s   OKs: 0
902s   Standard error:
902s     *** buffer overflow detected ***: terminated
902s     Aborted (core dumped)
902s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reindex.py" [OK] 0.1s
902s   Time:  0.10
902s   Return code: 0
902s   OKs: 1
902s   Standard out:
902s     Skipping
902s     OK
905s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
905s 139
905s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
905s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_symmetry.py" [FAIL] 5.7s
905s   Time:  5.70
905s   Return code: 139
905s   OKs: 0
905s   Standard error:
905s     Segmentation fault (core dumped)
908s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
908s 139
908s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
908s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_editor.py" [FAIL] 6.5s
908s   Time:  6.51
908s   Return code: 139
908s   OKs: 0
908s   Standard error:
908s     Segmentation fault (core dumped)
909s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_as_fasta.py" [OK] 0.3s
909s   Time:  0.33
909s   Return code: 0
909s   OKs: 1
909s   Standard out:
909s     OK
909s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_link_records.py" [OK] 0.3s
909s   Time:  0.35
909s   Return code: 0
909s   OKs: 0
909s   Standard out:
909s     Can not initialize monomer_library, skipping test.
909s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_merging_statistics.py" [OK] 0.2s
909s   Time:  0.24
909s   Return code: 0
909s   OKs: 1
909s   Standard out:
909s     phenix_regression not configured, skipping.
909s     OK
915s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
915s 1
915s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
915s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py" [FAIL] 10.0s
915s   Time: 10.00
915s   Return code: 1
915s   OKs: 0
915s   Standard error:
915s     Traceback (most recent call last):
915s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py", line 60, in <module>
915s         exercise()
915s         ~~~~~~~~^^
915s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py", line 48, in exercise
915s         assert (len(out.stdout_lines) == 2) and (len(out.stderr_lines) == 0)
915s                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
915s     AssertionError
916s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
916s 139
916s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
916s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_map_coefficients.py" [FAIL] 6.3s
916s   Time:  6.32
916s   Return code: 139
916s   OKs: 0
916s   Standard error:
916s     Segmentation fault (core dumped)
916s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_xparm.py" [OK] 0.1s
916s   Time:  0.10
916s   Return code: 0
916s   OKs: 3
916s   Standard out:
916s     OK
916s     OK
916s     OK
916s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_xds_inp.py" [OK] 0.1s
916s   Time:  0.11
916s   Return code: 0
916s   OKs: 1
916s   Standard out:
916s     OK
923s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
923s 1
923s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
923s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py" [FAIL] 8.1s
923s   Time:  8.08
923s   Return code: 1
923s   OKs: 0
923s   Standard out:
923s     iotbx.pdb.sort_atoms tst_sort_atoms_1.pdb
923s   Standard error:
923s     Segmentation fault (core dumped)
923s     Traceback (most recent call last):
923s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py", line 815, in <module>
923s         exercise_1()
923s         ~~~~~~~~~~^^
923s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py", line 806, in exercise_1
923s         assert not easy_run.call(cmd)
923s                ^^^^^^^^^^^^^^^^^^^^^^
923s     AssertionError
923s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_spots_xds.py" [OK] 0.1s
923s   Time:  0.10
923s   Return code: 0
923s   OKs: 1
923s   Standard out:
923s     OK
924s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_as_cif.py" [OK] 0.5s
924s   Time:  0.46
924s   Return code: 0
924s   OKs: 1
924s   Standard out:
924s     Can not initialize monomer_library, skipping tst_pdb_as_cif.
924s     OK
924s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
924s 139
924s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
924s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_integrate_hkl.py" [FAIL] 8.5s
924s   Time:  8.50
924s   Return code: 139
924s   OKs: 0
924s   Standard error:
924s     Segmentation fault (core dumped)
928s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
928s 139
928s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
928s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_no_merge_original_index.py" [FAIL] 4.3s
928s   Time:  4.34
928s   Return code: 139
928s   OKs: 0
928s   Standard error:
928s     Segmentation fault (core dumped)
932s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
932s 139
932s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
932s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_export_scalepack_unmerged.py" [FAIL] 7.3s
932s   Time:  7.29
932s   Return code: 139
932s   OKs: 0
932s   Standard error:
932s     Segmentation fault (core dumped)
932s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_mtrix_biomt_cmdl.py" [OK] 0.3s
932s   Time:  0.33
932s   Return code: 0
932s   OKs: 0
932s   Standard out:
932s     Skipping tests: phenix not found
933s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_mmcif_biomt_reduction_output.py" [OK] 0.8s
933s   Time:  0.81
933s   Return code: 0
933s   OKs: 0
933s   Standard out:
933s     chem_data is not available, skipping
935s   Standard error:
935s     Segmentation fault (core dumped)
935s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
935s 139
935s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
935s libtbx.python "/usr/lib/python3/dist-packages/iotbx/dsn6/tst.py" P31 [FAIL] 6.9s
935s   Time:  6.90
935s   Return code: 139
935s   OKs: 0
938s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
938s 139
938s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
938s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_ligs.py" [FAIL] 5.7s
938s   Time:  5.69
938s   Return code: 139
938s   OKs: 0
938s   Standard error:
938s     Segmentation fault (core dumped)
942s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
942s 139
942s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
942s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_broken_chain.py" [FAIL] 7.3s
942s   Time:  7.33
942s   Return code: 139
942s   OKs: 0
942s   Standard error:
942s     Segmentation fault (core dumped)
946s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
946s 139
946s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
946s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_shortcut_1.py" [FAIL] 7.5s
946s   Time:  7.51
946s   Return code: 139
946s   OKs: 0
946s   Standard error:
946s     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/iotbx/regression/ncs/tst_ncs_groups_preprocessing.py" [FAIL] 7.9s
950s   Time:  7.94
950s   Return code: 139
950s   OKs: 0
950s   Standard error:
950s     Segmentation fault (core dumped)
954s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
954s 139
954s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
954s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_input.py" [FAIL] 8.2s
954s   Time:  8.23
954s   Return code: 139
954s   OKs: 0
954s   Standard error:
954s     Segmentation fault (core dumped)
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/iotbx/regression/ncs/tst_ncs_user_selections.py" [FAIL] 7.8s
958s   Time:  7.79
958s   Return code: 139
958s   OKs: 0
958s   Standard error:
958s     Segmentation fault (core dumped)
962s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
962s 139
962s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
962s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs.py" [FAIL] 8.0s
962s   Time:  8.01
962s   Return code: 139
962s   OKs: 0
962s   Standard error:
962s     Segmentation fault (core dumped)
966s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
966s 139
966s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
966s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_without_validation.py" [FAIL] 8.1s
966s   Time:  8.08
966s   Return code: 139
966s   OKs: 0
966s   Standard error:
966s     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/iotbx/pdb/tst_read_mtrix_records_from_cif.py" [FAIL] 7.7s
970s   Time:  7.65
970s   Return code: 139
970s   OKs: 0
970s   Standard error:
970s     Segmentation fault (core dumped)
974s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
974s 139
974s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
974s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_show_systematic_absences.py" [FAIL] 7.6s
974s   Time:  7.61
974s   Return code: 139
974s   OKs: 0
974s   Standard error:
974s     Segmentation fault (core dumped)
974s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_reader.py" [OK] 0.4s
974s   Time:  0.43
974s   Return code: 0
974s   OKs: 1
974s   Standard out:
974s     OK
977s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
977s 139
977s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
977s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_miller_sort_asu.py" [FAIL] 7.0s
977s   Time:  7.03
977s   Return code: 139
977s   OKs: 0
977s   Standard error:
977s     Segmentation fault (core dumped)
977s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_alignment_as_hsearch.py" [OK] 0.1s
977s   Time:  0.13
977s   Return code: 0
977s   OKs: 0
977s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_ebi_wu_blast_xml.py" [OK] 0.1s
977s   Time:  0.13
977s   Return code: 0
977s   OKs: 0
977s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_ncbi_blast_xml.py" [OK] 0.1s
977s   Time:  0.13
977s   Return code: 0
977s   OKs: 0
978s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/pdb_info.py" [OK] 0.9s
978s   Time:  0.90
978s   Return code: 0
978s   OKs: 0
981s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
981s 134
981s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
981s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_xray_scale.py" [FAIL] 7.2s
981s   Time:  7.16
981s   Return code: 134
981s   OKs: 0
981s   Standard error:
981s     *** buffer overflow detected ***: terminated
981s     Aborted (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/iotbx/regression/tst_cif_as_pdb_1atom.py" [FAIL] 6.9s
985s   Standard error:
985s     Segmentation fault (core dumped)
985s   Time:  6.89
985s   Return code: 139
985s   OKs: 0
989s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
989s 139
989s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
989s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_1.py" [FAIL] 7.9s
989s   Time:  7.91
989s   Return code: 139
989s   OKs: 0
989s   Standard error:
989s     Segmentation fault (core dumped)
997s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
997s 1
997s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
997s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py" [FAIL] 11.5s
997s   Time: 11.47
997s   Return code: 1
997s   OKs: 0
997s   Standard error:
997s     Traceback (most recent call last):
997s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py", line 395, in <module>
997s         tst_1()
997s         ~~~~~^^
997s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py", line 370, in tst_1
997s         assert os.path.isfile('%s.cif_%s_000.mtz' % (prefix, bn))
997s                ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
997s     AssertionError
998s   Standard error:
998s     *** buffer overflow detected ***: terminated
998s     Aborted (core dumped)
998s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
998s 134
998s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
998s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_all_chain_ids.py" [FAIL] 8.8s
998s   Time:  8.80
998s   Return code: 134
998s   OKs: 0
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/iotbx/regression/tst_extract_xtal_data.py" [FAIL] 5.1s
1002s   Time:  5.07
1002s   Return code: 139
1002s   OKs: 0
1002s   Standard error:
1002s     Segmentation fault (core dumped)
1002s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mtz_as_cif.py" [OK] 0.4s
1002s   Time:  0.45
1002s   Return code: 0
1002s   OKs: 1
1002s   Standard out:
1002s     Skipping 1akg.mtz test: input file not available
1002s     Skipping 1zff.mtz test: input file not available
1002s     Skipping l.mtz test: input file not available
1002s     Skipping outside_4_exptl_fobs_phases_freeR_flags.mtz test: input file not available
1002s     Skipping r1wqzsf.mtz test: input file not available
1002s     Skipping ur0013.sf.mtz test: input file not available
1002s     Skipping 1aba_test.mtz test: input file not available
1002s     OK
1002s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_group_rounding.py" [OK] 0.3s
1002s   Time:  0.34
1002s   Return code: 0
1002s   OKs: 0
1006s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1006s 139
1006s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1006s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cli_parser.py" [FAIL] 7.8s
1006s   Time:  7.84
1006s   Return code: 139
1006s   OKs: 0
1006s   Standard error:
1006s     Segmentation fault (core dumped)
1006s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_merge_atoms_at_end_to_residues.py" [OK] 0.3s
1006s   Time:  0.33
1006s   Return code: 0
1006s   OKs: 1
1006s   Standard out:
1006s     [('1', 22), ('3', 17), ('1', 1), ('3', 1)]
1006s     [('1', 22), ('3', 18), ('1', 1)]
1006s     OK
1007s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_chain_ids_1.py" [OK] 1.2s
1007s   Time:  1.15
1007s   Return code: 0
1007s   OKs: 1
1007s   Standard out:
1007s     
1007s     total number of:
1007s       models:       1
1007s       chains:       3
1007s       alt. conf.:   0
1007s       residues:    12
1007s       atoms:      174
1007s       anisou:       0
1007s     number of atom element+charge types: 4
1007s     histogram of atom element+charge frequency:
1007s       " H  " 78
1007s       " C  " 60
1007s       " O  " 21
1007s       " N  " 15
1007s     residue name classes:
1007s       "common_amino_acid" 12
1007s     number of chain ids: 3
1007s     histogram of chain id frequency:
1007s       "A"   1
1007s       "A-2" 1
1007s       "A-5" 1
1007s     number of alt. conf. ids: 0
1007s     number of residue names: 4
1007s     histogram of residue name frequency:
1007s       "ASN" 3
1007s       "PHE" 3
1007s       "SER" 3
1007s       "THR" 3
1007s     Can not initialize monomer_library, skipping test.
1007s     OK. Time:    0.414
1008s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_1.py" [OK] 0.7s
1008s   Time:  0.70
1008s   Return code: 0
1008s   OKs: 1
1008s   Standard out:
1008s     OK. Time:    0.373
1009s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_2.py" [OK] 0.7s
1009s   Time:  0.74
1009s   Return code: 0
1009s   OKs: 1
1009s   Standard out:
1009s     Can not initialize monomer_library, skipping test.
1009s     OK. Time:    0.014
1009s   Standard error:
1009s     *** buffer overflow detected ***: terminated
1009s     Aborted (core dumped)
1009s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1009s 134
1009s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1009s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_occupancies_rounding.py" [FAIL] 6.8s
1009s   Time:  6.76
1009s   Return code: 134
1009s   OKs: 0
1009s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_3.py" [OK] 0.8s
1009s   Time:  0.75
1009s   Return code: 0
1009s   OKs: 1
1009s   Standard out:
1009s     Can not initialize monomer_library, skipping test.
1009s     OK. Time:    0.015
1010s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_copy_select.py" [OK] 0.3s
1010s   Time:  0.35
1010s   Return code: 0
1010s   OKs: 1
1010s   Standard out:
1010s     There is no info: pdb=" N             "
1010s     And no parent: None
1010s     Info is gone: pdb=" N             "
1010s     Info is still here: pdb=" N   GLY A   1 "
1010s     OK. Time:    0.030
1010s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_4.py" [OK] 0.8s
1010s   Time:  0.76
1010s   Return code: 0
1010s   OKs: 1
1010s   Standard out:
1010s     Can not initialize monomer_library, skipping test.
1010s     OK. Time:    0.015
1010s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_id_str.py" [OK] 0.3s
1010s   Time:  0.33
1010s   Return code: 0
1010s   OKs: 0
1010s   Standard out:
1010s     u+s,u,s: 0.25 0.21 0.04
1010s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_altlocs.py" [OK] 0.3s
1010s   Time:  0.31
1010s   Return code: 0
1010s   OKs: 1
1010s   Standard out:
1010s     OK
1014s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1014s 139
1014s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1014s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_debug_write.py" [FAIL] 3.4s
1014s   Time:  3.43
1014s   Return code: 139
1014s   OKs: 0
1014s   Standard error:
1014s     Segmentation fault (core dumped)
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/iotbx/regression/ncs/tst_ncs_reordered_chains.py" [EXPECTED FAIL] 4.0s
1018s   Time:  3.97
1018s   Return code: 139
1018s   OKs: 0
1018s   Standard error:
1018s     Segmentation fault (core dumped)
1022s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1022s 134
1022s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1022s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_to_from_hierarchy.py" [EXPECTED FAIL] 4.4s
1022s   Time:  4.39
1022s   Return code: 134
1022s   OKs: 0
1022s   Standard error:
1022s     *** buffer overflow detected ***: terminated
1022s     Aborted (core dumped)
1022s libtbx.python "/usr/lib/python3/dist-packages/libtbx/metric_prefixes.py" [OK] 0.0s
1022s   Time:  0.04
1022s   Return code: 0
1022s   OKs: 1
1022s   Standard out:
1022s     OK
1027s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_utils.py" [OK] 4.4s
1027s   Time:  4.38
1027s   Return code: 0
1027s   OKs: 0
1027s   Standard out:
1027s     Skipping exercise_retrieve_unless_exists
1027s     ### USER = ubuntu
1027s     ### PID = 11018
1027s     multiprocessing problem: None
1027s     base36_timestamp(): 00m878nn1r now
1027s     base36_timestamp(): zzydazd000 year 115855 CE
1027s     get_svn_revision(): None
1027s     get_build_tag(): None
1027s     u+s,u,s: 0.15 0.11 0.04
1027s libtbx.python "/usr/lib/python3/dist-packages/libtbx/test_utils/__init__.py" [OK] 0.7s
1027s   Time:  0.71
1027s   Return code: 0
1027s   OKs: 1
1027s   Standard out:
1027s     OK
1027s libtbx.python "/usr/lib/python3/dist-packages/libtbx/queuing_system_utils/pbs_utils.py" [OK] 0.0s
1027s   Time:  0.03
1027s   Return code: 0
1027s   OKs: 1
1027s   Standard out:
1027s     *** MY_PBS_ARRAY_SIZE = None
1027s     *** MY_PBS_ARRAYID_OFFSET = None
1027s     *** PBS_ARRAYID = None
1027s     *** OMPI_MCA_ns_nds_num_procs = None
1027s     *** OMPI_MCA_ns_nds_vpid = None
1027s     n,i: 1 0
1027s     OK
1027s libtbx.python "/usr/lib/python3/dist-packages/libtbx/queuing_system_utils/sge_utils.py" [OK] 0.0s
1027s   Time:  0.04
1027s   Return code: 0
1027s   OKs: 1
1027s   Standard out:
1027s     *** JOB_ID = None
1027s     *** SGE_ARCH = None
1027s     *** SGE_TASK_FIRST = None
1027s     *** SGE_TASK_LAST = None
1027s     *** SGE_TASK_ID = None
1027s     OK
1027s libtbx.python "/usr/lib/python3/dist-packages/libtbx/introspection.py" [OK] 0.1s
1027s   Time:  0.06
1027s   Return code: 0
1027s   OKs: 1
1027s   Standard out:
1027s     number of processors: 2
1027s     Virtual memory size: 21,204,992
1027s     Resident set size:   12,296,192
1027s     Stack size:             139,264
1027s     Virtual memory size: 21,331,968     exact max: 29,335,552
1027s     Resident set size:   12,816,384   approx. max: 20,733,952
1027s     Stack size:             139,264   approx. max:    139,264
1027s     Memory total:  4,088,070,144
1027s     Memory free:     102,522,880
1027s     OK
1049s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_thread_utils.py" [OK] 21.4s
1049s   Time: 21.43
1049s   Return code: 0
1049s   OKs: 1
1049s   Standard out:
1049s     OK
1052s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp.py" [OK] 3.5s
1052s   Time:  3.54
1052s   Return code: 0
1052s   OKs: 1
1052s   Standard out:
1052s     multiprocessing pool size: 2
1052s     wall clock time: 0.01 seconds
1052s     OK
1053s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp_state.py" [OK] 0.7s
1053s   Time:  0.70
1053s   Return code: 0
1053s   OKs: 3
1053s   Standard out:
1053s     Running threading test with 1 processes, 1 threads, 3 tasks
1053s     (0xefa8a6e1eba0-12237) object in state -init-
1053s     (0xefa8a6e1eba0-12237) changing state from -init- to E0QB08
1053s     (0xefa8a6e1eba0-12237) changing state from E0QB08 to FEXUY6
1053s     (0xefa8a6e1eba0-12237) changing state from FEXUY6 to 3N0I82
1053s     (0xefa8a6e1eba0-12237) object in state 3N0I82
1053s     OK
1053s     Running threading test with 2 processes, 1 threads, 3 tasks
1053s     (0xefa8a6d09d10-12237) object in state -init-
1053s     (0xefa8a6d09d10-12237) changing state from -init- to V1BS0Z
1053s     (0xefa8a6d09d10-12237) changing state from V1BS0Z to 9Q5D5T
1053s     (0xefa8a6d09d10-12237) changing state from 9Q5D5T to OYCKQ5
1053s     (0xefa8a6d09d10-12237) object in state OYCKQ5
1053s     OK
1053s     Running multiprocessing test with 1 processes, 1 threads, 3 tasks
1053s     (0xefa8a6d09d10-12237) object in state -init-
1053s     (0xefa8a6d09d10-12237) changing state from -init- to ZLV4P8
1053s     (0xefa8a6d09d10-12237) changing state from ZLV4P8 to FCN05H
1053s     (0xefa8a6d09d10-12237) changing state from FCN05H to UH5BTD
1053s     (0xefa8a6d09d10-12237) object in state UH5BTD
1053s     OK
1053s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_pickle.py" [OK] 0.1s
1053s   Time:  0.07
1053s   Return code: 0
1053s   OKs: 1
1053s   Standard out:
1053s     test.dat
1053s       dump: 0.00 s
1053s       load buffered: 0.00 s
1053s       load direct: 0.00 s
1053s     test.dat.gz
1053s       dump: 0.00 s
1053s       load buffered: 0.00 s
1053s       load direct: 0.00 s
1053s     dumps/loads
1053s       dump: 0.00 s
1053s       load buffered: 0.00 s
1053s     OK
1053s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_fully_buffered_timeout.py" [OK] 0.1s
1053s   Time:  0.10
1053s   Return code: 0
1053s   OKs: 0
1053s   Standard out:
1053s     Skipping test: probe not configured
1057s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_fetch.py" [OK] 47.2s
1057s   Time: 47.17
1057s   Return code: 0
1057s   OKs: 1
1057s   Standard out:
1057s     data_r1yjpsf
1057s     # 
1057s     loop_
1057s     _audit.revision_id 
1057s     _audit.creation_date 
1057s     _audit.update_record 
1057s     1_0 2005-06-14 'Initial release'                              
1057s     1_1 2013-05-08 'Status correction and format standardization' 
1057s     # 
1057s     _cell.entry_id      1yjp 
1057s     _cell.length_a      21.937 
1057s     _cell.length_b      4.866 
1057s     _cell.length_c      23.477 
1057s     _cell.angle_alpha   90.000 
1057s     _cell.angle_beta    107.080 
1057s     _cell.angle_gamma   90.000 
1057s     # 
1057s     _diffrn_radiation_wavelength.id           1 
1057s     _diffrn_radiation_wavelength.wavelength   0.97500 
1057s     # 
1057s     _entry.id   1yjp 
1057s     # 
1057s     _exptl_crystal.id   1 
1057s     # 
1057s     _reflns_scale.group_code   1 
1057s     # 
1057s     _symmetry.entry_id               1yjp 
1057s     _symmetry.space_group_name_H-M   'P 1 21 1' 
1057s     # 
1057s     #
1057s     loop_
1057s     _refln.crystal_id
1057s     _refln.wavelength_id
1057s     _refln.scale_group_code
1057s     _refln.index_h
1057s     _refln.index_k
1057s     _refln.index_l
1057s     _refln.status
1057s     _refln.F_meas_au
1057s     _refln.F_meas_sigma_au
1057s     1 1 1  -12    0    2 o     3.49   2.34 
1057s     1 1 1  -12    0    3 o     3.31   2.43 
1057s     1 1 1  -12    0    4 o     7.32   4.25 
1057s     1 1 1  -12    0    5 o     8.88   5.39 
1057s     1 1 1  -11    0    1 o     9.46   4.13 
1057s     1 1 1  -11    0    2 o     4.91   3.21 
1057s     1 1 1  -11    0    3 o     6.37   3.70 
1057s     1 1 1  -11    0    4 o     8.50   4.91 
1057s     1 1 1  -11    0    5 o    17.44   8.06 
1057s     1 1 1  -11    0    6 o     5.89   3.64 
1057s     1 1 1  -11    0    8 o     6.39   3.90 
1057s     1 1 1  -11    1    2 o     5.69   2.18 
1057s     1 1 1  -11    1    3 o     6.53   2.53 
1057s     1 1 1  -11    1    5 o     7.26   3.20 
1057s     1 1 1  -11    1    6 o    11.05   3.47 
1057s     1 1 1  -10    0    2 o     6.32   3.74 
1057s     1 1 1  -10    0    3 o     9.36   4.67 
1057s     1 1 1  -10    0    5 o     7.20   4.12 
1057s     1 1 1  -10    0    6 o     4.88   3.25 
1057s     1 1 1  -10    0    7 o    11.84   5.41 
1057s     1 1 1  -10    0    8 o    14.49   6.53 
1057s     1 1 1  -10    0    9 o     6.21   3.91 
1057s     1 1 1  -10    0   10 o     5.55   3.37 
1057s     1 1 1  -10    1    1 o     4.58   1.49 
1057s     1 1 1  -10    1    3 o    12.40   3.65 
1057s     1 1 1  -10    1    4 o     9.07   2.47 
1057s     1 1 1  -10    1    5 o    17.23   6.02 
1057s     1 1 1  -10    1    6 o     4.60   2.10 
1057s     1 1 1  -10    1    7 o     6.34   2.43 
1057s     1 1 1  -10    1    8 o     9.04   2.92 
1057s     1 1 1   -9    0    2 o     8.10   3.98 
1057s     1 1 1   -9    0    3 o    14.22   5.11 
1057s     1 1 1   -9    0    5 o     6.01   3.78 
1057s     1 1 1   -9    0    6 o    10.48   4.68 
1057s     1 1 1   -9    0    7 o     8.79   4.52 
1057s     1 1 1   -9    0    8 o     6.15   3.63 
1057s     1 1 1   -9    0    9 o    10.27   4.16 
1057s     1 1 1   -9    0   10 o     4.38   3.04 
1057s     1 1 1   -9    0   11 o     7.27   4.16 
1057s     1 1 1   -9    1    3 o    10.75   2.38 
1057s     1 1 1   -9    1    4 o    11.86   1.95 
1057s     1 1 1   -9    1    5 o    10.95   3.27 
1057s     1 1 1   -9    1    6 o    13.31   2.59 
1057s     1 1 1   -9    1    7 o     8.06   2.92 
1057s     1 1 1   -9    1    8 o    14.75   2.87 
1057s     1 1 1   -9    1    9 o     9.04   2.82 
1057s     1 1 1   -8    0    2 f    15.88   3.97 
1057s     1 1 1   -8    0    3 o    26.78   5.79 
1057s     1 1 1   -8    0    5 o    32.83   7.52 
1057s     1 1 1   -8    0    7 o    12.74   3.54 
1057s     1 1 1   -8    0    8 o    29.46   9.29 
1057s     1 1 1   -8    0    9 f    22.09   3.59 
1057s     1 1 1   -8    0   10 o    18.81   5.24 
1057s     1 1 1   -8    0   11 o    12.76   7.11 
1057s     1 1 1   -8    1    1 o     6.26   2.08 
1057s     1 1 1   -8    1    2 o     6.97   2.14 
1057s     1 1 1   -8    1    4 o    19.24   4.18 
1057s     1 1 1   -8    1    5 o    15.46   2.43 
1057s     1 1 1   -8    1    6 o    16.87   2.78 
1057s     1 1 1   -8    1    7 o    15.66   2.34 
1057s     1 1 1   -8    1    8 o     7.07   2.43 
1057s     1 1 1   -8    1    9 o     8.81   2.80 
1057s     1 1 1   -8    1   10 o     8.61   3.09 
1057s     1 1 1   -8    2    1 o     4.39   1.52 
1057s     1 1 1   -8    2    2 o     4.20   1.87 
1057s     1 1 1   -8    2    3 o     6.14   1.87 
1057s     1 1 1   -8    2    4 o     9.38   2.80 
1057s     1 1 1   -7    0    3 o    23.46   3.83 
1057s     1 1 1   -7    0    4 o    37.35   7.40 
1057s     1 1 1   -7    0    6 o     7.44   3.60 
1057s     1 1 1   -7    0    7 o    43.94   5.36 
1057s     1 1 1   -7    0    8 o    18.96   2.98 
1057s     1 1 1   -7    0    9 o     4.95   3.22 
1057s     1 1 1   -7    0   10 o    31.73   4.61 
1057s     1 1 1   -7    0   11 o     6.31   3.82 
1057s     1 1 1   -7    0   12 o     5.05   3.33 
1057s     1 1 1   -7    1    1 o     8.89   1.60 
1057s     1 1 1   -7    1    2 o    13.70   1.71 
1057s     1 1 1   -7    1    3 o    21.03   2.45 
1057s     1 1 1   -7    1    4 f     7.57   2.36 
1057s     1 1 1   -7    1    5 o    11.31   3.34 
1057s     1 1 1   -7    1    6 o    19.93   3.06 
1057s     1 1 1   -7    1    7 o    22.86   3.28 
1057s     1 1 1   -7    1    8 o    10.32   2.58 
1057s     1 1 1   -7    1    9 f     5.13   2.34 
1057s     1 1 1   -7    1   10 o     9.91   3.03 
1057s     1 1 1   -7    1   11 o     5.61   2.33 
1057s     1 1 1   -7    2    1 o    12.28   3.86 
1057s     1 1 1   -7    2    2 o    11.29   3.50 
1057s     1 1 1   -7    2    3 f     7.22   2.40 
1057s     1 1 1   -7    2    4 o    11.13   2.74 
1057s     1 1 1   -7    2    5 o     7.86   2.92 
1057s     1 1 1   -7    2    6 o     5.23   2.15 
1057s     1 1 1   -6    0    2 o    35.03   5.13 
1057s     1 1 1   -6    0    3 o    15.64   3.61 
1057s     1 1 1   -6    0    4 o    12.60   4.22 
1057s     1 1 1   -6    0    5 o    21.36   2.47 
1057s     1 1 1   -6    0    6 o    31.19   3.17 
1057s     1 1 1   -6    0    7 o    33.66   3.99 
1057s     1 1 1   -6    0    8 o    13.70   4.22 
1057s     1 1 1   -6    0    9 o    10.99   4.16 
1057s     1 1 1   -6    0   10 o    24.56   3.98 
1057s     1 1 1   -6    0   11 o     4.41   3.08 
1057s     1 1 1   -6    0   12 o     4.07   2.83 
1057s     1 1 1   -6    1    1 o    10.24   1.40 
1057s     1 1 1   -6    1    2 o    20.59   2.28 
1057s     1 1 1   -6    1    3 o    32.14   3.57 
1057s     1 1 1   -6    1    4 f    11.60   2.18 
1057s     1 1 1   -6    1    5 o    22.15   2.66 
1057s     1 1 1   -6    1    6 o     7.68   2.64 
1057s     1 1 1   -6    1    7 o     6.39   2.58 
1057s     1 1 1   -6    1    8 o     6.60   2.60 
1057s     1 1 1   -6    1    9 o     8.21   2.82 
1057s     1 1 1   -6    1   10 o    13.25   3.07 
1057s     1 1 1   -6    1   11 o    10.62   3.80 
1057s     1 1 1   -6    2    1 o    13.78   2.98 
1057s     1 1 1   -6    2    2 o     5.95   2.11 
1057s     1 1 1   -6    2    3 o     8.96   3.00 
1057s     1 1 1   -6    2    4 o     4.88   2.17 
1057s     1 1 1   -6    2    5 o     7.35   2.58 
1057s     1 1 1   -6    2    6 o     6.93   2.91 
1057s     1 1 1   -6    2    7 o     8.14   2.74 
1057s     1 1 1   -5    0    2 o    44.04   6.46 
1057s     1 1 1   -5    0    3 o    15.30   3.69 
1057s     1 1 1   -5    0    4 o    16.95   2.51 
1057s     1 1 1   -5    0    5 o    14.82   4.54 
1057s     1 1 1   -5    0    6 o    29.73   3.15 
1057s     1 1 1   -5    0    7 f    55.71  13.43 
1057s     1 1 1   -5    0    8 o    15.06   3.67 
1057s     1 1 1   -5    0    9 o     8.76   4.15 
1057s     1 1 1   -5    0   10 o     4.69   3.13 
1057s     1 1 1   -5    0   11 o    16.56   5.19 
1057s     1 1 1   -5    0   12 o     5.59   3.77 
1057s     1 1 1   -5    1    1 o    26.70   2.49 
1057s     1 1 1   -5    1    2 o    38.67   3.63 
1057s     1 1 1   -5    1    3 o    20.45   2.09 
1057s     1 1 1   -5    1    4 o     6.46   2.54 
1057s     1 1 1   -5    1    5 o    20.55   2.58 
1057s     1 1 1   -5    1    6 o    28.68   2.67 
1057s     1 1 1   -5    1    7 o     5.68   2.48 
1057s     1 1 1   -5    1    8 o     6.99   2.70 
1057s     1 1 1   -5    1    9 o    20.74   2.59 
1057s     1 1 1   -5    1   10 o    14.70   3.00 
1057s     1 1 1   -5    1   11 o     8.62   2.89 
1057s     1 1 1   -5    2    1 o     6.26   2.16 
1057s     1 1 1   -5    2    2 o     7.93   2.10 
1057s     1 1 1   -5    2    3 o    19.90   4.18 
1057s     1 1 1   -5    2    4 o     4.98   2.02 
1057s     1 1 1   -5    2    5 o    16.85   3.60 
1057s     1 1 1   -5    2    7 o     8.15   2.74 
1057s     1 1 1   -5    2    8 o     8.89   2.75 
1057s     1 1 1   -4    0    2 o     4.55   2.74 
1057s     1 1 1   -4    0    3 o    23.50   2.52 
1057s     1 1 1   -4    0    4 o    19.15   3.81 
1057s     1 1 1   -4    0    7 o    20.06   2.98 
1057s     1 1 1   -4    0    8 o    28.85   3.55 
1057s     1 1 1   -4    0    9 o     5.36   3.45 
1057s     1 1 1   -4    0   10 o    25.68   3.87 
1057s     1 1 1   -4    0   11 o    23.28   3.81 
1057s     1 1 1   -4    0   12 o    11.39   4.82 
1057s     1 1 1   -4    0   13 o     7.07   3.96 
1057s     1 1 1   -4    1    1 o    31.99   4.35 
1057s     1 1 1   -4    1    2 o    18.48   1.94 
1057s     1 1 1   -4    1    3 f    18.93   2.01 
1057s     1 1 1   -4    1    4 o    38.05   3.65 
1057s     1 1 1   -4    1    5 o    36.34   3.49 
1057s     1 1 1   -4    1    6 o    18.08   3.24 
1057s     1 1 1   -4    1    7 o    20.11   2.29 
1057s     1 1 1   -4    1    8 o    11.25   2.61 
1057s     1 1 1   -4    1    9 o    27.09   3.02 
1057s     1 1 1   -4    1   10 o    17.78   3.55 
1057s     1 1 1   -4    1   11 o    10.45   3.55 
1057s     1 1 1   -4    1   12 o     7.42   2.61 
1057s     1 1 1   -4    2    1 o     7.72   2.01 
1057s     1 1 1   -4    2    2 o    30.88   3.36 
1057s     1 1 1   -4    2    3 o    19.14   2.65 
1057s     1 1 1   -4    2    4 o     4.44   2.00 
1057s     1 1 1   -4    2    5 f    26.44   8.10 
1057s     1 1 1   -4    2    6 o    10.83   3.21 
1057s     1 1 1   -4    2    7 o     6.03   2.73 
1057s     1 1 1   -4    2    8 o    12.78   2.87 
1057s     1 1 1   -3    0    2 o     3.40   2.13 
1057s     1 1 1   -3    0    3 o     5.40   2.78 
1057s     1 1 1   -3    0    4 o    11.52   2.39 
1057s     1 1 1   -3    0    5 o    55.13   5.36 
1057s     1 1 1   -3    0    6 f    31.55   3.22 
1057s     1 1 1   -3    0    7 o     6.95   4.11 
1057s     1 1 1   -3    0    8 o     6.00   3.79 
1057s     1 1 1   -3    0    9 o    23.03   3.41 
1057s     1 1 1   -3    0   10 o     4.79   3.36 
1057s     1 1 1   -3    0   11 o    10.46   5.21 
1057s     1 1 1   -3    0   12 o    11.53   6.07 
1057s     1 1 1   -3    0   13 o     3.22   2.15 
1057s     1 1 1   -3    1    1 o    53.95   5.22 
1057s     1 1 1   -3    1    2 o    21.50   3.03 
1057s     1 1 1   -3    1    3 o    42.88   4.08 
1057s     1 1 1   -3    1    4 o    42.70   6.13 
1057s     1 1 1   -3    1    5 o    41.12   3.18 
1057s     1 1 1   -3    1    6 o    17.31   2.67 
1057s     1 1 1   -3    1    7 o    35.59   4.21 
1057s     1 1 1   -3    1    8 o    18.53   2.36 
1057s     1 1 1   -3    1    9 o    11.55   2.71 
1057s     1 1 1   -3    1   10 o    11.41   2.79 
1057s     1 1 1   -3    1   11 o     6.92   2.69 
1057s     1 1 1   -3    1   12 o     7.03   2.45 
1057s     1 1 1   -3    2    1 o    18.65   2.01 
1057s     1 1 1   -3    2    2 o    16.33   1.93 
1057s     1 1 1   -3    2    3 o    32.88   5.01 
1057s     1 1 1   -3    2    4 o     9.99   2.93 
1057s     1 1 1   -3    2    5 o    20.62   2.93 
1057s     1 1 1   -3    2    6 o     9.18   3.06 
1057s     1 1 1   -3    2    7 o     6.90   2.83 
1057s     1 1 1   -3    2    8 o     5.26   2.23 
1057s     1 1 1   -2    0    1 o    37.92   5.29 
1057s     1 1 1   -2    0    2 o    25.98   3.53 
1057s     1 1 1   -2    0    3 o    20.20   2.27 
1057s     1 1 1   -2    0    4 o    43.74   4.27 
1057s     1 1 1   -2    0    5 o    32.34   3.28 
1057s     1 1 1   -2    0    6 o    61.28   6.06 
1057s     1 1 1   -2    0    7 o    39.92   3.91 
1057s     1 1 1   -2    0    8 o     5.73   3.51 
1057s     1 1 1   -2    0    9 o    34.44   8.22 
1057s     1 1 1   -2    0   10 o     5.00   3.24 
1057s     1 1 1   -2    0   11 o     5.95   3.63 
1057s     1 1 1   -2    0   12 o     7.57   4.58 
1057s     1 1 1   -2    1    1 o     5.64   1.74 
1057s     1 1 1   -2    1    2 o    27.80   2.66 
1057s     1 1 1   -2    1    3 f    58.08   5.70 
1057s     1 1 1   -2    1    4 o    17.13   2.16 
1057s     1 1 1   -2    1    5 o    17.82   1.84 
1057s     1 1 1   -2    1    6 o    38.29   4.36 
1057s     1 1 1   -2    1    7 o    21.32   2.41 
1057s     1 1 1   -2    1    8 o    14.24   2.30 
1057s     1 1 1   -2    1    9 o    23.48   2.71 
1057s     1 1 1   -2    1   10 f    12.02   2.17 
1057s     1 1 1   -2    1   11 o    15.91   5.89 
1057s     1 1 1   -2    1   12 o     7.00   2.53 
1057s     1 1 1   -2    2    1 o    15.73   2.27 
1057s     1 1 1   -2    2    2 o    24.74   2.59 
1057s     1 1 1   -2    2    3 o    16.53   2.59 
1057s     1 1 1   -2    2    4 o     6.46   2.78 
1057s     1 1 1   -2    2    5 o    13.27   4.40 
1057s     1 1 1   -2    2    6 o     5.58   2.29 
1057s     1 1 1   -2    2    7 o     6.76   2.38 
1057s     1 1 1   -2    2    8 o     5.29   2.14 
1057s     1 1 1   -1    0    1 o    28.12   3.79 
1057s     1 1 1   -1    0    2 o    21.59   2.21 
1057s     1 1 1   -1    0    3 o    33.14   3.24 
1057s     1 1 1   -1    0    4 o    43.39   4.18 
1057s     1 1 1   -1    0    5 f    46.52   4.56 
1057s     1 1 1   -1    0    6 o    76.28  14.50 
1057s     1 1 1   -1    0    7 o     5.12   3.18 
1057s     1 1 1   -1    0    9 o    37.08   8.90 
1057s     1 1 1   -1    0   10 o     6.65   3.72 
1057s     1 1 1   -1    0   11 o     6.86   4.45 
1057s     1 1 1   -1    0   12 o     4.18   2.86 
1057s     1 1 1   -1    1    1 o    36.99   3.46 
1057s     1 1 1   -1    1    2 o    40.11   3.76 
1057s     1 1 1   -1    1    3 o    15.12   3.05 
1057s     1 1 1   -1    1    4 o    11.44   2.42 
1057s     1 1 1   -1    1    5 f     7.66   2.37 
1057s     1 1 1   -1    1    6 o    37.21   3.40 
1057s     1 1 1   -1    1    7 o    13.99   2.19 
1057s     1 1 1   -1    1    8 o    23.42   2.40 
1057s     1 1 1   -1    1    9 o    12.59   2.48 
1057s     1 1 1   -1    1   10 o    14.84   2.83 
1057s     1 1 1   -1    1   11 o    13.90   3.02 
1057s     1 1 1   -1    2    1 o     7.71   2.59 
1057s     1 1 1   -1    2    2 o     5.95   2.09 
1057s     1 1 1   -1    2    3 o    25.96   3.59 
1057s     1 1 1   -1    2    4 o    16.53   2.52 
1057s     1 1 1   -1    2    5 o    12.51   2.97 
1057s     1 1 1   -1    2    6 o    12.40   3.34 
1057s     1 1 1   -1    2    7 o     5.97   2.01 
1057s     1 1 1   -1    2    8 o     8.24   2.40 
1057s     1 1 1    0    0    1 o    40.04   3.82 
1057s     1 1 1    0    0    2 o    58.22   5.69 
1057s     1 1 1    0    0    3 o    47.47   4.60 
1057s     1 1 1    0    0    4 o     7.98   2.75 
1057s     1 1 1    0    0    5 o    50.74   7.60 
1057s     1 1 1    0    0    6 o    14.87   1.94 
1057s     1 1 1    0    0    7 o     3.62   2.41 
1057s     1 1 1    0    0    8 o    36.19   7.98 
1057s     1 1 1    0    0    9 o    10.11   5.01 
1057s     1 1 1    0    0   10 o    18.08   3.24 
1057s     1 1 1    0    0   11 o    12.35   4.26 
1057s     1 1 1    0    0   12 o     9.41   4.38 
1057s     1 1 1    0    1    1 o    92.10  11.26 
1057s     1 1 1    0    1    2 o    47.48   4.50 
1057s     1 1 1    0    1    3 o    22.08   2.22 
1057s     1 1 1    0    1    4 o     8.62   2.51 
1057s     1 1 1    0    1    5 o    24.16   1.98 
1057s     1 1 1    0    1    6 o    16.72   1.95 
1057s     1 1 1    0    1    7 o     5.50   2.46 
1057s     1 1 1    0    1    8 o    21.06   2.19 
1057s     1 1 1    0    1    9 o     5.99   2.45 
1057s     1 1 1    0    1   10 o     8.62   3.03 
1057s     1 1 1    0    1   11 o     9.15   3.06 
1057s     1 1 1    0    2    0 o    27.82   5.58 
1057s     1 1 1    0    2    1 o    29.68   4.10 
1057s     1 1 1    0    2    2 o    37.82   4.30 
1057s     1 1 1    0    2    3 o    14.42   1.91 
1057s     1 1 1    0    2    4 o    13.55   2.70 
1057s     1 1 1    0    2    5 o     8.67   3.07 
1057s     1 1 1    0    2    6 o    22.77   5.53 
1057s     1 1 1    0    2    7 o     5.74   2.12 
1057s     1 1 1    0    2    8 o     9.78   2.64 
1057s     1 1 1    1    0    1 o    10.19   1.09 
1057s     1 1 1    1    0    2 o    20.07   1.88 
1057s     1 1 1    1    0    3 o    28.76   2.81 
1057s     1 1 1    1    0    4 o     3.16   2.18 
1057s     1 1 1    1    0    5 o    35.75   3.54 
1057s     1 1 1    1    0    6 f    52.32   5.12 
1057s     1 1 1    1    0    7 o    37.09   5.54 
1057s     1 1 1    1    0    8 o     6.52   3.32 
1057s     1 1 1    1    0    9 o     3.67   2.45 
1057s     1 1 1    1    0   10 o     6.03   3.17 
1057s     1 1 1    1    0   11 o     3.13   2.20 
1057s     1 1 1    1    0   12 o     4.06   2.74 
1057s     1 1 1    1    1    0 o    34.97   2.64 
1057s     1 1 1    1    1    1 o    15.45   1.46 
1057s     1 1 1    1    1    2 o    27.96   2.66 
1057s     1 1 1    1    1    3 o    55.14   5.35 
1057s     1 1 1    1    1    4 o    14.46   1.65 
1057s     1 1 1    1    1    5 o     7.23   2.19 
1057s     1 1 1    1    1    6 o    10.31   2.54 
1057s     1 1 1    1    1    7 o    11.70   2.22 
1057s     1 1 1    1    1    8 o    11.24   2.14 
1057s     1 1 1    1    1    9 o     7.60   2.88 
1057s     1 1 1    1    1   10 o     8.83   2.34 
1057s     1 1 1    1    1   11 o    12.55   3.17 
1057s     1 1 1    1    2    0 o    24.36   5.60 
1057s     1 1 1    1    2    1 o    13.12   2.09 
1057s     1 1 1    1    2    2 o    10.37   2.52 
1057s     1 1 1    1    2    3 o    14.39   1.98 
1057s     1 1 1    1    2    4 o    26.67   8.23 
1057s     1 1 1    1    2    5 o    22.53   5.20 
1057s     1 1 1    1    2    6 o    13.94   2.61 
1057s     1 1 1    1    2    7 o     7.45   2.38 
1057s     1 1 1    1    2    8 o     4.51   2.05 
1057s     1 1 1    2    0    1 o    13.06   1.30 
1057s     1 1 1    2    0    2 o    10.37   1.36 
1057s     1 1 1    2    0    3 o    20.89   2.04 
1057s     1 1 1    2    0    4 o    45.12   4.31 
1057s     1 1 1    2    0    5 o    15.37   1.91 
1057s     1 1 1    2    0    6 o    28.38   2.79 
1057s     1 1 1    2    0    7 o    16.02   2.31 
1057s     1 1 1    2    0    8 o     3.40   2.35 
1057s     1 1 1    2    0    9 o     4.23   2.72 
1057s     1 1 1    2    0   10 o     3.89   2.43 
1057s     1 1 1    2    0   11 o    10.26   3.01 
1057s     1 1 1    2    1    0 o    34.61   2.64 
1057s     1 1 1    2    1    1 o    53.93   5.22 
1057s     1 1 1    2    1    2 o    20.62   2.08 
1057s     1 1 1    2    1    3 o    44.45   3.37 
1057s     1 1 1    2    1    4 o    24.41   2.00 
1057s     1 1 1    2    1    5 o    40.33   4.58 
1057s     1 1 1    2    1    6 o    41.76   5.03 
1057s     1 1 1    2    1    7 o    28.20   3.43 
1057s     1 1 1    2    1    8 o    33.56   3.76 
1057s     1 1 1    2    1    9 o     4.41   1.97 
1057s     1 1 1    2    1   10 o    15.24   3.10 
1057s     1 1 1    2    2    0 o    25.09   3.38 
1057s     1 1 1    2    2    1 o     9.96   2.30 
1057s     1 1 1    2    2    2 o    15.79   2.28 
1057s     1 1 1    2    2    3 f    23.73   2.57 
1057s     1 1 1    2    2    4 o    31.55   3.47 
1057s     1 1 1    2    2    5 o    22.42   5.53 
1057s     1 1 1    2    2    6 o    21.84   3.98 
1057s     1 1 1    2    2    7 o    11.92   3.24 
1057s     1 1 1    3    0    1 o    20.22   2.60 
1057s     1 1 1    3    0    2 o    15.58   1.67 
1057s     1 1 1    3    0    3 o    43.75   4.24 
1057s     1 1 1    3    0    4 o    53.24   5.13 
1057s     1 1 1    3    0    5 o     9.04   2.60 
1057s     1 1 1    3    0    6 o    16.05   2.16 
1057s     1 1 1    3    0    7 o    10.18   3.61 
1057s     1 1 1    3    0    8 f    21.57   2.93 
1057s     1 1 1    3    0    9 o     5.10   2.75 
1057s     1 1 1    3    0   10 o     9.06   4.48 
1057s     1 1 1    3    0   11 o     7.20   4.29 
1057s     1 1 1    3    1    0 o     6.01   1.35 
1057s     1 1 1    3    1    1 o    38.17   5.32 
1057s     1 1 1    3    1    2 o    88.61  10.65 
1057s     1 1 1    3    1    3 o    46.76   4.49 
1057s     1 1 1    3    1    4 o    21.38   1.98 
1057s     1 1 1    3    1    5 o    10.82   1.68 
1057s     1 1 1    3    1    6 o     9.92   1.96 
1057s     1 1 1    3    1    7 o    13.79   1.74 
1057s     1 1 1    3    1    8 o    18.26   2.25 
1057s     1 1 1    3    1    9 o    10.74   2.36 
1057s     1 1 1    3    1   10 o     4.53   1.95 
1057s     1 1 1    3    2    0 o    36.54   6.90 
1057s     1 1 1    3    2    1 o     7.87   2.79 
1057s     1 1 1    3    2    2 o    18.30   2.61 
1057s     1 1 1    3    2    3 o    17.39   2.45 
1057s     1 1 1    3    2    4 o    17.18   2.74 
1057s     1 1 1    3    2    5 o    13.02   2.60 
1057s     1 1 1    3    2    6 o     4.72   1.98 
1057s     1 1 1    4    0    1 o     3.64   2.08 
1057s     1 1 1    4    0    2 o    63.80   6.24 
1057s     1 1 1    4    0    3 o    19.19   1.93 
1057s     1 1 1    4    0    4 o    63.44   6.28 
1057s     1 1 1    4    0    5 o    30.78   6.03 
1057s     1 1 1    4    0    6 o     9.03   2.53 
1057s     1 1 1    4    0    7 o    18.16   2.40 
1057s     1 1 1    4    0    8 o     8.94   3.14 
1057s     1 1 1    4    0    9 o     6.87   3.36 
1057s     1 1 1    4    0   10 o     9.58   4.40 
1057s     1 1 1    4    1    0 o    24.37   2.38 
1057s     1 1 1    4    1    1 o    49.48   4.80 
1057s     1 1 1    4    1    2 o    10.45   1.03 
1057s     1 1 1    4    1    3 o    15.01   1.64 
1057s     1 1 1    4    1    4 o     4.52   1.88 
1057s     1 1 1    4    1    5 f    35.40   3.27 
1057s     1 1 1    4    1    6 o     8.15   2.10 
1057s     1 1 1    4    1    7 o     9.72   1.59 
1057s     1 1 1    4    1    8 o     5.93   1.88 
1057s     1 1 1    4    1    9 o    13.31   3.66 
1057s     1 1 1    4    2    0 o    12.03   2.31 
1057s     1 1 1    4    2    1 o    13.76   1.98 
1057s     1 1 1    4    2    2 o    10.87   2.55 
1057s     1 1 1    4    2    3 o     7.78   2.40 
1057s     1 1 1    4    2    4 o    19.45   4.53 
1057s     1 1 1    4    2    5 o    11.32   4.24 
1057s     1 1 1    4    2    6 o     7.29   3.50 
1057s     1 1 1    5    0    1 o    67.42  11.14 
1057s     1 1 1    5    0    2 o    13.50   3.13 
1057s     1 1 1    5    0    3 o    22.37   2.21 
1057s     1 1 1    5    0    4 o    56.42   6.72 
1057s     1 1 1    5    0    5 o    25.46   3.07 
1057s     1 1 1    5    0    6 o    38.61   4.82 
1057s     1 1 1    5    0    7 o    14.33   2.65 
1057s     1 1 1    5    0    8 f     4.56   2.78 
1057s     1 1 1    5    0    9 o     8.50   3.26 
1057s     1 1 1    5    1    0 o    21.65   2.85 
1057s     1 1 1    5    1    1 o    12.29   1.67 
1057s     1 1 1    5    1    2 o    11.21   3.27 
1057s     1 1 1    5    1    3 o     9.29   2.49 
1057s     1 1 1    5    1    4 o    12.76   2.42 
1057s     1 1 1    5    1    5 o     4.61   0.86 
1057s     1 1 1    5    1    6 o    21.81   2.38 
1057s     1 1 1    5    1    7 o    11.05   2.11 
1057s     1 1 1    5    1    8 o     4.27   1.64 
1057s     1 1 1    5    2    0 o    17.82   3.76 
1057s     1 1 1    5    2    1 o    13.94   3.96 
1057s     1 1 1    5    2    2 o    14.67   2.97 
1057s     1 1 1    5    2    3 o    12.27   4.35 
1057s     1 1 1    5    2    4 o    12.90   2.88 
1057s     1 1 1    5    2    5 o     8.21   2.77 
1057s     1 1 1    6    0    1 o     4.02   2.51 
1057s     1 1 1    6    0    2 o    14.11   3.04 
1057s     1 1 1    6    0    4 o    44.86   5.41 
1057s     1 1 1    6    0    5 f    22.85   4.74 
1057s     1 1 1    6    0    6 o    41.69   6.63 
1057s     1 1 1    6    0    7 o     7.42   2.96 
1057s     1 1 1    6    0    8 o    13.47   5.61 
1057s     1 1 1    6    1    0 o    25.42   2.26 
1057s     1 1 1    6    1    1 o     9.87   3.01 
1057s     1 1 1    6    1    2 o    28.37   5.85 
1057s     1 1 1    6    1    3 o    16.66   3.91 
1057s     1 1 1    6    1    4 o    23.02   5.62 
1057s     1 1 1    6    1    6 o    26.51   4.88 
1057s     1 1 1    6    1    7 o     3.67   1.58 
1057s     1 1 1    6    2    0 o     8.22   2.50 
1057s     1 1 1    6    2    2 o     9.67   2.35 
1057s     1 1 1    6    2    3 o     3.73   1.60 
1057s     1 1 1    7    0    1 o    10.99   3.37 
1057s     1 1 1    7    0    2 o    17.23   3.99 
1057s     1 1 1    7    0    3 o     5.15   2.69 
1057s     1 1 1    7    0    4 o     5.19   3.01 
1057s     1 1 1    7    0    5 o    23.76   3.00 
1057s     1 1 1    7    0    6 o     5.48   3.05 
1057s     1 1 1    7    0    7 o     6.05   3.12 
1057s     1 1 1    7    0    8 o     7.94   3.69 
1057s     1 1 1    7    1    0 o    33.08   3.93 
1057s     1 1 1    7    1    1 o     8.43   3.00 
1057s     1 1 1    7    1    2 o    10.12   3.61 
1057s     1 1 1    7    1    3 o    14.66   3.85 
1057s     1 1 1    7    1    4 o     9.43   3.13 
1057s     1 1 1    7    1    6 o    14.64   4.20 
1057s     1 1 1    7    2    0 o    14.80   3.92 
1057s     1 1 1    7    2    1 o     6.02   2.00 
1057s     1 1 1    8    0    2 o    29.07   8.06 
1057s     1 1 1    8    0    3 o     5.29   2.84 
1057s     1 1 1    8    0    4 o    22.81   5.95 
1057s     1 1 1    8    0    5 o     4.11   2.70 
1057s     1 1 1    8    1    0 o     7.24   1.50 
1057s     1 1 1    8    1    1 o     8.85   3.06 
1057s     1 1 1    8    1    2 o     6.83   3.09 
1057s     1 1 1    8    1    3 o    18.14   5.99 
1057s     1 1 1    9    0    1 o    13.49   3.22 
1057s     1 1 1    9    0    2 o    11.72   3.95 
1057s     1 1 1   10    0    2 o     7.39   3.73 
1057s     1 1 1   10    1    0 o    16.08   6.44 
1057s     #END OF REFLECTIONS
1057s     
1057s     Starting iotbx.fetch_pdb
1057s     on Thu Mar 13 11:01:04 2025 by ubuntu
1057s     ===============================================================================
1057s     
1057s     Processing files:
1057s     -------------------------------------------------------------------------------
1057s     
1057s       No files found
1057s     
1057s     Processing PHIL parameters:
1057s     -------------------------------------------------------------------------------
1057s     
1057s       Adding command-line PHIL:
1057s       -------------------------
1057s         action=all
1057s     
1057s     Final processed PHIL parameters:
1057s     -------------------------------------------------------------------------------
1057s       fetch {
1057s         pdb_ids = "6yvd"
1057s         action = model data sequence half_maps *all
1057s       }
1057s     
1057s     
1057s     Starting job
1057s     ===============================================================================
1057s     Validating inputs:
1057s     
1057s     Model in PDB format saved to /tmp/autopkgtest.r32aCk/autopkgtest_tmp/python3.13/6yvd.pdb
1057s     Model in mmCIF format saved to /tmp/autopkgtest.r32aCk/autopkgtest_tmp/python3.13/6yvd.cif
1057s     Couldn't download sf for 6yvd at https://files.rcsb.org/download/6yvd-sf.cif.gz.
1057s     Cryo-EM map saved to /tmp/autopkgtest.r32aCk/autopkgtest_tmp/python3.13/emd_10944.map.gz
1057s     Cryo-EM half map 1 saved to /tmp/autopkgtest.r32aCk/autopkgtest_tmp/python3.13/emd_10944_half_map_1.map.gz
1057s     Cryo-EM half map 2 saved to /tmp/autopkgtest.r32aCk/autopkgtest_tmp/python3.13/emd_10944_half_map_2.map.gz
1057s     Sequence saved to /tmp/autopkgtest.r32aCk/autopkgtest_tmp/python3.13/6yvd.fa
1057s     
1057s     ===============================================================================
1057s     Job complete
1057s     Total CPU time: 0.60 seconds
1057s     Starting iotbx.fetch_pdb
1057s     on Thu Mar 13 11:01:17 2025 by ubuntu
1057s     ===============================================================================
1057s     
1057s     Processing files:
1057s     -------------------------------------------------------------------------------
1057s     
1057s       No files found
1057s     
1057s     Processing PHIL parameters:
1057s     -------------------------------------------------------------------------------
1057s     
1057s       Adding command-line PHIL:
1057s       -------------------------
1057s         action=model
1057s     
1057s     Final processed PHIL parameters:
1057s     -------------------------------------------------------------------------------
1057s       fetch {
1057s         pdb_ids = "6yvd"
1057s       }
1057s     
1057s     
1057s     Starting job
1057s     ===============================================================================
1057s     Validating inputs:
1057s     
1057s     Model in PDB format saved to /tmp/autopkgtest.r32aCk/autopkgtest_tmp/python3.13/6yvd.pdb
1057s     Model in mmCIF format saved to /tmp/autopkgtest.r32aCk/autopkgtest_tmp/python3.13/6yvd.cif
1057s     
1057s     ===============================================================================
1057s     Job complete
1057s     Total CPU time: 0.48 seconds
1057s     Starting iotbx.fetch_pdb
1057s     on Thu Mar 13 11:01:20 2025 by ubuntu
1057s     ===============================================================================
1057s     
1057s     Processing files:
1057s     -------------------------------------------------------------------------------
1057s     
1057s       No files found
1057s     
1057s     Processing PHIL parameters:
1057s     -------------------------------------------------------------------------------
1057s     
1057s       Adding command-line PHIL:
1057s       -------------------------
1057s         action=model
1057s     
1057s     Final processed PHIL parameters:
1057s     -------------------------------------------------------------------------------
1057s       fetch {
1057s         pdb_ids = "6yvd"
1057s       }
1057s     
1057s     
1057s     Starting job
1057s     ===============================================================================
1057s     Validating inputs:
1057s     
1057s     Model in PDB format saved to /tmp/autopkgtest.r32aCk/autopkgtest_tmp/python3.13/6yvd.pdb
1057s     Model in mmCIF format saved to /tmp/autopkgtest.r32aCk/autopkgtest_tmp/python3.13/6yvd.cif
1057s     
1057s     ===============================================================================
1057s     Job complete
1057s     Total CPU time: 0.47 seconds
1057s     Starting iotbx.fetch_pdb
1057s     on Thu Mar 13 11:01:23 2025 by ubuntu
1057s     ===============================================================================
1057s     
1057s     Processing files:
1057s     -------------------------------------------------------------------------------
1057s     
1057s       No files found
1057s     
1057s     Processing PHIL parameters:
1057s     -------------------------------------------------------------------------------
1057s     
1057s       Adding command-line PHIL:
1057s       -------------------------
1057s         action=data
1057s     
1057s     Final processed PHIL parameters:
1057s     -------------------------------------------------------------------------------
1057s       fetch {
1057s         pdb_ids = "6yvd"
1057s         action = model *data sequence half_maps all
1057s       }
1057s     
1057s     
1057s     Starting job
1057s     ===============================================================================
1057s     Validating inputs:
1057s     
1057s     Couldn't download sf for 6yvd at https://files.rcsb.org/download/6yvd-sf.cif.gz.
1057s     Cryo-EM map saved to /tmp/autopkgtest.r32aCk/autopkgtest_tmp/python3.13/emd_10944.map.gz
1057s     
1057s     ===============================================================================
1057s     Job complete
1057s     Total CPU time: 0.42 seconds
1057s     Starting iotbx.fetch_pdb
1057s     on Thu Mar 13 11:01:28 2025 by ubuntu
1057s     ===============================================================================
1057s     
1057s     Processing files:
1057s     -------------------------------------------------------------------------------
1057s     
1057s       No files found
1057s     
1057s     Processing PHIL parameters:
1057s     -------------------------------------------------------------------------------
1057s     
1057s       Adding command-line PHIL:
1057s       -------------------------
1057s         action=half_maps
1057s     
1057s     Final processed PHIL parameters:
1057s     -------------------------------------------------------------------------------
1057s       fetch {
1057s         pdb_ids = "6yvd"
1057s         action = model data sequence *half_maps all
1057s       }
1057s     
1057s     
1057s     Starting job
1057s     ===============================================================================
1057s     Validating inputs:
1057s     
1057s     Cryo-EM half map 1 saved to /tmp/autopkgtest.r32aCk/autopkgtest_tmp/python3.13/emd_10944_half_map_1.map.gz
1057s     Cryo-EM half map 2 saved to /tmp/autopkgtest.r32aCk/autopkgtest_tmp/python3.13/emd_10944_half_map_2.map.gz
1057s     
1057s     ===============================================================================
1057s     Job complete
1057s     Total CPU time: 0.48 seconds
1057s     Starting iotbx.fetch_pdb
1057s     on Thu Mar 13 11:01:33 2025 by ubuntu
1057s     ===============================================================================
1057s     
1057s     Processing files:
1057s     -------------------------------------------------------------------------------
1057s     
1057s       No files found
1057s     
1057s     Processing PHIL parameters:
1057s     -------------------------------------------------------------------------------
1057s     
1057s       Adding command-line PHIL:
1057s       -------------------------
1057s         action=sequence
1057s     
1057s     Final processed PHIL parameters:
1057s     -------------------------------------------------------------------------------
1057s       fetch {
1057s         pdb_ids = "6yvd"
1057s         action = model data *sequence half_maps all
1057s       }
1057s     
1057s     
1057s     Starting job
1057s     ===============================================================================
1057s     Validating inputs:
1057s     
1057s     Sequence saved to /tmp/autopkgtest.r32aCk/autopkgtest_tmp/python3.13/6yvd.fa
1057s     
1057s     ===============================================================================
1057s     Job complete
1057s     Total CPU time: 0.46 seconds
1057s     Starting iotbx.fetch_pdb
1057s     on Thu Mar 13 11:01:34 2025 by ubuntu
1057s     ===============================================================================
1057s     
1057s     Processing files:
1057s     -------------------------------------------------------------------------------
1057s     
1057s       No files found
1057s     
1057s     Processing PHIL parameters:
1057s     -------------------------------------------------------------------------------
1057s     
1057s       Adding command-line PHIL:
1057s       -------------------------
1057s         action=all
1057s     
1057s     Final processed PHIL parameters:
1057s     -------------------------------------------------------------------------------
1057s       fetch {
1057s         pdb_ids = "6yvd"
1057s         action = model data sequence half_maps *all
1057s       }
1057s     
1057s     
1057s     Starting job
1057s     ===============================================================================
1057s     Validating inputs:
1057s     
1057s     Model in PDB format saved to /tmp/autopkgtest.r32aCk/autopkgtest_tmp/python3.13/6yvd.pdb
1057s     Model in mmCIF format saved to /tmp/autopkgtest.r32aCk/autopkgtest_tmp/python3.13/6yvd.cif
1057s     Couldn't download sf for 6yvd at https://files.rcsb.org/download/6yvd-sf.cif.gz.
1057s     Cryo-EM map saved to /tmp/autopkgtest.r32aCk/autopkgtest_tmp/python3.13/emd_10944.map.gz
1057s     Cryo-EM half map 1 saved to /tmp/autopkgtest.r32aCk/autopkgtest_tmp/python3.13/emd_10944_half_map_1.map.gz
1057s     Cryo-EM half map 2 saved to /tmp/autopkgtest.r32aCk/autopkgtest_tmp/python3.13/emd_10944_half_map_2.map.gz
1057s     Sequence saved to /tmp/autopkgtest.r32aCk/autopkgtest_tmp/python3.13/6yvd.fa
1057s     
1057s     ===============================================================================
1057s     Job complete
1057s     Total CPU time: 0.63 seconds
1057s     OK
1057s     u+s,u,s: 0.39 0.33 0.06
1059s libtbx.python "/usr/lib/python3/dist-packages/libtbx/easy_run.py" [OK] 2.1s
1059s   Time:  2.14
1059s   Return code: 0
1059s   OKs: 1
1059s   Standard out:
1059s     OK
1059s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_containers.py" [OK] 0.0s
1059s   Time:  0.03
1059s   Return code: 0
1059s   OKs: 1
1059s   Standard out:
1059s     OK
1060s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_path.py" [OK] 0.1s
1060s   Time:  0.07
1060s   Return code: 0
1060s   OKs: 1
1060s   Standard out:
1060s     OK
1060s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_math_utils.py" [OK] 0.3s
1060s   Time:  0.33
1060s   Return code: 0
1060s   OKs: 1
1060s   Standard out:
1060s     OK
1060s libtbx.python "/usr/lib/python3/dist-packages/libtbx/assert_utils.py" [OK] 0.2s
1060s   Time:  0.17
1060s   Return code: 0
1060s   OKs: 1
1060s   Standard out:
1060s     OK
1060s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_str_utils.py" [OK] 0.3s
1060s   Time:  0.32
1060s   Return code: 0
1060s   OKs: 1
1060s   Standard out:
1060s     OK
1060s libtbx.python "/usr/lib/python3/dist-packages/libtbx/table_utils.py" [OK] 0.0s
1060s   Time:  0.04
1060s   Return code: 0
1060s   OKs: 1
1060s   Standard out:
1060s     OK
1061s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_scheduling.py" [OK] 7.6s
1061s   Time:  7.63
1061s   Return code: 0
1061s   OKs: 0
1061s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_tokenizer.py" [OK] 0.1s
1061s   Time:  0.07
1061s   Return code: 0
1061s   OKs: 1
1061s   Standard out:
1061s     OK
1061s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst.py" [OK] 0.2s
1061s   Time:  0.23
1061s   Return code: 0
1061s   OKs: 1
1061s   Standard out:
1061s     OK
1061s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_experimental.py" [OK] 0.1s
1061s   Time:  0.07
1061s   Return code: 0
1061s   OKs: 1
1061s   Standard out:
1061s     OK
1061s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_interface.py" [OK] 0.1s
1061s   Time:  0.12
1061s   Return code: 0
1061s   OKs: 1
1061s   Standard out:
1061s     phenix module not available: skipping advanced tests
1061s     phaser module not available: skipping advanced tests
1061s     OK
1061s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_object_oriented_patterns.py" [OK] 0.1s
1061s   Time:  0.09
1061s   Return code: 0
1061s   OKs: 0
1061s libtbx.python "/usr/lib/python3/dist-packages/libtbx/find_reference_cycles.py" [OK] 0.0s
1061s   Time:  0.05
1061s   Return code: 0
1061s   OKs: 1
1061s   Standard out:
1061s     OK
1061s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_binary_search.py" [OK] 0.0s
1061s   Time:  0.04
1061s   Return code: 0
1061s   OKs: 1
1061s   Standard out:
1061s     OK
1062s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_topological_sort.py" [OK] 0.0s
1062s   Time:  0.04
1062s   Return code: 0
1062s   OKs: 1
1062s   Standard out:
1062s     OK
1062s libtbx.python "/usr/lib/python3/dist-packages/libtbx/clusterTests.py" [OK] 0.2s
1062s   Time:  0.16
1062s   Return code: 0
1062s   OKs: 1
1062s   Standard out:
1062s     ----------------------------------------------------------------------
1062s     Ran 13 tests in 0.079s
1062s     
1062s     OK
1062s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_citations.py" [OK] 0.2s
1062s   Time:  0.18
1062s   Return code: 0
1062s   OKs: 1
1062s   Standard out:
1062s     OK
1062s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_python_code_parsing.py" [OK] 0.0s
1062s   Time:  0.05
1062s   Return code: 0
1062s   OKs: 1
1062s   Standard out:
1062s     OK
1062s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_representation.py" [OK] 0.0s
1062s   Time:  0.04
1062s   Return code: 0
1062s   OKs: 0
1062s   Standard out:
1062s     99999999999999950039963891867
1062s     99999999999999963917751699682
1062s     99999999999999977795539507496
1062s     99999999999999991673327315311
1062s     100000000000000005551115123125
1062s     100000000000000019428902930940
1062s     100000000000000033306690738754
1062s     100000000000000047184478546569
1062s     100000000000000061062266354383
1062s     100000000000000074940054162198
1062s     100000000000000088817841970012
1062s     100000000000000102695629777826
1062s     100000000000000116573417585641
1062s     100000000000000130451205393455
1062s     100000000000000144328993201270
1062s     100000000000000158206781009084
1062s     100000000000000172084568816899
1062s     100000000000000185962356624713
1062s     100000000000000199840144432528
1062s     100000000000000213717932240342
1062s     100000000000000227595720048157
1062s     100000000000000241473507855971
1062s     100000000000000255351295663786
1062s     100000000000000269229083471600
1062s     100000000000000283106871279414
1062s     100000000000000296984659087229
1062s     100000000000000310862446895043
1062s     100000000000000324740234702858
1062s     100000000000000338618022510672
1062s     100000000000000352495810318487
1062s     BEst 450359962737049.6
1062s          900719925474099.2
1062s     55.32192809488736
1062s     56.32192809488736
1062s     True
1062s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_find_unused_imports.py" [OK] 0.0s
1062s   Time:  0.04
1062s   Return code: 0
1062s   OKs: 1
1062s   Standard out:
1062s     OK
1062s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_program_template.py" [OK] 0.3s
1062s   Time:  0.32
1062s   Return code: 0
1062s   OKs: 0
1062s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_version.py" [OK] 0.1s
1062s   Time:  0.09
1062s   Return code: 0
1062s   OKs: 0
1062s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_dlite.py" [OK] 2.1s
1062s   Time:  2.07
1062s   Return code: 0
1062s   OKs: 1
1062s   Standard out:
1062s     OK
1063s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp_multicore.py" [OK] 0.4s
1063s   Time:  0.38
1063s   Return code: 0
1063s   OKs: 0
1063s   Standard out:
1063s     [1] 1
1063s     [2] 2
1063s     [3] 6
1063s     [4] 24
1063s     [5] 120
1063s     [6] 720
1063s     [7] 5040
1066s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1066s 1
1066s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1066s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_xmlrpc_utils.py" [EXPECTED FAIL] 3.1s
1066s   Time:  3.14
1066s   Return code: 1
1066s   OKs: 0
1066s   Standard error:
1066s     Traceback (most recent call last):
1066s       File "/usr/lib/python3/dist-packages/libtbx/tst_xmlrpc_utils.py", line 42, in <module>
1066s         exercise()
1066s         ~~~~~~~~^^
1066s       File "/usr/lib/python3/dist-packages/libtbx/tst_xmlrpc_utils.py", line 15, in exercise
1066s         server = xmlrpc_utils.external_program_server(command=full_cmd,
1066s                                                       program_id="TEST",
1066s                                                       timeout=None,
1066s                                                       cache_requests=True,
1066s                                                       log=log)
1066s     TypeError: external_program_server.__init__() got an unexpected keyword argument 'command'
1068s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_runtime_utils.py" [OK] 6.0s
1068s   Time:  6.02
1068s   Return code: 0
1068s   OKs: 1
1068s   Standard out:
1068s     OK
1070s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1070s 139
1070s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1070s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_smoothing.py" [FAIL] 4.0s
1070s   Time:  4.01
1070s   Return code: 139
1070s   OKs: 0
1070s   Standard error:
1070s     Segmentation fault (core dumped)
1074s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1074s 139
1074s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1074s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_genetic_algorithm_with_mp.py" [FAIL] 5.1s
1074s   Time:  5.10
1074s   Return code: 139
1074s   OKs: 0
1074s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_1" [OK] 0.0s
1074s   Time:  0.01
1074s   Return code: 0
1074s   OKs: 1
1074s   Standard out:
1074s     Total OK: 511
1074s   Standard error:
1074s     Segmentation fault (core dumped)
1074s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_2" [OK] 0.0s
1074s   Time:  0.01
1074s   Return code: 0
1074s   OKs: 1
1074s   Standard out:
1074s     Total OK: 268
1074s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_3" [OK] 0.0s
1074s   Time:  0.01
1074s   Return code: 0
1074s   OKs: 1
1074s   Standard out:
1074s     Total OK: 164
1074s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_4" [OK] 0.0s
1074s   Time:  0.01
1074s   Return code: 0
1074s   OKs: 1
1074s   Standard out:
1074s     Total OK: 1420
1074s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_5" [OK] 0.0s
1074s   Time:  0.01
1074s   Return code: 0
1074s   OKs: 1
1074s   Standard out:
1074s     Total OK: 23
1074s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_vec3" [OK] 0.0s
1074s   Time:  0.01
1074s   Return code: 0
1074s   OKs: 1
1074s   Standard out:
1074s     Total OK: 83
1074s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_unsigned_float_arithmetic" [OK] 0.0s
1074s   Time:  0.01
1074s   Return code: 0
1074s   OKs: 1
1074s   Standard out:
1074s     OK
1074s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_mat3" [OK] 0.0s
1074s   Time:  0.01
1074s   Return code: 0
1074s   OKs: 1
1074s   Standard out:
1074s     Total OK: 129
1074s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_sym_mat3" [OK] 0.0s
1074s   Time:  0.01
1074s   Return code: 0
1074s   OKs: 1
1074s   Standard out:
1074s     Total OK: 91
1074s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_ref_matrix_facet" [OK] 0.0s
1074s   Time:  0.01
1074s   Return code: 0
1074s   OKs: 1
1074s   Standard out:
1074s     OK
1074s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_accessors" [OK] 0.0s
1074s   Time:  0.01
1074s   Return code: 0
1074s   OKs: 1
1074s   Standard out:
1074s     Total OK: 1730
1074s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_optional_copy" [OK] 0.0s
1074s   Time:  0.01
1074s   Return code: 0
1074s   OKs: 1
1074s   Standard out:
1074s     OK
1074s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_rectangular_full_packed" [OK] 0.0s
1074s   Time:  0.01
1074s   Return code: 0
1074s   OKs: 0
1074s   Standard out:
1074s     Test of accessor for rectangular full packed format skipped
1074s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex_argument_passing.py" [OK] 0.2s
1074s   Time:  0.17
1074s   Return code: 0
1074s   OKs: 1
1074s   Standard out:
1074s     OK
1074s "/usr/lib/cctbx/python3.13/scitbx/serialization/tst_base_256" [OK] 0.3s
1074s   Time:  0.27
1074s   Return code: 0
1074s   OKs: 1
1074s   Standard out:
1074s     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/scitbx/tests/tst_basic.py" [FAIL] 7.2s
1077s   Time:  7.16
1077s   Return code: 139
1077s   OKs: 1
1077s   Standard out:
1077s     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'
1077s     Size of an empty container.
1077s     Some of those containers store a pointer to a raw storage:
1077s     the 'cumulative' entry refers to the total memory footprint
1077s     whereas the other entry does not include the raw storage.
1077s     
1077s                                               int : 4
1077s                                      af::ref<int> : 32
1077s                           scitbx::auto_array<int> : 8
1077s                          boost::shared_array<int> : 16
1077s                            boost::ptr_vector<int> : 24
1077s                                  std::vector<int> : 24
1077s                                   af::shared<int> : 16
1077s                           af::shared [cumulative] : 64
1077s                                std::valarray<int> : 16
1077s                                    af::versa<int> : 24
1077s                  af::versa<int, af::flex_grid<> > : 280
1077s     af::versa<int, af::flex_grid<> > [cumulative] : 328
1077s     
1077s                                               double : 8
1077s                                      af::ref<double> : 32
1077s                           scitbx::auto_array<double> : 8
1077s                          boost::shared_array<double> : 16
1077s                            boost::ptr_vector<double> : 24
1077s                                  std::vector<double> : 24
1077s                                   af::shared<double> : 16
1077s                              af::shared [cumulative] : 64
1077s                                std::valarray<double> : 16
1077s                                    af::versa<double> : 24
1077s                  af::versa<double, af::flex_grid<> > : 280
1077s     af::versa<double, af::flex_grid<> > [cumulative] : 328
1077s     
1077s     OK
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/scitbx/math/tests/tst_minimum_covering_ellipsoid.py" [FAIL] 6.3s
1080s   Time:  6.26
1080s   Return code: 139
1080s   OKs: 0
1080s   Standard error:
1080s     Segmentation fault (core dumped)
1084s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1084s 139
1084s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1084s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian_fit_1d_analytical.py" [FAIL] 6.5s
1084s   Time:  6.54
1084s   Return code: 139
1084s   OKs: 0
1084s   Standard error:
1084s     Segmentation fault (core dumped)
1084s "/usr/lib/cctbx/python3.13/scitbx/math/tests/tst" [OK] 0.0s
1084s   Time:  0.01
1084s   Return code: 0
1084s   OKs: 2
1084s   Standard out:
1084s     copysign(3.f, +0.f) = 3 instead of 0.f as per C99
1084s     copysign(3.f, -0.f) = -3 instead of -0.f as per C99
1084s     linear interpolation test OK
1084s     OK
1084s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_givens" [OK] 0.0s
1084s   Time:  0.01
1084s   Return code: 0
1084s   OKs: 1
1084s   Standard out:
1084s     OK
1084s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_householder" [OK] 0.0s
1084s   Time:  0.01
1084s   Return code: 0
1084s   OKs: 1
1084s   Standard out:
1084s     OK
1084s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_svd" [OK] 0.0s
1084s   Time:  0.01
1084s   Return code: 0
1084s   OKs: 1
1084s   Standard out:
1084s     OK
1084s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_cholesky" [OK] 0.1s
1084s   Time:  0.11
1084s   Return code: 0
1084s   OKs: 1
1084s   Standard out:
1084s     Exercising sizes up to 100
1084s     Hilbert
1084s     Condition 1
1084s     Condition 2
1084s     Condition 3
1084s     Condition 4
1084s     OK
1084s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/tests/tst_row_echelon.py" [OK] 0.1s
1084s   Time:  0.09
1084s   Return code: 0
1084s   OKs: 1
1084s   Standard out:
1084s     OK
1084s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/tests/tst_householder.py" [OK] 0.2s
1084s   Time:  0.21
1084s   Return code: 0
1084s   OKs: 1
1084s   Standard out:
1084s     OK
1084s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_matrix.py" [OK] 0.2s
1084s   Time:  0.23
1084s   Return code: 0
1084s   OKs: 1
1084s   Standard out:
1084s     OK
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/scitbx/math/tests/tst_cubic_equation.py" [FAIL] 6.6s
1087s   Time:  6.60
1087s   Return code: 139
1087s   OKs: 0
1087s   Standard error:
1087s     Segmentation fault (core dumped)
1091s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1091s 139
1091s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1091s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_cholesky.py" [FAIL] 6.3s
1091s   Standard error:
1091s   Time:  6.29
1091s   Return code: 139
1091s   OKs: 0
1091s     Segmentation fault (core dumped)
1094s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1094s 139
1094s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1094s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_svd.py" [FAIL] 7.4s
1094s   Time:  7.40
1094s   Return code: 139
1094s   OKs: 0
1094s   Standard error:
1094s     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/scitbx/linalg/tests/tst_eigensystem.py" [FAIL] 7.5s
1098s   Time:  7.46
1098s   Return code: 139
1098s   OKs: 0
1098s   Standard error:
1098s     Segmentation fault (core dumped)
1101s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1101s 139
1101s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1101s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_svd.py" [FAIL] 6.7s
1101s   Time:  6.72
1101s   Return code: 139
1101s   OKs: 0
1101s   Standard error:
1101s     Segmentation fault (core dumped)
1101s libtbx.python "/usr/lib/python3/dist-packages/scitbx/error/tst_error.py" [OK] 0.1s
1101s   Time:  0.10
1101s   Return code: 0
1101s   OKs: 1
1101s   Standard out:
1101s     OK
1101s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_map.py" [OK] 0.1s
1101s   Time:  0.07
1101s   Return code: 0
1101s   OKs: 1
1101s   Standard out:
1101s     OK
1101s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_set.py" [OK] 0.1s
1101s   Time:  0.07
1101s   Return code: 0
1101s   OKs: 1
1101s   Standard out:
1101s     OK
1101s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_vector.py" [OK] 0.1s
1101s   Time:  0.07
1101s   Return code: 0
1101s   OKs: 1
1101s   Standard out:
1101s     OK
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/scitbx/linalg/tests/tst_lapack_dsyev.py" [FAIL] 6.5s
1105s   Time:  6.51
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/scitbx/array_family/boost_python/regression_test.py" [FAIL] 6.7s
1108s   Time:  6.68
1108s   Return code: 139
1108s   OKs: 0
1108s   Standard error:
1108s     Segmentation fault (core dumped)
1112s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1112s 139
1112s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1112s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex.py" [FAIL] 7.2s
1112s   Time:  7.22
1112s   Return code: 139
1112s   OKs: 0
1112s   Standard error:
1112s     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/scitbx/array_family/boost_python/tst_numpy_bridge.py" [FAIL] 7.0s
1115s   Time:  7.00
1115s   Return code: 139
1115s   OKs: 0
1115s   Standard error:
1115s     Segmentation fault (core dumped)
1119s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1119s 139
1119s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1119s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_smart_selection.py" [FAIL] 7.0s
1119s   Standard error:
1119s     Segmentation fault (core dumped)
1119s   Time:  6.96
1119s   Return code: 139
1119s   OKs: 0
1122s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1122s 139
1122s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1122s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_shared.py" [FAIL] 7.4s
1122s   Time:  7.35
1122s   Return code: 139
1122s   OKs: 0
1122s   Standard error:
1122s     Segmentation fault (core dumped)
1126s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_cost_of_m_handle_in_af_shared.py" [OK] 3.1s
1126s   Time:  3.10
1126s   Return code: 0
1126s   OKs: 1
1126s   Standard out:
1126s     Loop over af::shared<double>:
1126s     data_size=1000, n_repeats=30000
1126s     size+begin inside  loop: 0.28 s
1126s          begin outside loop: 0.21 s
1126s     size+begin outside loop: 0.11 s
1126s     
1126s     data_size=10000, n_repeats=3000
1126s     size+begin inside  loop: 0.24 s
1126s          begin outside loop: 0.17 s
1126s     size+begin outside loop: 0.11 s
1126s     
1126s     data_size=100000, n_repeats=300
1126s     size+begin inside  loop: 0.24 s
1126s          begin outside loop: 0.17 s
1126s     size+begin outside loop: 0.11 s
1126s     
1126s     data_size=1000000, n_repeats=30
1126s     size+begin inside  loop: 0.24 s
1126s          begin outside loop: 0.18 s
1126s     size+begin outside loop: 0.11 s
1126s     
1126s     data_size=10000000, n_repeats=3
1126s     size+begin inside  loop: 0.29 s
1126s          begin outside loop: 0.18 s
1126s     size+begin outside loop: 0.11 s
1126s     
1126s     OK
1126s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_cubicle_neighbors.py" [OK] 0.2s
1126s   Time:  0.19
1126s   Return code: 0
1126s   OKs: 1
1126s   Standard out:
1126s     OK
1126s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_r3_utils.py" [OK] 0.2s
1126s   Time:  0.22
1126s   Return code: 0
1126s   OKs: 1
1126s   Standard out:
1126s     OK
1127s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_regular_grid_on_unit_sphere.py" [OK] 0.6s
1127s   Time:  0.65
1127s   Return code: 0
1127s   OKs: 0
1131s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1131s 139
1131s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1131s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/__init__.py" [FAIL] 4.2s
1131s   Time:  4.19
1131s   Return code: 139
1131s   OKs: 0
1131s   Standard error:
1131s     Segmentation fault (core dumped)
1135s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1135s 139
1135s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1135s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_random_transform.py" [FAIL] 4.1s
1135s   Time:  4.13
1135s   Return code: 139
1135s   OKs: 0
1135s   Standard error:
1135s     Segmentation fault (core dumped)
1135s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_graph.py" [OK] 0.1s
1135s   Time:  0.07
1135s   Return code: 0
1135s   OKs: 1
1135s   Standard out:
1135s     OK
1135s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_robust.py" [OK] 0.2s
1135s   Time:  0.19
1135s   Return code: 0
1135s   OKs: 1
1135s   Standard out:
1135s     OK
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/scitbx/math/superpose.py" [FAIL] 3.7s
1139s   Time:  3.75
1139s   Return code: 139
1139s   OKs: 0
1139s   Standard error:
1139s     Segmentation fault (core dumped)
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/scitbx/math/spe.py" [FAIL] 3.5s
1142s   Time:  3.46
1142s   Return code: 139
1142s   OKs: 0
1142s   Standard error:
1142s     Segmentation fault (core dumped)
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/scitbx/math/incremental_SO3_sampling.py" [FAIL] 4.8s
1147s   Time:  4.82
1147s   Return code: 139
1147s   OKs: 0
1147s   Standard error:
1147s     Segmentation fault (core dumped)
1147s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_integer_offsets_vs_pointers.py" [OK] 28.6s
1147s   Time: 28.64
1147s   Return code: 0
1147s   OKs: 1
1147s   Standard out:
1147s     data_size = 1000 n_repeats = 30000
1147s       use_pointers = False
1147s         use_iterators = 0 time = 0.34 s overhead = 0.00 s (d[p[i]] 2.72849e-08)
1147s         use_iterators = 1 time = 0.13 s overhead = 0.00 s (d[*p++] 2.72849e-08)
1147s       use_pointers = True
1147s         use_iterators = 0 time = 0.28 s overhead = 0.00 s (*dp[i]  2.72849e-08)
1147s         use_iterators = 1 time = 0.46 s overhead = 0.00 s (**dpi++ 2.72849e-08)
1147s         use_iterators = 2 time = 0.04 s overhead = 0.00 s (**dpp++ 2.72849e-08)
1147s     data_size = 10000 n_repeats = 3000
1147s       use_pointers = False
1147s         use_iterators = 0 time = 0.33 s overhead = 0.00 s (d[p[i]] -4.09276e-08)
1147s         use_iterators = 1 time = 0.14 s overhead = 0.00 s (d[*p++] -4.09276e-08)
1147s       use_pointers = True
1147s         use_iterators = 0 time = 0.25 s overhead = 0.00 s (*dp[i]  -4.09276e-08)
1147s         use_iterators = 1 time = 0.47 s overhead = 0.00 s (**dpi++ -4.09276e-08)
1147s         use_iterators = 2 time = 0.04 s overhead = 0.00 s (**dpp++ -4.09276e-08)
1147s     data_size = 100000 n_repeats = 300
1147s       use_pointers = False
1147s         use_iterators = 0 time = 0.54 s overhead = 0.00 s (d[p[i]] -3.49263e-08)
1147s         use_iterators = 1 time = 0.32 s overhead = 0.00 s (d[*p++] -3.49263e-08)
1147s       use_pointers = True
1147s         use_iterators = 0 time = 0.37 s overhead = 0.00 s (*dp[i]  -3.49263e-08)
1147s         use_iterators = 1 time = 0.76 s overhead = 0.00 s (**dpi++ -3.49263e-08)
1147s         use_iterators = 2 time = 0.11 s overhead = 0.00 s (**dpp++ -3.49263e-08)
1147s     data_size = 1000000 n_repeats = 30
1147s       use_pointers = False
1147s         use_iterators = 0 time = 2.52 s overhead = 0.02 s (d[p[i]] 4.2958e-07)
1147s         use_iterators = 1 time = 1.54 s overhead = 0.01 s (d[*p++] 4.2958e-07)
1147s       use_pointers = True
1147s         use_iterators = 0 time = 1.62 s overhead = 0.02 s (*dp[i]  4.2958e-07)
1147s         use_iterators = 1 time = 3.59 s overhead = 0.01 s (**dpi++ 4.2958e-07)
1147s         use_iterators = 2 time = 0.48 s overhead = 0.01 s (**dpp++ 4.2958e-07)
1147s     data_size = 10000000 n_repeats = 3
1147s       use_pointers = False
1147s         use_iterators = 0 time = 2.82 s overhead = 0.20 s (d[p[i]] -5.53288e-07)
1147s         use_iterators = 1 time = 1.75 s overhead = 0.18 s (d[*p++] -5.53288e-07)
1147s       use_pointers = True
1147s         use_iterators = 0 time = 1.80 s overhead = 0.18 s (*dp[i]  -5.53288e-07)
1147s         use_iterators = 1 time = 4.10 s overhead = 0.18 s (**dpi++ -5.53288e-07)
1147s         use_iterators = 2 time = 0.67 s overhead = 0.19 s (**dpp++ -5.53288e-07)
1147s     OK
1151s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1151s 139
1151s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1151s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_curve_fitting.py" [FAIL] 3.9s
1151s   Time:  3.86
1151s   Return code: 139
1151s   OKs: 0
1151s   Standard error:
1151s     Segmentation fault (core dumped)
1151s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_similarity_indices.py" [OK] 0.2s
1151s   Time:  0.19
1151s   Return code: 0
1151s   OKs: 1
1151s   Standard out:
1151s     OK
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/scitbx/math/tests/tst_weighted_correlation.py" [FAIL] 7.4s
1155s   Time:  7.41
1155s   Return code: 139
1155s   OKs: 0
1155s   Standard error:
1155s     Segmentation fault (core dumped)
1155s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_fit_quadratic_function.py" [OK] 0.3s
1155s   Time:  0.26
1155s   Return code: 0
1155s   OKs: 1
1155s   Standard out:
1155s     OK
1156s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gcd.py" [OK] 0.6s
1156s   Time:  0.58
1156s   Return code: 0
1156s   OKs: 1
1156s   Standard out:
1156s     compare_with_boost_rational_gcd(gcd_int_simple)
1156s     compare_with_boost_rational_gcd(gcd_long_simple)
1156s     compare_with_boost_rational_gcd(gcd_long_binary)
1156s     gcd_int_boost            999 w=0.04 u+s=0.03
1156s     gcd_int_simple           999 w=0.02 u+s=0.03
1156s     gcd_long_boost           999 w=0.04 u+s=0.03
1156s     gcd_long_simple          999 w=0.02 u+s=0.03
1156s     gcd_unsigned_long_binary 999 w=0.08 u+s=0.08
1156s     gcd_long_binary          999 w=0.08 u+s=0.08
1156s     OK
1159s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1159s 139
1159s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1159s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_exp_functions.py" [FAIL] 7.2s
1159s   Time:  7.18
1159s   Return code: 139
1159s   OKs: 0
1159s   Standard error:
1159s     Segmentation fault (core dumped)
1161s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_r3_rotation.py" [OK] 2.7s
1161s   Time:  2.67
1161s   Return code: 0
1161s   OKs: 0
1161s   Standard out:
1161s     times unit quaternion <-> matrix
1161s          py: 0.03 0.02 s
1161s         c++: 0.05 0.06 s
1161s       ratio: 0.63 0.38
1161s     u+s,u,s: 2.60 2.57 0.03
1162s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1162s 139
1162s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1162s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_math.py" [FAIL] 6.7s
1162s   Time:  6.72
1162s   Return code: 139
1162s   OKs: 0
1162s   Standard error:
1162s     Segmentation fault (core dumped)
1163s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_line_search.py" [OK] 0.2s
1163s   Time:  0.24
1163s   Return code: 0
1163s   OKs: 1
1163s   Standard out:
1163s     OK
1166s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1166s 139
1166s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1166s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_resample.py" [FAIL] 4.8s
1166s   Time:  4.79
1166s   Return code: 139
1166s   OKs: 0
1166s   Standard error:
1166s     Segmentation fault (core dumped)
1169s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1169s 139
1169s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1169s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian.py" [FAIL] 6.9s
1169s   Time:  6.88
1169s   Return code: 139
1169s   OKs: 0
1169s   Standard error:
1169s     Segmentation fault (core dumped)
1170s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_bessel.py" [OK] 0.2s
1170s   Time:  0.22
1170s   Return code: 0
1170s   OKs: 0
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/scitbx/math/tests/tst_quadrature.py" [FAIL] 6.9s
1173s   Time:  6.91
1173s   Return code: 139
1173s   OKs: 0
1173s   Standard error:
1173s     Segmentation fault (core dumped)
1174s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_euler_angles.py" [OK] 0.8s
1174s   Time:  0.76
1174s   Return code: 0
1174s   OKs: 0
1174s   Standard out:
1174s     u+s,u,s: 0.69 0.67 0.02
1174s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_superpose.py" [OK] 0.3s
1174s   Time:  0.30
1174s   Return code: 0
1174s   OKs: 1
1174s   Standard out:
1174s     OK
1174s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_uniform_rotation_matrix.py" [OK] 0.2s
1174s   Time:  0.22
1174s   Return code: 0
1174s   OKs: 1
1174s   Standard out:
1174s     OK
1176s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1176s 139
1176s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1176s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_halton.py" [FAIL] 6.3s
1176s   Time:  6.29
1176s   Return code: 139
1176s   OKs: 0
1176s   Standard error:
1176s     Segmentation fault (core dumped)
1176s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike_mom.py" [OK] 0.2s
1176s   Time:  0.22
1176s   Return code: 0
1176s   OKs: 1
1176s   Standard out:
1176s     OK
1176s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/sieve_of_eratosthenes.py" [OK] 0.0s
1176s   Time:  0.04
1176s   Return code: 0
1176s   OKs: 1
1176s   Standard out:
1176s     OK
1176s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/besselk.py" [OK] 0.0s
1176s   Time:  0.04
1176s   Return code: 0
1176s   OKs: 1
1176s   Standard out:
1176s     OK
1180s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1180s 139
1180s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1180s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/scale_curves.py" [FAIL] 3.6s
1180s   Time:  3.59
1180s   Return code: 139
1180s   OKs: 0
1180s   Standard error:
1180s     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/scitbx/math/tests/tst_fit_peak.py" [FAIL] 3.7s
1184s   Time:  3.72
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/scitbx/math/tests/tst_clustering.py" [FAIL] 3.4s
1187s   Time:  3.37
1187s   Return code: 139
1187s   OKs: 0
1187s   Standard error:
1187s     Segmentation fault (core dumped)
1187s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_orthonormal_basis.py" [OK] 0.2s
1187s   Time:  0.23
1187s   Return code: 0
1187s   OKs: 1
1187s   Standard out:
1187s     OK
1187s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_g_function.py" [OK] 0.2s
1187s   Time:  0.23
1187s   Return code: 0
1187s   OKs: 0
1188s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_angle_derivative.py" [OK] 0.2s
1188s   Time:  0.23
1188s   Return code: 0
1188s   OKs: 1
1188s   Standard out:
1188s     OK
1191s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1191s 139
1191s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1191s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike.py" [FAIL] 16.5s
1191s   Time: 16.45
1191s   Return code: 139
1191s   OKs: 0
1191s   Standard error:
1191s     Segmentation fault (core dumped)
1194s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1194s 139
1194s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1194s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_periodogram.py" [FAIL] 6.1s
1194s   Time:  6.14
1194s   Return code: 139
1194s   OKs: 0
1194s   Standard error:
1194s     Segmentation fault (core dumped)
1194s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_tetrahedron.py" [OK] 0.2s
1194s   Time:  0.25
1194s   Return code: 0
1194s   OKs: 1
1194s   Standard out:
1194s     OK
1194s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_undirected_graph.py" [OK] 0.2s
1194s   Time:  0.21
1194s   Return code: 0
1194s   OKs: 0
1195s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_so3_lie_algebra.py" [OK] 0.2s
1195s   Time:  0.21
1195s   Return code: 0
1195s   OKs: 0
1195s libtbx.python "/usr/lib/python3/dist-packages/scitbx/minpack/tst.py" [OK] 0.2s
1195s   Time:  0.23
1195s   Return code: 0
1195s   OKs: 1
1195s   Standard out:
1195s     OK
1195s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_ext.py"  [OK] 0.2s
1195s   Time:  0.20
1195s   Return code: 0
1195s   OKs: 1
1195s   Standard out:
1195s     OK
1197s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1197s 139
1197s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1197s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_error_propagation_matrix_inverse.py" [FAIL] 6.5s
1197s   Time:  6.49
1197s   Return code: 139
1197s   OKs: 0
1197s   Standard error:
1197s     Segmentation fault (core dumped)
1200s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1200s 139
1200s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1200s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_curvatures.py" [FAIL] 5.4s
1200s   Time:  5.35
1200s   Return code: 139
1200s   OKs: 0
1200s   Standard error:
1200s     Segmentation fault (core dumped)
1201s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_func_free_line_search.py" [OK] 0.2s
1201s   Time:  0.22
1201s   Return code: 0
1201s   OKs: 1
1201s   Standard out:
1201s     The answer is: [2, -5, 500] 
1201s     The start value is: [-100, 203, 999]
1201s     scitbx.lbfgs: use gradient_only line search:  True
1201s     scitbx.lbfgs: use gradient_only line search:  False
1201s     OK
1201s "/usr/lib/cctbx/python3.13/scitbx/lbfgs/tst_lbfgs" [OK] 0.0s
1201s   Time:  0.01
1201s   Return code: 0
1201s   OKs: 0
1201s   Standard out:
1201s     n: 100
1201s     m: 5
1201s     xtol: 1e-16
1201s     f: 254.065 gnorm: 325.365
1201s      1 2 0.000607303
1201s     f: 207.819 gnorm: 54.5204
1201s      2 3 1
1201s     f: 206.329 gnorm: 12.6873
1201s      3 4 1
1201s     f: 206.158 gnorm: 12.9705
1201s      4 5 1
1201s     f: 204.568 gnorm: 36.0649
1201s      5 6 1
1201s     f: 201.009 gnorm: 69.9702
1201s      6 7 1
1201s     f: 132.076 gnorm: 99.1014
1201s      7 11 2.30835
1201s     f: 131.557 gnorm: 80.1033
1201s      8 13 0.152436
1201s     f: 120.196 gnorm: 66.244
1201s      9 15 5
1201s     f: 105.948 gnorm: 116.627
1201s      10 16 1
1201s     f: 87.4002 gnorm: 17.1325
1201s      11 17 1
1201s     f: 72.7773 gnorm: 32.6968
1201s      12 18 1
1201s     f: 67.7306 gnorm: 49.5851
1201s      13 20 0.213662
1201s     f: 60.0913 gnorm: 52.8678
1201s      14 21 1
1201s     f: 45.9493 gnorm: 28.0796
1201s      15 22 1
1201s     f: 37.3669 gnorm: 39.3487
1201s      16 23 1
1201s     f: 23.0492 gnorm: 14.5867
1201s      17 24 1
1201s     f: 19.8468 gnorm: 17.9762
1201s      18 26 0.156708
1201s     f: 17.6677 gnorm: 48.6045
1201s      19 27 1
1201s     f: 13.9465 gnorm: 22.2498
1201s      20 28 1
1201s     f: 9.11604 gnorm: 28.0105
1201s      21 29 1
1201s     f: 5.82159 gnorm: 10.2151
1201s      22 30 1
1201s     f: 4.75971 gnorm: 28.511
1201s      23 32 0.436181
1201s     f: 2.35807 gnorm: 22.65
1201s      24 33 1
1201s     f: 1.55734 gnorm: 15.4752
1201s      25 34 1
1201s     f: 0.810498 gnorm: 2.3865
1201s      26 36 0.404632
1201s     f: 0.508703 gnorm: 9.94499
1201s      27 38 0.247512
1201s     f: 0.363447 gnorm: 15.2129
1201s      28 39 1
1201s     f: 0.167247 gnorm: 9.7728
1201s      29 40 1
1201s     f: 0.0372373 gnorm: 1.32586
1201s      30 41 1
1201s     f: 0.0098316 gnorm: 4.14194
1201s      31 42 1
1201s     f: 0.000471098 gnorm: 0.567595
1201s      32 43 1
1201s     f: 3.2788e-06 gnorm: 0.027547
1201s      33 44 1
1201s     f: 2.34044e-08 gnorm: 0.00607363
1201s      34 45 1
1201s     f: 2.09469e-13 gnorm: 1.31535e-05
1201s      35 46 1
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/scitbx/lbfgsb/boost_python/tst_lbfgsb.py" [FAIL] 3.6s
1204s   Time:  3.62
1204s   Return code: 139
1204s   OKs: 0
1204s   Standard error:
1204s     Segmentation fault (core dumped)
1208s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1208s 139
1208s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1208s libtbx.python "/usr/lib/python3/dist-packages/scitbx/fftpack/boost_python/tst_fftpack.py"  [FAIL] 3.5s
1208s   Time:  3.52
1208s   Return code: 139
1208s   OKs: 0
1208s   Standard error:
1208s     Segmentation fault (core dumped)
1211s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" [OK] 13.7s
1211s   Time: 13.70
1211s   Return code: 0
1211s   OKs: 1
1211s   Standard out:
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 5 -1 0
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 5 -1 0
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 5 -1 0
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 4 -1 1
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 4 -1 1
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 4 -1 1
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 5 -1 2
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 5 -1 2
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 5 -1 2
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 5 -1 3
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 5 -1 3
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 5 -1 3
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 6 0 0
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 6 0 0
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 6 0 0
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 6 0 1
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 6 0 1
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 6 0 1
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 4 0 2
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 4 0 2
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 4 0 2
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 2 0 3
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 2 0 3
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 2 0 3
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 6 1 0
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 6 1 0
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 6 1 0
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 4 1 1
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 4 1 1
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 4 1 1
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 7 1 2
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 7 1 2
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 7 1 2
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 7 1 3
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 7 1 3
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 7 1 3
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 5 2 0
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 5 2 0
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 5 2 0
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 4 2 1
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 4 2 1
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 4 2 1
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 4 2 2
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 4 2 2
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 4 2 2
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 6 2 3
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 6 2 3
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 6 2 3
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 5 3 0
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 5 3 0
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 5 3 0
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 2 3 1
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 2 3 1
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 2 3 1
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 2 3 2
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 2 3 2
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 2 3 2
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 7 3 3
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 7 3 3
1211s     scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 7 3 3
1211s     usr+sys time: 0.40 seconds
1211s     wall clock time: 13.48 seconds
1211s     OK
1211s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_array_loops.py" [OK] 0.2s
1211s   Time:  0.17
1211s   Return code: 0
1211s   OKs: 1
1211s   Standard out:
1211s     10.0
1211s     11.0
1211s     12.0
1211s     
1211s     10.0
1211s     11.0
1211s     12.0
1211s     
1211s     0 10.0
1211s     1 11.0
1211s     2 12.0
1211s     
1211s     100.0
1211s     110.0
1211s     120.0
1211s     
1211s     200.0
1211s     210.0
1211s     220.0
1211s     
1211s     OK
1211s   Standard error:
1211s     Segmentation fault (core dumped)
1211s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1211s 139
1211s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1211s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_grid.py" [FAIL] 3.4s
1211s   Time:  3.36
1211s   Return code: 139
1211s   OKs: 0
1211s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/principal_axes_of_inertia.py" [OK] 0.2s
1211s   Time:  0.19
1211s   Return code: 0
1211s   OKs: 0
1211s   Standard out:
1211s     (7.796692307692308, 1.365076923076923, 8.357692307692307)
1211s     (38.140037692307715, 97.02526753846156, 79.0222196923077, -19.808558307692305, 35.14258523076924, 7.6620366923076935)
1211s     [104.22746487361265, 97.26642591377534, 12.693634135689015]
1211s     [-0.43905397167468396, 0.8222124337102901, -0.36221309171382476, 0.3037216796237081, 0.5152398514117881, 0.8014243799908461, 0.8455677094610694, 0.24185658843488295, -0.4759418445014057]
1211s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_recipe.py" [OK] 0.2s
1211s   Time:  0.18
1211s   Return code: 0
1211s   OKs: 1
1211s   Standard out:
1211s     refinery
1211s     compute_functional_and_gradients
1211s     callback_after_step
1211s     OK
1214s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1214s 139
1214s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1214s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_linear_least_squares_fit.py" [FAIL] 3.2s
1214s   Time:  3.17
1214s   Return code: 139
1214s   OKs: 0
1214s   Standard error:
1214s     Segmentation fault (core dumped)
1217s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1217s 139
1217s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1217s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/chebyshev_lsq_example.py" [FAIL] 6.2s
1217s   Time:  6.21
1217s   Return code: 139
1217s   OKs: 0
1217s   Standard error:
1217s     Segmentation fault (core dumped)
1218s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/rigid_body_refinement_core.py" [OK] 0.2s
1218s   Time:  0.17
1218s   Return code: 0
1218s   OKs: 1
1218s   Standard out:
1218s     an ea: [0.0, 0.0, 0.0]
1218s     fd ea: [2.9856131013692537e-15, 8.482502921596884e-16, 3.956636706594845e-15]
1218s     an lt: [-0.0, -0.0, -0.0]
1218s     fd lt: [0.0, 0.0, 0.0]
1218s     
1218s     an ea: [1.4293798315070272, -4.7699199336056015, -3.2848275925325994]
1218s     fd ea: [1.4293798322739804, -4.769919932368083, -3.284827593041939]
1218s     an lt: [-2.6395370381698946, 3.8546779254822816, -3.7648774634679576]
1218s     fd lt: [-2.6395370364973303, 3.8546779261849906, -3.764877463563465]
1218s     
1218s     an ea: [-4.386454471339835, 2.1848899436111178, 5.0802158076235635]
1218s     fd ea: [-4.386454468985335, 2.184889945411328, 5.080215810693289]
1218s     an lt: [-4.688132824683539, -10.874759921610867, -1.9393316543209416]
1218s     fd lt: [-4.688132825947378, -10.874759922785415, -1.939331655265164]
1218s     
1218s     an ea: [-5.097458993694191, 2.0225151159319297, 4.479103261227751]
1218s     fd ea: [-5.097458993574833, 2.0225151207142744, 4.479103258958617]
1218s     an lt: [-2.8154365578392593, -5.157085781215166, -17.014046644874668]
1218s     fd lt: [-2.8154365576682494, -5.157085780638226, -17.014046648000658]
1218s     
1218s     OK
1220s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1220s 139
1220s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1220s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/immoptibox_ports.py" [FAIL] 6.1s
1220s   Time:  6.08
1220s   Return code: 139
1220s   OKs: 0
1220s   Standard error:
1220s     Segmentation fault (core dumped)
1223s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1223s 139
1223s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1223s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/integrating_a_weighted_sinc_function.py" [FAIL] 5.8s
1223s   Time:  5.80
1223s   Return code: 139
1223s   OKs: 0
1223s   Standard error:
1223s     Segmentation fault (core dumped)
1223s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_utils.py" [OK] 0.0s
1223s   Time:  0.04
1223s   Return code: 0
1223s   OKs: 1
1223s   Standard out:
1223s     OK
1223s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/rigidity.py" [OK] 0.0s
1223s   Time:  0.04
1223s   Return code: 0
1223s   OKs: 0
1223s   Standard out:
1223s     double banana 3D dof (method=integer): 7
1223s     double banana 3D dof (method=float): 7
1224s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_rigidity.py" [OK] 0.2s
1224s   Time:  0.21
1224s   Return code: 0
1224s   OKs: 0
1224s   Standard out:
1224s     repeat_log = {0: 85}
1224s     u+s,u,s: 0.18 0.18 0.00
1224s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/rigidity_matrix_symbolic.py" [OK] 0.2s
1224s   Time:  0.20
1224s   Return code: 0
1224s   OKs: 0
1224s   Standard out:
1224s     u+s,u,s: 0.18 0.18 0.00
1226s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree_find_paths.py" [OK] 1.9s
1226s   Time:  1.89
1226s   Return code: 0
1226s   OKs: 1
1226s   Standard out:
1226s     OK
1226s   Standard error:
1226s     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/scitbx/examples/minimizer_comparisons.py" [FAIL] 6.0s
1226s   Time:  6.01
1226s   Return code: 139
1226s   OKs: 0
1227s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/test_cases_tardy_pdb.py" [OK] 0.1s
1227s   Time:  0.07
1227s   Return code: 0
1227s   OKs: 0
1230s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1230s 139
1230s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1230s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree.py" [FAIL] 3.8s
1230s   Time:  3.83
1230s   Return code: 139
1230s   OKs: 0
1230s   Standard error:
1230s     Segmentation fault (core dumped)
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/scitbx/rigid_body/essence/tst_basic.py" [FAIL] 6.1s
1233s   Time:  6.12
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/scitbx/rigid_body/essence/tst_tardy.py" [FAIL] 6.3s
1236s   Time:  6.26
1236s   Return code: 139
1236s   OKs: 0
1236s   Standard error:
1236s     Segmentation fault (core dumped)
1239s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1239s 139
1239s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1239s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_energy_plots.py" [FAIL] 6.4s
1239s   Time:  6.39
1239s   Return code: 139
1239s   OKs: 0
1239s   Standard error:
1239s     Segmentation fault (core dumped)
1239s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/free_motion_reference_impl.py" [OK] 0.0s
1239s   Time:  0.04
1239s   Return code: 0
1239s   OKs: 1
1239s   Standard out:
1239s     e_kin tot ang lin: 0.04066059413038476 0.012310594130384761 0.02835
1239s                 e_pot: 0.6403087877704161
1239s                 e_tot: 0.6809693819008009
1239s     ang acc 3D: (0.4499405243671747, -0.22736369685250066, -0.6859763000328927)
1239s     lin acc 3D: (0.2108121283092794, 0.3044814367238479, -0.7824311428947446)
1239s     
1239s     e_kin tot ang lin: 0.043334386720177365 0.012335145793951681 0.030999240926225684
1239s                 e_pot: 0.6375204431681878
1239s                 e_tot: 0.6808548298883652
1239s     ang acc 3D: (0.4491523283824315, -0.2233952828755118, -0.688364609039924)
1239s     lin acc 3D: (0.2063305410676703, 0.3022012812609254, -0.7827791077048256)
1239s     
1239s     e_kin tot ang lin: 0.04624491637806352 0.012390841212545118 0.0338540751655184
1239s                 e_pot: 0.6344966498401754
1239s                 e_tot: 0.6807415662182389
1239s     ang acc 3D: (0.4482905223840879, -0.2193464063160701, -0.6906197519803725)
1239s     lin acc 3D: (0.20168867739512958, 0.299808900299363, -0.7830079270607541)
1239s     
1239s     e_kin tot ang lin: 0.049389854602061224 0.01247763222642335 0.036912222375637876
1239s                 e_pot: 0.6312398275384674
1239s                 e_tot: 0.6806296821405287
1239s     ang acc 3D: (0.44735466644443667, -0.21521902126722914, -0.692740958483326)
1239s     lin acc 3D: (0.19688964121862268, 0.29730414639378616, -0.7831155604559972)
1239s     
1239s     e_kin tot ang lin: 0.05276668787891577 0.012595448079626585 0.04017123979928919
1239s                 e_pot: 0.6277525800757479
1239s                 e_tot: 0.6805192679546637
1239s     ang acc 3D: (0.4463443200247767, -0.2110151239756078, -0.694727476553102)
1239s     lin acc 3D: (0.1919366941490876, 0.29468687861617315, -0.783099948460292)
1239s     
1239s     e_kin tot ang lin: 0.05637271969939971 0.012744195480724368 0.043628524218675344
1239s                 e_pot: 0.6240376932449352
1239s                 e_tot: 0.6804104129443349
1239s     ang acc 3D: (0.4452590426839754, -0.2067367517215091, -0.6965785731789051)
1239s     lin acc 3D: (0.18683325327725137, 0.29195696483157874, -0.7829590159403469)
1239s     
1239s     e_kin tot ang lin: 0.060205072713709167 0.012923758676161239 0.04728131403754793
1239s                 e_pot: 0.6200981325993219
1239s                 e_tot: 0.680303205313031
1239s     ang acc 3D: (0.44409839480429714, -0.20238598167333133, -0.6982935349568492)
1239s     lin acc 3D: (0.18158288880693388, 0.2891142841060344, -0.7826906753299725)
1239s     
1239s     e_kin tot ang lin: 0.06426069102522652 0.013133999536143382 0.051126691489083144
1239s                 e_pot: 0.6159370410950341
1239s                 e_tot: 0.6801977321202606
1239s     ang acc 3D: (0.4428619383337592, -0.1979649297164907, -0.6998716687235316)
1239s     lin acc 3D: (0.17618932152521946, 0.2861587292410898, -0.7822928299444691)
1239s     
1239s     e_kin tot ang lin: 0.06853634262082685 0.013374757653013635 0.05516158496781321
1239s                 e_pot: 0.6115577365976127
1239s                 e_tot: 0.6800940792184396
1239s     ang acc 3D: (0.4415492375442347, -0.1934757492571058, -0.7013123022002559)
1239s     lin acc 3D: (0.17065642010895676, 0.2830902094290727, -0.7817633773339945)
1239s     
1239s     e_kin tot ang lin: 0.07302862193581516 0.013645850452066947 0.059382771483748216
1239s                 e_pot: 0.6069637092547071
1239s                 e_tot: 0.6799923311905223
1239s     ang acc 3D: (0.44015985980451133, -0.18892063000069204, -0.702614784647033)
1239s     lin acc 3D: (0.16498819826718966, 0.2799086530227533, -0.7811002126706817)
1239s     
1239s     OK
1242s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1242s 139
1242s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1242s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/tst.py" [FAIL] 6.1s
1242s   Time:  6.14
1242s   Return code: 139
1242s   OKs: 0
1242s   Standard error:
1242s     Segmentation fault (core dumped)
1245s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1245s 139
1245s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1245s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_featherstone.py" [FAIL] 6.0s
1245s   Time:  5.97
1245s   Return code: 139
1245s   OKs: 0
1245s   Standard error:
1245s     Segmentation fault (core dumped)
1248s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1248s 139
1248s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1248s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion.py" [FAIL] 5.9s
1248s   Time:  5.94
1248s   Return code: 139
1248s   OKs: 0
1248s   Standard error:
1248s     Segmentation fault (core dumped)
1251s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1251s 139
1251s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1251s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion_hard.py" [FAIL] 5.9s
1251s   Time:  5.89
1251s   Return code: 139
1251s   OKs: 0
1251s   Standard error:
1251s     Segmentation fault (core dumped)
1254s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1254s 139
1254s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1254s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_joint_lib.py" [FAIL] 6.0s
1254s   Time:  6.03
1254s   Return code: 139
1254s   OKs: 0
1254s   Standard error:
1254s     Segmentation fault (core dumped)
1254s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_spherical_refinement.py" [OK] 0.3s
1254s   Time:  0.33
1254s   Return code: 0
1254s   OKs: 1
1254s   Standard out:
1254s     OK
1254s     usr+sys time: 0.27 seconds
1254s     wall clock time: 0.27 seconds
1257s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1257s 139
1257s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1257s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_singular.py" [FAIL] 6.2s
1257s   Standard error:
1257s     Segmentation fault (core dumped)
1257s   Time:  6.24
1257s   Return code: 139
1257s   OKs: 0
1260s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1260s 139
1260s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1260s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_molecules.py" [FAIL] 5.8s
1260s   Time:  5.81
1260s   Return code: 139
1260s   OKs: 0
1260s   Standard error:
1260s     Segmentation fault (core dumped)
1263s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1263s 139
1263s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1263s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_sparse.py" [FAIL] 6.2s
1263s   Time:  6.15
1263s   Return code: 139
1263s   OKs: 0
1263s   Standard error:
1263s     Segmentation fault (core dumped)
1266s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1266s 139
1266s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1266s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_lu_factorization.py" [FAIL] 6.2s
1266s   Time:  6.16
1266s   Return code: 139
1266s   OKs: 0
1266s   Standard error:
1266s     Segmentation fault (core dumped)
1269s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1269s 139
1269s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1269s libtbx.python "/usr/lib/python3/dist-packages/scitbx/iso_surface/tst_iso_surface.py" [FAIL] 5.9s
1269s   Time:  5.91
1269s   Return code: 139
1269s   OKs: 0
1269s   Standard error:
1269s     Segmentation fault (core dumped)
1272s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1272s 139
1272s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1272s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/simplex.py" [FAIL] 5.8s
1272s   Time:  5.82
1272s   Return code: 139
1272s   OKs: 0
1272s   Standard error:
1272s     Segmentation fault (core dumped)
1272s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/golden_section_search.py" [OK] 0.0s
1272s   Time:  0.03
1272s   Return code: 0
1272s   OKs: 0
1275s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1275s 139
1275s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1275s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/differential_evolution.py" [FAIL] 5.8s
1275s   Time:  5.76
1275s   Return code: 139
1275s   OKs: 0
1275s   Standard error:
1275s     Segmentation fault (core dumped)
1278s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1278s 139
1278s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1278s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/direct_search_simulated_annealing.py" [FAIL] 5.8s
1278s   Time:  5.78
1278s   Return code: 139
1278s   OKs: 0
1278s   Standard error:
1278s     Segmentation fault (core dumped)
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/scitbx/random/tests/tst_random.py" [FAIL] 6.3s
1281s   Time:  6.27
1281s   Return code: 139
1281s   OKs: 0
1281s   Standard error:
1281s     Segmentation fault (core dumped)
1281s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/test_problems.py" [OK] 0.2s
1281s   Time:  0.19
1281s   Return code: 0
1281s   OKs: 0
1284s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1284s 139
1284s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1284s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/tst_normal_equations.py" [FAIL] 6.4s
1284s   Time:  6.38
1284s   Return code: 139
1284s   OKs: 0
1284s   Standard error:
1284s     Segmentation fault (core dumped)
1287s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1287s 139
1287s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1287s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_basic.py" [FAIL] 3.0s
1287s   Time:  3.02
1287s   Return code: 139
1287s   OKs: 0
1287s   Standard error:
1287s     Segmentation fault (core dumped)
1289s libtbx.python "/usr/lib/python3/dist-packages/scitbx/glmtbx/tests/tst.py" [OK] 7.2s
1289s   Time:  7.24
1289s   Return code: 0
1289s   OKs: 2
1289s   Standard out:
1289s     OK
1289s     OK
1290s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1290s 139
1290s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_booth.py" [FAIL] 3.1s
1290s   Time:  3.09
1290s   Return code: 139
1290s   OKs: 0
1290s   Standard error:
1290s     Segmentation fault (core dumped)
1291s libtbx.python "/usr/lib/python3/dist-packages/scitbx/suffixtree/test/tst_single.py" [OK] 0.1s
1291s   Time:  0.09
1291s   Return code: 0
1291s   OKs: 0
1293s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1293s 139
1293s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1293s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_twisted.py" [FAIL] 4.5s
1293s   Time:  4.54
1293s   Return code: 139
1293s   OKs: 0
1293s   Standard error:
1293s     Segmentation fault (core dumped)
1296s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1296s 139
1296s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1296s libtbx.python "/usr/lib/python3/dist-packages/smtbx/absolute_structure/tests/tst_absolute_structure.py" --fix_random_seeds [FAIL] 5.9s
1296s   Time:  5.95
1296s   Return code: 139
1296s   OKs: 0
1296s   Standard error:
1296s     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/smtbx/ab_initio/tests/tst_ab_initio_ext.py" [FAIL] 6.3s
1300s   Time:  6.26
1300s   Return code: 139
1300s   OKs: 0
1300s   Standard error:
1300s     Segmentation fault (core dumped)
1303s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1303s 139
1303s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1303s libtbx.python "/usr/lib/python3/dist-packages/smtbx/ab_initio/tests/tst_charge_flipping.py" --fix_seed --on=E "hall: P 1" "hall: P 3" "hall: -P 2ybc" [FAIL] 6.3s
1303s   Time:  6.27
1303s   Return code: 139
1303s   OKs: 0
1303s   Standard error:
1303s     Segmentation fault (core dumped)
1306s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1306s 139
1306s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1306s libtbx.python "/usr/lib/python3/dist-packages/smtbx/masks/tests/tst_masks.py" [FAIL] 6.6s
1306s   Time:  6.62
1306s   Return code: 139
1306s   OKs: 0
1306s   Standard error:
1306s     Segmentation fault (core dumped)
1310s   Standard error:
1310s     Segmentation fault (core dumped)
1310s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1310s 139
1310s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1310s libtbx.python "/usr/lib/python3/dist-packages/smtbx/structure_factors/direct/tests/tst_standard_xray.py" [FAIL] 7.5s
1310s   Time:  7.45
1310s   Return code: 139
1310s   OKs: 0
1314s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1314s 139
1314s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_weighting_schemes.py" --fix_random_seeds [FAIL] 7.6s
1314s   Time:  7.64
1314s   Return code: 139
1314s   OKs: 0
1314s   Standard error:
1314s     Segmentation fault (core dumped)
1314s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_reparametrisation" [OK] 0.0s
1314s   Time:  0.01
1314s   Return code: 0
1314s   OKs: 1
1314s   Standard out:
1314s     sizeof(parameter) = 32
1314s     OK
1317s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1317s 139
1317s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1317s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_lbfgs.py" [FAIL] 7.3s
1317s   Time:  7.28
1317s   Return code: 139
1317s   OKs: 0
1317s   Standard error:
1317s     Segmentation fault (core dumped)
1317s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens" [OK] 0.0s
1317s   Time:  0.01
1317s   Return code: 0
1317s   OKs: 1
1317s   Standard out:
1317s     OK
1321s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1321s 139
1321s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1321s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_occupancies.py" [FAIL] 7.3s
1321s   Time:  7.29
1321s   Return code: 139
1321s   OKs: 0
1321s   Standard error:
1321s     Segmentation fault (core dumped)
1321s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_special_position" [OK] 0.0s
1321s   Time:  0.01
1321s   Return code: 0
1321s   OKs: 1
1321s   Standard out:
1321s     OK
1325s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1325s 139
1325s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1325s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_same_group.py" [FAIL] 7.1s
1325s   Time:  7.12
1325s   Return code: 139
1325s   OKs: 0
1325s   Standard error:
1325s     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/smtbx/refinement/constraints/tests/tst_reparametrisation.py" [FAIL] 7.0s
1328s   Time:  7.00
1328s   Return code: 139
1328s   OKs: 0
1328s   Standard error:
1328s     Segmentation fault (core dumped)
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/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=naive [FAIL] 7.0s
1332s   Time:  7.02
1332s   Return code: 139
1332s   OKs: 0
1332s   Standard error:
1332s     Segmentation fault (core dumped)
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/smtbx/refinement/constraints/tests/tst_disorder.py" [FAIL] 7.1s
1335s   Time:  7.14
1335s   Return code: 139
1335s   OKs: 0
1335s   Standard error:
1335s     Segmentation fault (core dumped)
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/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=levenberg-marquardt [FAIL] 3.7s
1335s   Time:  3.66
1335s   Return code: 139
1335s   OKs: 0
1335s   Standard error:
1335s     Segmentation fault (core dumped)
1339s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1339s 139
1339s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1339s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_direction.py" [FAIL] 4.1s
1339s   Time:  4.10
1339s   Return code: 139
1339s   OKs: 0
1339s   Standard error:
1339s     Segmentation fault (core dumped)
1343s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1343s 139
1343s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_rigid.py" [FAIL] 7.8s
1343s   Time:  7.84
1343s   Return code: 139
1343s   OKs: 0
1343s   Standard error:
1343s     Segmentation fault (core dumped)
1347s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1347s 139
1347s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1347s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_adp_restraints.py" [FAIL] 7.2s
1347s   Time:  7.21
1347s   Return code: 139
1347s   OKs: 0
1347s   Standard error:
1347s     Segmentation fault (core dumped)
1350s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1350s 139
1350s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1350s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_manager.py" [FAIL] 7.0s
1350s   Time:  7.02
1350s   Return code: 139
1350s   OKs: 0
1350s   Standard error:
1350s     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/smtbx/refinement/restraints/tests/tst_restraints.py" --verbose --scatterers=5 --resolution=0.2 [FAIL] 7.3s
1354s   Time:  7.29
1354s   Return code: 139
1354s   OKs: 0
1354s   Standard error:
1354s     Segmentation fault (core dumped)
1358s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1358s 139
1358s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1358s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_refine.py" [FAIL] 7.7s
1358s   Time:  7.67
1358s   Return code: 139
1358s   OKs: 0
1358s   Standard error:
1358s     Segmentation fault (core dumped)
1365s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1365s 1
1365s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1365s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py" [FAIL] 11.3s
1365s   Time: 11.34
1365s   Return code: 1
1365s   OKs: 0
1365s   Standard out:
1365s     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
1365s   Standard error:
1365s     Traceback (most recent call last):
1365s       File "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py", line 37, in <module>
1365s         run()
1365s         ~~~^^
1365s       File "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py", line 27, in run
1365s         run_buf.raise_if_errors()
1365s         ~~~~~~~~~~~~~~~~~~~~~~~^^
1365s       File "/usr/lib/python3/dist-packages/libtbx/easy_run.py", line 46, in raise_if_errors
1365s         raise Error(msg)
1365s     RuntimeError: child process stderr output:
1365s       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'
1365s       Segmentation fault (core dumped)
1366s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1366s 139
1366s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1366s libtbx.python "/usr/lib/python3/dist-packages/smtbx/tests/tst_utils.py" [FAIL] 8.2s
1366s   Time:  8.19
1366s   Return code: 139
1366s   OKs: 0
1366s   Standard error:
1366s     Segmentation fault (core dumped)
1370s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1370s 139
1370s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1370s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_least_squares.py" [EXPECTED UNSTABLE] 4.4s
1370s   Time:  4.41
1370s   Return code: 139
1370s   OKs: 0
1370s   Standard error:
1370s     Segmentation fault (core dumped)
1370s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_predict.py" [OK] 0.3s
1370s   Time:  0.27
1370s   Return code: 0
1370s   OKs: 1
1370s   Standard out:
1370s     OK
1370s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_ewald_sphere.py" [OK] 0.2s
1370s   Time:  0.25
1370s   Return code: 0
1370s   OKs: 1
1370s   Standard out:
1370s     OK
1370s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_partial_derivatives.py" [OK] 0.2s
1370s   Time:  0.23
1370s   Return code: 0
1370s   OKs: 1
1370s   Standard out:
1370s     OK
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/rstbx/dps_core/tst_iotbx_converter.py" [FAIL] 7.1s
1373s   Time:  7.14
1373s   Return code: 139
1373s   OKs: 0
1373s   Standard error:
1373s     Segmentation fault (core dumped)
1377s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1377s 139
1377s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1377s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/fastbragg/tst_bragg_minimal.py" [FAIL] 6.4s
1377s   Time:  6.35
1377s   Return code: 139
1377s   OKs: 0
1377s   Standard error:
1377s     Segmentation fault (core dumped)
1380s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 
1380s 139
1380s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 
1380s libtbx.python "/usr/lib/python3/dist-packages/rstbx/sublattice_support/tst_sublattice.py" [FAIL] 6.9s
1380s   Time:  6.94
1380s   Return code: 139
1380s   OKs: 0
1380s   Standard error:
1380s     Segmentation fault (core dumped)
1381s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/core_toolbox/boost_python/tst_small_image.py" [OK] 0.4s
1381s   Time:  0.45
1381s   Return code: 0
1381s   OKs: 1
1381s   Standard out:
1381s     OK
1381s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/diffraction/geometry.py" [OK] 0.2s
1381s   Time:  0.23
1381s   Return code: 0
1381s   OKs: 1
1381s   Standard out:
1381s     OK
1381s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/math_support/sphere_formulae.py" [OK] 0.0s
1381s   Time:  0.04
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 -c "from rstbx.run_tests import run; run()" [FAIL] 5.0s
1382s   Time:  4.98
1382s   Return code: 139
1382s   OKs: 0
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s ================================================================================
1382s 
1382s Tests finished. Elapsed time: 1124.17s
1382s 
1382s Distribution of test runtimes:
1382s   0.0s - 4.7s: 282
1382s   4.7s - 9.4s: 250
1382s   9.4s - 14.2s: 9
1382s   14.2s - 18.9s: 2
1382s   18.9s - 23.6s: 1
1382s   23.6s - 28.3s: 0
1382s   28.3s - 33.0s: 1
1382s   33.0s - 37.7s: 0
1382s   37.7s - 42.5s: 0
1382s   42.5s - 47.2s: 1
1382s 
1382s 
1382s Warning: the following are 5 longest jobs:
1382s   libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_fetch.py": 47.2s
1382s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_integer_offsets_vs_pointers.py": 28.6s
1382s   libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_thread_utils.py": 21.4s
1382s   libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike.py": 16.5s
1382s   libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_separate_files.py": 14.5s
1382s Please try to reduce overall runtime - consider splitting up these tests.
1382s 
1382s 
1382s Error: the following jobs returned non-zero exit codes or suspicious stderr output:
1382s 
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sf_low_res_accuracy.py" [FAIL] 5.5s
1382s   Time:  5.48
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_double_step_filtration.py" [FAIL] 5.3s
1382s   Time:  5.26
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_is_periodic.py" [FAIL] 8.3s
1382s   Time:  8.26
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_reindexing.py" [FAIL] 7.7s
1382s   Time:  7.73
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_data_manipulation.py" [FAIL] 7.3s
1382s   Time:  7.27
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_bfgs.py" [FAIL] 7.5s
1382s   Time:  7.45
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_dev.py" P31 [FAIL] 7.5s
1382s   Time:  7.46
1382s   Return code: 139
1382s   OKs: 0
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry/tests/tst_geometry.py" [FAIL] 7.9s
1382s   Time:  7.88
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/covariance/tests/tst_covariance.py" [FAIL] 7.7s
1382s   Time:  7.69
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_goodness_of_symmetry.py" [FAIL] 7.6s
1382s   Time:  7.63
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_from_map.py" P312 [FAIL] 7.7s
1382s   Time:  7.70
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_xray.py" [FAIL] 7.0s
1382s   Time:  7.01
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray.py" I41/acd [FAIL] 8.3s
1382s   Time:  8.33
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_r1.py" [FAIL] 8.0s
1382s   Time:  7.97
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_shelxl_wght_ls.py" [FAIL] 8.1s
1382s   Time:  8.10
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_f_model.py" [FAIL] 8.3s
1382s   Time:  8.30
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/array_family/boost_python/tst_flex.py" [FAIL] 7.5s
1382s   Time:  7.51
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_uctbx.py" [FAIL] 7.1s
1382s   Time:  7.06
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_crystal_orientation.py" [FAIL] 6.8s
1382s   Time:  6.76
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_sgtbx.py" [FAIL] 7.3s
1382s   Time:  7.28
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_ext.py" [FAIL] 7.6s
1382s   Time:  7.61
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_distance_based_connectivity.py" [FAIL] 7.5s
1382s   Time:  7.51
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_super_cell.py" [FAIL] 8.1s
1382s   Time:  8.14
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adptbx/boost_python/tst_adptbx.py" [FAIL] 8.3s
1382s   Time:  8.34
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/boost_python/tst_miller.py" [FAIL] 7.9s
1382s   Time:  7.87
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_xray_scattering.py" [FAIL] 7.4s
1382s   Time:  7.43
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_formula.py" [FAIL] 6.2s
1382s   Time:  6.17
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_attenuation_coefficient.py" [FAIL] 7.2s
1382s   Time:  7.19
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/boost_python/tst_maptbx.py" [FAIL] 7.3s
1382s   Time:  7.26
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_bcr.py" [FAIL] 8.0s
1382s   Time:  7.97
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_loft.py" [FAIL] 8.7s
1382s   Time:  8.71
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/dmtbx/boost_python/tst_dmtbx.py" [FAIL] 8.2s
1382s   Time:  8.17
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/translation_search/boost_python/tst_translation_search.py" [FAIL] 7.8s
1382s   Time:  7.84
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_ext.py" [FAIL] 7.9s
1382s   Time:  7.94
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_angle_derivs.py" [FAIL] 5.7s
1382s   Time:  5.69
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adp_restraints/tst_ext.py" [FAIL] 7.5s
1382s   Time:  7.50
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_krivy_gruber.py" --Quick [FAIL] 7.5s
1382s   Time:  7.54
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx.py" [FAIL] 7.2s
1382s   Time:  7.22
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_space_group_type_tidy_cb_op_t.py" [FAIL] 7.3s
1382s   Time:  7.32
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_denominators.py" P31 [FAIL] 7.3s
1382s   Time:  7.30
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_subgroups.py" [FAIL] 7.1s
1382s   Time:  7.12
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_lattice_symmetry.py" [FAIL] 7.1s
1382s   Time:  7.09
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints.py" P3 [FAIL] 6.9s
1382s   Time:  6.94
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints_cartesian.py" [FAIL] 6.7s
1382s   Time:  6.67
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reflection_statistics.py" [FAIL] 6.0s
1382s   Time:  6.05
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_harker.py" [FAIL] 6.5s
1382s   Time:  6.51
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_special_op_simplifier.py" [FAIL] 7.0s
1382s   Time:  6.97
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_twin_target.py" [FAIL] 7.4s
1382s   Time:  7.40
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/symbol_confidence.py" [FAIL] 7.0s
1382s   Time:  7.03
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/bravais_types.py" [FAIL] 6.6s
1382s   Time:  6.60
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_lookup_utils.py" [FAIL] 6.9s
1382s   Time:  6.92
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal.py" I41/acd [FAIL] 7.4s
1382s   Time:  7.35
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_direct_space_asu.py" I41/acd [FAIL] 7.0s
1382s   Time:  7.05
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pair_asu_table.py" [FAIL] 6.8s
1382s   Time:  6.80
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_asu_clusters.py" [FAIL] 6.7s
1382s   Time:  6.67
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_close_packing.py" R-3mr [FAIL] 6.4s
1382s   Time:  6.43
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fourier_transform_real_part_at_x.py" P31 [FAIL] 7.2s
1382s   Time:  7.17
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller.py" P31 [FAIL] 7.7s
1382s   Time:  7.73
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem.py" [FAIL] 8.4s
1382s   Time:  8.40
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reciprocal_space_asu.py" P312 [FAIL] 7.3s
1382s   Time:  7.33
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_triplet_generator.py" P41 [FAIL] 7.1s
1382s   Time:  7.13
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_emma.py" P31 [FAIL] 7.8s
1382s   Time:  7.81
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_expand_to_p1.py" P31 [FAIL] 7.9s
1382s   Time:  7.88
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_change_basis.py" P31 [FAIL] 7.2s
1382s   Time:  7.19
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wilson_plot.py" P31 [FAIL] 6.9s
1382s   Time:  6.88
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_derivatives.py" P31 [FAIL] 6.9s
1382s   Time:  6.93
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_fast_gradients.py" P31 [FAIL] 7.0s
1382s   Time:  7.01
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F P31 [FAIL] 7.1s
1382s   Time:  7.06
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F_sq P31 [FAIL] 3.6s
1382s   Time:  3.56
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_structure_factors.py" P31 [FAIL] 4.7s
1382s   Time:  4.68
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_weights_for_symmetry_summation.py" Pmmm [FAIL] 9.1s
1382s   Time:  9.11
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_real_space_refinement_simple.py" [FAIL] 8.5s
1382s   Time:  8.53
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation.py" [FAIL] 7.9s
1382s   Time:  7.86
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation_2.py" [FAIL] 7.8s
1382s   Time:  7.84
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_loc_res.py" [FAIL] 8.6s
1382s   Time:  8.58
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_target_and_gradients.py" [FAIL] 8.2s
1382s   Time:  8.19
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_merge_equivalents.py" P31 [FAIL] 7.2s
1382s   Time:  7.15
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grouped_data.py" P31 [FAIL] 7.4s
1382s   Time:  7.42
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_fft_map.py" P31 [FAIL] 7.8s
1382s   Time:  7.81
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sampled_model_density.py" P31 [FAIL] 8.1s
1382s   Time:  8.08
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fast_nv1995.py" F222 [FAIL] 8.5s
1382s   Time:  8.49
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_lbfgs.py" [FAIL] 7.5s
1382s   Time:  7.51
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_2.py" [FAIL] 8.2s
1382s   Time:  8.19
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_french_wilson.py" [FAIL] 7.3s
1382s   Time:  7.31
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/make_cns_input.py" P31 [FAIL] 7.3s
1382s   Time:  7.28
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pointgroup_tools.py" [FAIL] 6.2s
1382s   Time:  6.25
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/sub_lattice_tools.py" [FAIL] 7.3s
1382s   Time:  7.28
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/rational_matrices_point_groups.py" [FAIL] 7.8s
1382s   Time:  7.85
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/cosets.py" [FAIL] 7.7s
1382s   Time:  7.73
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_pg_tools.py" [FAIL] 7.4s
1382s   Time:  7.43
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_twin_laws.py" [FAIL] 7.3s
1382s   Time:  7.30
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_find_best_cell.py" [FAIL] 7.1s
1382s   Time:  7.11
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_amplitude_normalisation.py" [FAIL] 7.3s
1382s   Time:  7.34
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_statistics_graphs.py" [FAIL] 7.6s
1382s   Time:  7.63
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_web_change_basis.py" [FAIL] 8.1s
1382s   Time:  8.11
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/direct_space_asu/proto/tst_asu.py" [FAIL] 7.7s
1382s   Time:  7.67
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_tidy_pickling.py" [FAIL] 7.7s
1382s   Time:  7.68
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/masks/tests/tst_flood_fill.py" [FAIL] 8.1s
1382s   Time:  8.13
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_r_free_utils.py" [FAIL] 8.0s
1382s   Time:  8.01
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_ccp.py" [FAIL] 7.4s
1382s   Time:  7.43
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_mask.py" [FAIL] 7.3s
1382s   Time:  7.32
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_map_peak_3d_as_2d.py" [FAIL] 7.5s
1382s   Time:  7.55
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_asymmetric_map.py" [FAIL] 7.9s
1382s   Time:  7.87
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_peak_volume_estimate.py" [FAIL] 7.5s
1382s   Time:  7.48
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_resolution_from_map_and_model.py" [FAIL] 7.2s
1382s   Time:  7.15
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_curves.py" [FAIL] 7.0s
1382s   Time:  7.03
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_radius_as_central_peak_width.py" [FAIL] 7.0s
1382s   Time:  6.98
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_get_percentile_cutoffs.py" [FAIL] 7.3s
1382s   Time:  7.29
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sphericity.py" [FAIL] 5.6s
1382s   Time:  5.59
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_statistics.py" [FAIL] 7.0s
1382s   Time:  7.03
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity.py" [FAIL] 6.5s
1382s   Time:  6.49
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity_allsym.py" [FAIL] 7.0s
1382s   Time:  6.97
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py" [FAIL] 10.8s
1382s   Time: 10.82
1382s   Return code: 1
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_prepare_map_for_docking.py" [FAIL] 8.1s
1382s   Time:  8.06
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/cma_es/tst_cma_es.py" [FAIL] 5.9s
1382s   Time:  5.91
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mrc_io.py" [FAIL] 4.0s
1382s   Time:  3.99
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/gui_tools/tst.py" [FAIL] 4.2s
1382s   Time:  4.17
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phil.py" [FAIL] 5.7s
1382s   Time:  5.73
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_manager.py" [FAIL] 7.6s
1382s   Time:  7.65
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager_wrapping.py" [FAIL] 8.0s
1382s   Time:  8.02
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager.py" [FAIL] 7.9s
1382s   Time:  7.87
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry.py" [FAIL] 5.4s
1382s   Time:  5.41
1382s   Return code: 139
1382s   OKs: 0
1382s 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] 9.8s
1382s   Time:  9.80
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_tools.py" [FAIL] 7.7s
1382s   Time:  7.73
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_atom_selections_10k.py" [FAIL] 7.2s
1382s   Time:  7.25
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_crystal_symmetry_from_any.py" [FAIL] 7.7s
1382s   Time:  7.72
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/kriber/tst_strudat.py" [FAIL] 7.4s
1382s   Time:  7.41
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_geometry.py" [FAIL] 7.3s
1382s   Time:  7.25
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_lex_parse_build.py" [FAIL] 7.7s
1382s   Time:  7.68
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model.py" [FAIL] 7.8s
1382s   Time:  7.83
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py" [FAIL] 3.6s
1382s   Time:  3.57
1382s   Return code: 1
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_restraints.py" [FAIL] 7.9s
1382s   Time:  7.93
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_lex_parse_build.py" [FAIL] 4.2s
1382s   Time:  4.16
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_hklf.py" [FAIL] 7.7s
1382s   Time:  7.65
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_writer.py" [FAIL] 7.5s
1382s   Time:  7.50
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_fvar_encoding.py" [FAIL] 7.4s
1382s   Time:  7.39
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_pdb.py" [FAIL] 7.1s
1382s   Time:  7.15
1382s   Return code: 134
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy.py" [FAIL] 8.0s
1382s   Time:  8.02
1382s   Return code: 134
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy.py" [FAIL] 4.5s
1382s   Time:  4.52
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_ext.py" [FAIL] 6.7s
1382s   Time:  6.75
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection.py" [FAIL] 7.5s
1382s   Time:  7.48
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation.py" [FAIL] 6.3s
1382s   Time:  6.28
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection_string.py" [FAIL] 7.5s
1382s   Time:  7.47
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_utils.py" [FAIL] 7.8s
1382s   Time:  7.79
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_truncate_to_ala/tst.py" [FAIL] 5.5s
1382s   Time:  5.47
1382s   Return code: 134
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_examples.py" [FAIL] 8.1s
1382s   Time:  8.11
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/space_group_symbols.py" [FAIL] 8.3s
1382s   Time:  8.35
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/tst_cns.py" [FAIL] 8.3s
1382s   Time:  8.35
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_merge.py" P31 [FAIL] 7.9s
1382s   Time:  7.93
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/no_merge_original_index.py" [FAIL] 6.9s
1382s   Time:  6.88
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/ccp4_map/tst.py" [FAIL] 7.1s
1382s   Time:  7.08
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_ext.py" [FAIL] 7.8s
1382s   Time:  7.84
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_extract_from_symmetry_lib.py" [FAIL] 7.7s
1382s   Time:  7.73
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_dano.py" [FAIL] 7.0s
1382s   Time:  7.03
1382s   Return code: 139
1382s   OKs: 0
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s     Traceback (most recent call last):
1382s       File "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py", line 140, in <module>
1382s         exercise()
1382s         ~~~~~~~~^^
1382s       File "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py", line 126, in exercise
1382s         assert not easy_run.call(cmd)
1382s                ^^^^^^^^^^^^^^^^^^^^^^
1382s     AssertionError
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Traceback (most recent call last):
1382s       File "/usr/lib/python3.13/urllib/request.py", line 1541, in ftp_open
1382s         fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout)
1382s       File "/usr/lib/python3.13/urllib/request.py", line 1561, in connect_ftp
1382s         return ftpwrapper(user, passwd, host, port, dirs, timeout,
1382s                           persistent=False)
1382s       File "/usr/lib/python3.13/urllib/request.py", line 2409, in __init__
1382s         self.init()
1382s         ~~~~~~~~~^^
1382s       File "/usr/lib/python3.13/urllib/request.py", line 2418, in init
1382s         self.ftp.connect(self.host, self.port, self.timeout)
1382s         ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
1382s       File "/usr/lib/python3.13/ftplib.py", line 158, in connect
1382s         self.sock = socket.create_connection((self.host, self.port), self.timeout,
1382s                     ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
1382s                                              source_address=self.source_address)
1382s                                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
1382s       File "/usr/lib/python3.13/socket.py", line 864, in create_connection
1382s         raise exceptions[0]
1382s       File "/usr/lib/python3.13/socket.py", line 849, in create_connection
1382s         sock.connect(sa)
1382s         ~~~~~~~~~~~~^^^^
1382s     ConnectionRefusedError: [Errno 111] Connection refused
1382s     
1382s     The above exception was the direct cause of the following exception:
1382s     
1382s     Traceback (most recent call last):
1382s       File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 327, in <module>
1382s         exercise(sys.argv[1:])
1382s         ~~~~~~~~^^^^^^^^^^^^^^
1382s       File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 26, in exercise
1382s         exercise_validation()
1382s         ~~~~~~~~~~~~~~~~~~~^^
1382s       File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 29, in exercise_validation
1382s         cd = validation.smart_load_dictionary(name="cif_core.dic")
1382s       File "/usr/lib/python3/dist-packages/iotbx/cif/validation.py", line 111, in smart_load_dictionary
1382s         url = locate_dictionary(name, registry_location=registry_location)
1382s       File "/usr/lib/python3/dist-packages/iotbx/cif/validation.py", line 129, in locate_dictionary
1382s         cm = cif.reader(file_object=urlopen(registry_location)).model()
1382s                                     ~~~~~~~^^^^^^^^^^^^^^^^^^^
1382s       File "/usr/lib/python3.13/urllib/request.py", line 189, in urlopen
1382s         return opener.open(url, data, timeout)
1382s                ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^
1382s       File "/usr/lib/python3.13/urllib/request.py", line 489, in open
1382s         response = self._open(req, data)
1382s       File "/usr/lib/python3.13/urllib/request.py", line 506, in _open
1382s         result = self._call_chain(self.handle_open, protocol, protocol +
1382s                                   '_open', req)
1382s       File "/usr/lib/python3.13/urllib/request.py", line 466, in _call_chain
1382s         result = func(*args)
1382s       File "/usr/lib/python3.13/urllib/request.py", line 1558, in ftp_open
1382s         raise URLError(exp) from exp
1382s     urllib.error.URLError: <urlopen error [Errno 111] Connection refused>
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     *** buffer overflow detected ***: terminated
1382s     Aborted (core dumped)
1382s   Standard error:
1382s     *** buffer overflow detected ***: terminated
1382s     Aborted (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     *** buffer overflow detected ***: terminated
1382s     Aborted (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     /usr/lib/python3/dist-packages/ccp4io_adaptbx/__init__.py:25: UserWarning: ccp4io_adaptbx: cannot locate syminfo.lib
1382s       warnings.warn("ccp4io_adaptbx: cannot locate syminfo.lib")
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Traceback (most recent call last):
1382s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 477, in <module>
1382s         exercise(sys.argv[1:])
1382s         ~~~~~~~~^^^^^^^^^^^^^^
1382s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 22, in exercise
1382s           run_and_compare(
1382s           ~~~~~~~~~~~~~~~^
1382s             ['iotbx.lattice_symmetry'
1382s             ^^^^^^^^^^^^^^^^^^^^^^^^^
1382s         ...<31 lines>...
1382s         
1382s         
1382s         """)
1382s         ^^^^
1382s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 17, in run_and_compare
1382s         command=command).raise_if_errors().stdout_lines
1382s                          ~~~~~~~~~~~~~~~^^
1382s       File "/usr/lib/python3/dist-packages/libtbx/easy_run.py", line 46, in raise_if_errors
1382s         raise Error(msg)
1382s     RuntimeError: child process stderr output:
1382s       command: 'iotbx.lattice_symmetry --unit_cell="12.7923,12.8923,29.4356,102.846,103.846,22.7475"'
1382s       Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     *** buffer overflow detected ***: terminated
1382s     Aborted (core dumped)
1382s     Traceback (most recent call last):
1382s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py", line 138, in <module>
1382s         exercise()
1382s         ~~~~~~~~^^
1382s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py", line 48, in exercise
1382s         assert not easy_run.call("iotbx.pdb.box_around_molecule %s.pdb" % (
1382s                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
1382s             prefix))
1382s             ^^^^^^^^
1382s     AssertionError
1382s   Standard error:
1382s     *** buffer overflow detected ***: terminated
1382s     Aborted (core dumped)
1382s   Standard error:
1382s     *** buffer overflow detected ***: terminated
1382s     Aborted (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Traceback (most recent call last):
1382s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py", line 60, in <module>
1382s         exercise()
1382s         ~~~~~~~~^^
1382s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py", line 48, in exercise
1382s         assert (len(out.stdout_lines) == 2) and (len(out.stderr_lines) == 0)
1382s                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
1382s     AssertionError
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s     Traceback (most recent call last):
1382s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py", line 815, in <module>
1382s         exercise_1()
1382s         ~~~~~~~~~~^^
1382s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py", line 806, in exercise_1
1382s         assert not easy_run.call(cmd)
1382s                ^^^^^^^^^^^^^^^^^^^^^^
1382s     AssertionError
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     *** buffer overflow detected ***: terminated
1382s     Aborted (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Traceback (most recent call last):
1382s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py", line 395, in <module>
1382s         tst_1()
1382s         ~~~~~^^
1382s       File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py", line 370, in tst_1
1382s         assert os.path.isfile('%s.cif_%s_000.mtz' % (prefix, bn))
1382s                ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
1382s     AssertionError
1382s   Standard error:
1382s     *** buffer overflow detected ***: terminated
1382s     Aborted (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     *** buffer overflow detected ***: terminated
1382s     Aborted (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst.py" P31 [FAIL] 6.5s
1382s   Time:  6.47
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_utils.py" [FAIL] 6.9s
1382s   Time:  6.92
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xplor/tst_xplormap.py" [FAIL] 6.5s
1382s   Time:  6.47
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phases.py" P31 [FAIL] 6.6s
1382s   Time:  6.60
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py" [FAIL] 9.9s
1382s   Time:  9.90
1382s   Return code: 1
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_statistics.py" Fdd2 P31m [FAIL] 7.6s
1382s   Time:  7.64
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_file_reader.py" [FAIL] 4.4s
1382s   Time:  4.37
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py" [FAIL] 11.0s
1382s   Time: 11.04
1382s   Return code: 1
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_segids.py" [FAIL] 8.4s
1382s   Time:  8.37
1382s   Return code: 134
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_forward_compatible_pdb.py" [FAIL] 4.0s
1382s   Time:  3.97
1382s   Return code: 134
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_symmetry.py" [FAIL] 5.7s
1382s   Time:  5.70
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_editor.py" [FAIL] 6.5s
1382s   Time:  6.51
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py" [FAIL] 10.0s
1382s   Time: 10.00
1382s   Return code: 1
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_map_coefficients.py" [FAIL] 6.3s
1382s   Time:  6.32
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py" [FAIL] 8.1s
1382s   Time:  8.08
1382s   Return code: 1
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_integrate_hkl.py" [FAIL] 8.5s
1382s   Time:  8.50
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_no_merge_original_index.py" [FAIL] 4.3s
1382s   Time:  4.34
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_export_scalepack_unmerged.py" [FAIL] 7.3s
1382s   Time:  7.29
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/dsn6/tst.py" P31 [FAIL] 6.9s
1382s   Time:  6.90
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_ligs.py" [FAIL] 5.7s
1382s   Time:  5.69
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_broken_chain.py" [FAIL] 7.3s
1382s   Time:  7.33
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_shortcut_1.py" [FAIL] 7.5s
1382s   Time:  7.51
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_groups_preprocessing.py" [FAIL] 7.9s
1382s   Time:  7.94
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_input.py" [FAIL] 8.2s
1382s   Time:  8.23
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_user_selections.py" [FAIL] 7.8s
1382s   Time:  7.79
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs.py" [FAIL] 8.0s
1382s   Time:  8.01
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_without_validation.py" [FAIL] 8.1s
1382s   Time:  8.08
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_read_mtrix_records_from_cif.py" [FAIL] 7.7s
1382s   Time:  7.65
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_show_systematic_absences.py" [FAIL] 7.6s
1382s   Time:  7.61
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_miller_sort_asu.py" [FAIL] 7.0s
1382s   Time:  7.03
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_xray_scale.py" [FAIL] 7.2s
1382s   Time:  7.16
1382s   Return code: 134
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_as_pdb_1atom.py" [FAIL] 6.9s
1382s   Time:  6.89
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_1.py" [FAIL] 7.9s
1382s   Time:  7.91
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py" [FAIL] 11.5s
1382s   Time: 11.47
1382s   Return code: 1
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_all_chain_ids.py" [FAIL] 8.8s
1382s   Time:  8.80
1382s   Return code: 134
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_extract_xtal_data.py" [FAIL] 5.1s
1382s   Time:  5.07
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cli_parser.py" [FAIL] 7.8s
1382s   Time:  7.84
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_occupancies_rounding.py" [FAIL] 6.8s
1382s   Time:  6.76
1382s   Return code: 134
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_debug_write.py" [FAIL] 3.4s
1382s   Time:  3.43
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_smoothing.py" [FAIL] 4.0s
1382s   Time:  4.01
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_genetic_algorithm_with_mp.py" [FAIL] 5.1s
1382s   Time:  5.10
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_basic.py" [FAIL] 7.2s
1382s   Time:  7.16
1382s   Return code: 139
1382s   OKs: 1
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_minimum_covering_ellipsoid.py" [FAIL] 6.3s
1382s   Time:  6.26
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian_fit_1d_analytical.py" [FAIL] 6.5s
1382s   Time:  6.54
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_cubic_equation.py" [FAIL] 6.6s
1382s   Time:  6.60
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_cholesky.py" [FAIL] 6.3s
1382s   Time:  6.29
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_svd.py" [FAIL] 7.4s
1382s   Time:  7.40
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_eigensystem.py" [FAIL] 7.5s
1382s   Time:  7.46
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_svd.py" [FAIL] 6.7s
1382s   Time:  6.72
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_dsyev.py" [FAIL] 6.5s
1382s   Time:  6.51
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/regression_test.py" [FAIL] 6.7s
1382s   Time:  6.68
1382s   Return code: 139
1382s   OKs: 0
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex.py" [FAIL] 7.2s
1382s   Time:  7.22
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_numpy_bridge.py" [FAIL] 7.0s
1382s   Time:  7.00
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_smart_selection.py" [FAIL] 7.0s
1382s   Time:  6.96
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_shared.py" [FAIL] 7.4s
1382s   Time:  7.35
1382s   Return code: 139
1382s   OKs: 0
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/__init__.py" [FAIL] 4.2s
1382s   Time:  4.19
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_random_transform.py" [FAIL] 4.1s
1382s   Time:  4.13
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/superpose.py" [FAIL] 3.7s
1382s   Time:  3.75
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/spe.py" [FAIL] 3.5s
1382s   Time:  3.46
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/incremental_SO3_sampling.py" [FAIL] 4.8s
1382s   Time:  4.82
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_curve_fitting.py" [FAIL] 3.9s
1382s   Time:  3.86
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_weighted_correlation.py" [FAIL] 7.4s
1382s   Time:  7.41
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_exp_functions.py" [FAIL] 7.2s
1382s   Time:  7.18
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_math.py" [FAIL] 6.7s
1382s   Time:  6.72
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_resample.py" [FAIL] 4.8s
1382s   Time:  4.79
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian.py" [FAIL] 6.9s
1382s   Time:  6.88
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_quadrature.py" [FAIL] 6.9s
1382s   Time:  6.91
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_halton.py" [FAIL] 6.3s
1382s   Time:  6.29
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/scale_curves.py" [FAIL] 3.6s
1382s   Time:  3.59
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_fit_peak.py" [FAIL] 3.7s
1382s   Time:  3.72
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_clustering.py" [FAIL] 3.4s
1382s   Time:  3.37
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike.py" [FAIL] 16.5s
1382s   Time: 16.45
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_periodogram.py" [FAIL] 6.1s
1382s   Time:  6.14
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_error_propagation_matrix_inverse.py" [FAIL] 6.5s
1382s   Time:  6.49
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_curvatures.py" [FAIL] 5.4s
1382s   Time:  5.35
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgsb/boost_python/tst_lbfgsb.py" [FAIL] 3.6s
1382s   Time:  3.62
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/fftpack/boost_python/tst_fftpack.py"  [FAIL] 3.5s
1382s   Time:  3.52
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_grid.py" [FAIL] 3.4s
1382s   Time:  3.36
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_linear_least_squares_fit.py" [FAIL] 3.2s
1382s   Time:  3.17
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/chebyshev_lsq_example.py" [FAIL] 6.2s
1382s   Time:  6.21
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/immoptibox_ports.py" [FAIL] 6.1s
1382s   Time:  6.08
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/integrating_a_weighted_sinc_function.py" [FAIL] 5.8s
1382s   Time:  5.80
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/minimizer_comparisons.py" [FAIL] 6.0s
1382s   Time:  6.01
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree.py" [FAIL] 3.8s
1382s   Time:  3.83
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_basic.py" [FAIL] 6.1s
1382s   Time:  6.12
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_tardy.py" [FAIL] 6.3s
1382s   Time:  6.26
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_energy_plots.py" [FAIL] 6.4s
1382s   Time:  6.39
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/tst.py" [FAIL] 6.1s
1382s   Time:  6.14
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_featherstone.py" [FAIL] 6.0s
1382s   Time:  5.97
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion.py" [FAIL] 5.9s
1382s   Time:  5.94
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion_hard.py" [FAIL] 5.9s
1382s   Time:  5.89
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_joint_lib.py" [FAIL] 6.0s
1382s   Time:  6.03
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_singular.py" [FAIL] 6.2s
1382s   Time:  6.24
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_molecules.py" [FAIL] 5.8s
1382s   Time:  5.81
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_sparse.py" [FAIL] 6.2s
1382s   Time:  6.15
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_lu_factorization.py" [FAIL] 6.2s
1382s   Time:  6.16
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/iso_surface/tst_iso_surface.py" [FAIL] 5.9s
1382s   Time:  5.91
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/simplex.py" [FAIL] 5.8s
1382s   Time:  5.82
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/differential_evolution.py" [FAIL] 5.8s
1382s   Time:  5.76
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/direct_search_simulated_annealing.py" [FAIL] 5.8s
1382s   Time:  5.78
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/random/tests/tst_random.py" [FAIL] 6.3s
1382s   Time:  6.27
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/tst_normal_equations.py" [FAIL] 6.4s
1382s   Time:  6.38
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_basic.py" [FAIL] 3.0s
1382s   Time:  3.02
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_booth.py" [FAIL] 3.1s
1382s   Time:  3.09
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_twisted.py" [FAIL] 4.5s
1382s   Time:  4.54
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/absolute_structure/tests/tst_absolute_structure.py" --fix_random_seeds [FAIL] 5.9s
1382s   Time:  5.95
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/ab_initio/tests/tst_ab_initio_ext.py" [FAIL] 6.3s
1382s   Time:  6.26
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/ab_initio/tests/tst_charge_flipping.py" --fix_seed --on=E "hall: P 1" "hall: P 3" "hall: -P 2ybc" [FAIL] 6.3s
1382s   Time:  6.27
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/masks/tests/tst_masks.py" [FAIL] 6.6s
1382s   Time:  6.62
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/structure_factors/direct/tests/tst_standard_xray.py" [FAIL] 7.5s
1382s   Time:  7.45
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_weighting_schemes.py" --fix_random_seeds [FAIL] 7.6s
1382s   Time:  7.64
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_lbfgs.py" [FAIL] 7.3s
1382s   Time:  7.28
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_occupancies.py" [FAIL] 7.3s
1382s   Time:  7.29
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_same_group.py" [FAIL] 7.1s
1382s   Time:  7.12
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_reparametrisation.py" [FAIL] 7.0s
1382s   Time:  7.00
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=naive [FAIL] 7.0s
1382s   Time:  7.02
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_disorder.py" [FAIL] 7.1s
1382s   Time:  7.14
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=levenberg-marquardt [FAIL] 3.7s
1382s   Time:  3.66
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_direction.py" [FAIL] 4.1s
1382s   Time:  4.10
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_rigid.py" [FAIL] 7.8s
1382s   Time:  7.84
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_adp_restraints.py" [FAIL] 7.2s
1382s   Time:  7.21
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_manager.py" [FAIL] 7.0s
1382s   Time:  7.02
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_restraints.py" --verbose --scatterers=5 --resolution=0.2 [FAIL] 7.3s
1382s   Time:  7.29
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_refine.py" [FAIL] 7.7s
1382s   Time:  7.67
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py" [FAIL] 11.3s
1382s   Time: 11.34
1382s   Return code: 1
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/smtbx/tests/tst_utils.py" [FAIL] 8.2s
1382s   Time:  8.19
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/rstbx/dps_core/tst_iotbx_converter.py" [FAIL] 7.1s
1382s   Time:  7.14
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/fastbragg/tst_bragg_minimal.py" [FAIL] 6.4s
1382s   Time:  6.35
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python "/usr/lib/python3/dist-packages/rstbx/sublattice_support/tst_sublattice.py" [FAIL] 6.9s
1382s   Time:  6.94
1382s   Return code: 139
1382s   OKs: 0
1382s libtbx.python -c "from rstbx.run_tests import run; run()" [FAIL] 5.0s
1382s   Time:  4.98
1382s   Return code: 139
1382s   OKs: 0
1382s 
1382s Please verify these tests manually.
1382s 
1382s Summary:
1382s   Tests run                    : 546
1382s   Failures                     : 284
1382s   Warnings (possible failures) : 0
1382s   Known Failures (  4)         : 4
1382s   Known Unstable (  3)         : 2
1382s   Stderr output (discouraged)  : 291
1382s 
1382s See run_tests_parallel_zlog for full output.
1382s 
1382s 
1382s ********************************************************************************
1382s ERROR: 284 TEST FAILURES.  PLEASE FIX BEFORE COMMITTING CODE.
1382s ********************************************************************************
1382s 
1382s     Segmentation fault (core dumped)
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1382s     Segmentation fault (core dumped)
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1382s   Standard error:
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1382s   Standard error:
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1382s   Standard error:
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1382s   Standard error:
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1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
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1382s   Standard error:
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1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
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1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Traceback (most recent call last):
1382s       File "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py", line 37, in <module>
1382s         run()
1382s         ~~~^^
1382s       File "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py", line 27, in run
1382s         run_buf.raise_if_errors()
1382s         ~~~~~~~~~~~~~~~~~~~~~~~^^
1382s       File "/usr/lib/python3/dist-packages/libtbx/easy_run.py", line 46, in raise_if_errors
1382s         raise Error(msg)
1382s     RuntimeError: child process stderr output:
1382s       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'
1382s       Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s   Standard error:
1382s     Segmentation fault (core dumped)
1382s autopkgtest [11:07:11]: test cctbx: -----------------------]
1383s cctbx                FAIL non-zero exit status 1
1383s autopkgtest [11:07:12]: test cctbx:  - - - - - - - - - - results - - - - - - - - - -
1383s autopkgtest [11:07:12]: test dxtbx: preparing testbed
1478s autopkgtest [11:08:47]: testbed dpkg architecture: arm64
1478s autopkgtest [11:08:47]: testbed apt version: 2.9.32ubuntu1
1478s autopkgtest [11:08:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup
1479s autopkgtest [11:08:48]: testbed release detected to be: plucky
1479s autopkgtest [11:08:48]: updating testbed package index (apt update)
1480s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB]
1480s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
1480s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
1480s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
1480s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [11.5 kB]
1480s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [43.9 kB]
1480s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [396 kB]
1480s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [54.8 kB]
1480s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [340 kB]
1480s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [3244 B]
1481s Fetched 960 kB in 1s (1191 kB/s)
1481s Reading package lists...
1482s Reading package lists...
1482s Building dependency tree...
1482s Reading state information...
1483s Calculating upgrade...
1483s Calculating upgrade...
1483s The following packages will be upgraded:
1483s   gir1.2-glib-2.0 htop libglib2.0-0t64 libglib2.0-data
1483s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1483s Need to get 1982 kB of archives.
1483s After this operation, 0 B of additional disk space will be used.
1483s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 gir1.2-glib-2.0 arm64 2.84.0-1 [185 kB]
1484s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libglib2.0-0t64 arm64 2.84.0-1 [1571 kB]
1484s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libglib2.0-data all 2.84.0-1 [53.0 kB]
1484s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 htop arm64 3.4.0-2 [173 kB]
1484s Fetched 1982 kB in 1s (3240 kB/s)
1485s (Reading database ... 
(Reading database ... 5%
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(Reading database ... 100%
(Reading database ... 117763 files and directories currently installed.)
1485s Preparing to unpack .../gir1.2-glib-2.0_2.84.0-1_arm64.deb ...
1485s Unpacking gir1.2-glib-2.0:arm64 (2.84.0-1) over (2.83.5-1) ...
1485s Preparing to unpack .../libglib2.0-0t64_2.84.0-1_arm64.deb ...
1485s Unpacking libglib2.0-0t64:arm64 (2.84.0-1) over (2.83.5-1) ...
1485s Preparing to unpack .../libglib2.0-data_2.84.0-1_all.deb ...
1485s Unpacking libglib2.0-data (2.84.0-1) over (2.83.5-1) ...
1485s Preparing to unpack .../htop_3.4.0-2_arm64.deb ...
1485s Unpacking htop (3.4.0-2) over (3.4.0-1) ...
1485s Setting up htop (3.4.0-2) ...
1485s Setting up libglib2.0-0t64:arm64 (2.84.0-1) ...
1485s No schema files found: doing nothing.
1485s Setting up libglib2.0-data (2.84.0-1) ...
1485s Setting up gir1.2-glib-2.0:arm64 (2.84.0-1) ...
1485s Processing triggers for man-db (2.13.0-1) ...
1486s Processing triggers for libc-bin (2.41-1ubuntu1) ...
1486s Reading package lists...
1486s Building dependency tree...
1486s Reading state information...
1486s Solving dependencies...
1487s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1487s autopkgtest [11:08:56]: upgrading testbed (apt dist-upgrade and autopurge)
1487s Reading package lists...
1487s Building dependency tree...
1487s Reading state information...
1488s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
1488s Starting 2 pkgProblemResolver with broken count: 0
1488s Done
1489s Entering ResolveByKeep
1489s 
1489s Calculating upgrade...
1489s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1490s Reading package lists...
1490s Building dependency tree...
1490s Reading state information...
1490s Starting pkgProblemResolver with broken count: 0
1490s Starting 2 pkgProblemResolver with broken count: 0
1490s Done
1491s Solving dependencies...
1491s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1494s Reading package lists...
1494s Building dependency tree...
1494s Reading state information...
1494s Starting pkgProblemResolver with broken count: 0
1495s Starting 2 pkgProblemResolver with broken count: 0
1495s Done
1495s The following NEW packages will be installed:
1495s   adwaita-icon-theme at-spi2-common bitshuffle blt dconf-gsettings-backend
1495s   dconf-service fontconfig fontconfig-config fonts-dejavu-core
1495s   fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lyx
1495s   gtk-update-icon-cache hicolor-icon-theme libaec0 libamd-comgr2 libamdhip64-5
1495s   libann-cctbx-dev libann-cctbx0 libantlr3c-3.4-0 libasan8
1495s   libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 libavahi-client3
1495s   libavahi-common-data libavahi-common3 libblas3 libboost-numpy1.83.0
1495s   libboost-python-dev libboost-python1.83-dev libboost-python1.83.0
1495s   libboost-thread1.83.0 libboost-timer1.83.0 libboost1.83-dev
1495s   libcairo-gobject2 libcairo2 libcbf1t64 libccp4-data libccp4-dev libccp4c0t64
1495s   libccp4f0t64 libcctbx-dev libcctbx0 libcolord2 libcups2t64 libdatrie1
1495s   libdconf1 libdeflate0 libdouble-conversion3 libegl-mesa0 libegl1 libepoxy0
1495s   libevent-pthreads-2.1-7t64 libexpat1-dev libfabric1 libfontconfig1 libgbm1
1495s   libgcc-14-dev libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5
1495s   libgl1 libgl1-mesa-dri libglew2.2 libglu1-mesa libglvnd0 libglx-mesa0
1495s   libglx0 libgomp1 libgraphite2-3 libgtk-3-0t64 libgtk-3-common libharfbuzz0b
1495s   libhdf5-310 libhdf5-hl-310 libhdf5-openmpi-310 libhsa-runtime64-1 libhsakmt1
1495s   libhwasan0 libhwloc-plugins libhwloc15 libibmad5 libibumad3 libice6
1495s   libimagequant0 libinput-bin libinput10 libitm1 libjbig0 libjpeg-turbo8
1496s   libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore
1496s   liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libllvm17t64 liblsan0 liblzf1
1496s   libmd4c0 libmmdb2-0 libmtdev1t64 libmunge2 libnetcdf22 libnotify4 libopengl0
1496s   libopenjp2-7 libopenmpi40 libpango-1.0-0 libpangocairo-1.0-0
1496s   libpangoft2-1.0-0 libpciaccess0 libpcre2-16-0 libpcre2-32-0 libpixman-1-0
1496s   libpmix2t64 libpython3-dev libpython3.13-dev libqhull-r8.0 libqt5core5t64
1496s   libqt5dbus5t64 libqt5designer5 libqt5gui5t64 libqt5help5 libqt5network5t64
1496s   libqt5opengl5t64 libqt5printsupport5t64 libqt5sql5t64 libqt5test5t64
1496s   libqt5widgets5t64 libqt5xml5t64 libraqm0 librdmacm1t64 libsharpyuv0 libsm6
1496s   libssm2 libstdc++-14-dev libsz2 libtcl8.6 libthai-data libthai0 libtiff6
1496s   libtk8.6 libtsan2 libubsan1 libucx0 libvulkan1 libwacom-common libwacom9
1496s   libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0
1496s   libwebp7 libwebpdemux2 libwebpmux3 libwxbase3.2-1t64 libwxgtk-gl3.2-1t64
1496s   libwxgtk3.2-1t64 libx11-xcb1 libxcb-dri3-0 libxcb-glx0 libxcb-icccm4
1496s   libxcb-image0 libxcb-keysyms1 libxcb-present0 libxcb-randr0
1496s   libxcb-render-util0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1
1496s   libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1
1496s   libxcomposite1 libxcursor1 libxdamage1 libxfixes3 libxft2 libxi6
1496s   libxinerama1 libxkbcommon-x11-0 libxnvctrl0 libxrandr2 libxrender1
1496s   libxshmfence1 libxslt1.1 libxss1 libxtst6 libxxf86vm1 mesa-libgallium
1496s   ocl-icd-libopencl1 pymol-data python-matplotlib-data python3-all
1496s   python3-brotli python3-cctbx python3-contourpy python3-cycler
1496s   python3-dateutil python3-decorator python3-dev python3-dials-data
1496s   python3-flexcache python3-flexparser python3-fonttools python3-fs
1496s   python3-h5py python3-h5py-serial python3-hdf5plugin
1496s   python3-importlib-resources python3-iniconfig python3-kiwisolver
1496s   python3-legacy-cgi python3-lxml python3-lz4 python3-matplotlib
1496s   python3-mpmath python3-mrcfile python3-natsort python3-numpy
1496s   python3-numpy-dev python3-nxmx python3-opengl python3-ordered-set
1496s   python3-packaging python3-pil python3-pil.imagetk python3-pint
1496s   python3-platformdirs python3-pluggy python3-procrunner python3-pycbf
1496s   python3-pymol python3-pyqt5 python3-pyqt5.qtopengl python3-pyqt5.sip
1496s   python3-pytest python3-pytest-datadir python3-pytest-mock
1496s   python3-pytest-regressions python3-scipy python3-six python3-sympy
1496s   python3-tk python3-tqdm python3-ufolib2 python3-wxgtk4.0 python3.12-tk
1496s   python3.13-dev python3.13-tk sphinx-rtd-theme-common tk8.6-blt2.5
1496s   unicode-data x11-common zlib1g-dev
1496s 0 upgraded, 264 newly installed, 0 to remove and 0 not upgraded.
1496s Need to get 255 MB of archives.
1496s After this operation, 1274 MB of additional disk space will be used.
1496s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-lato all 2.015-1 [2781 kB]
1496s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-4 [146 kB]
1496s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB]
1496s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB]
1496s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB]
1496s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:2.2.3+ds-4 [3982 kB]
1496s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [8004 B]
1496s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB]
1496s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
1496s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB]
1496s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB]
1496s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB]
1496s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB]
1496s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB]
1496s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB]
1496s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-2 [147 kB]
1496s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 gtk-update-icon-cache arm64 4.17.5+ds-3ubuntu1 [52.9 kB]
1497s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 hicolor-icon-theme all 0.18-2 [13.3 kB]
1497s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 adwaita-icon-theme all 48~beta-3 [578 kB]
1497s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 at-spi2-common all 2.55.90-1 [9072 B]
1497s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB]
1497s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B]
1497s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-310 arm64 1.14.5+repack-3 [1331 kB]
1497s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [59.8 kB]
1497s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B]
1497s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.13.0-1 [1126 kB]
1497s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.13.0-1 [7978 B]
1497s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB]
1497s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10 [7922 B]
1497s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 librdmacm1t64 arm64 55.0-1ubuntu1 [71.5 kB]
1497s Get:31 http://ftpmaster.internal/ubuntu plucky/universe arm64 libfabric1 arm64 1.17.0-3.1 [542 kB]
1497s Get:32 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhwloc15 arm64 2.12.0-1 [162 kB]
1497s Get:33 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmunge2 arm64 0.5.16-1 [15.2 kB]
1497s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libpciaccess0 arm64 0.17-3build1 [18.9 kB]
1497s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu4 [12.4 kB]
1497s Get:36 http://ftpmaster.internal/ubuntu plucky/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1build1 [37.6 kB]
1497s Get:37 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhwloc-plugins arm64 2.12.0-1 [15.9 kB]
1497s Get:38 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpmix2t64 arm64 5.0.6-5 [666 kB]
1497s Get:39 http://ftpmaster.internal/ubuntu plucky/universe arm64 libllvm17t64 arm64 1:17.0.6-21 [24.9 MB]
1498s Get:40 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3build2 [14.1 MB]
1498s Get:41 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhsakmt1 arm64 5.7.0-1build1 [63.6 kB]
1498s Get:42 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhsa-runtime64-1 arm64 5.7.1-2build1 [286 kB]
1498s Get:43 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamdhip64-5 arm64 5.7.1-5 [9704 kB]
1499s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libibumad3 arm64 55.0-1ubuntu1 [29.8 kB]
1499s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libibmad5 arm64 55.0-1ubuntu1 [43.3 kB]
1499s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 libucx0 arm64 1.18.1+ds-2 [1161 kB]
1499s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenmpi40 arm64 5.0.7-1 [2419 kB]
1499s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-openmpi-310 arm64 1.14.5+repack-3 [1388 kB]
1499s Get:49 http://ftpmaster.internal/ubuntu plucky/universe arm64 bitshuffle arm64 0.5.2-1build2 [157 kB]
1499s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB]
1499s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
1499s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
1499s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB]
1499s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB]
1499s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB]
1499s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB]
1499s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
1499s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B]
1499s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB]
1499s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-8 [624 kB]
1499s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-8 [4824 B]
1499s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 libdconf1 arm64 0.40.0-5 [40.0 kB]
1499s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 dconf-service arm64 0.40.0-5 [27.1 kB]
1499s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 dconf-gsettings-backend arm64 0.40.0-5 [22.3 kB]
1499s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB]
1499s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB]
1499s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.3-1 [171 kB]
1499s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 libann-cctbx0 arm64 1.1.2+doc-9build1 [32.8 kB]
1499s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 libann-cctbx-dev arm64 1.1.2+doc-9build1 [45.1 kB]
1499s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 libantlr3c-3.4-0 arm64 3.4+dfsg-4build2 [45.7 kB]
1499s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250222-0ubuntu1 [2924 kB]
1499s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libatk1.0-0t64 arm64 2.55.90-1 [55.3 kB]
1499s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libxi6 arm64 2:1.8.2-1 [32.4 kB]
1499s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libatspi2.0-0t64 arm64 2.55.90-1 [84.4 kB]
1499s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libatk-bridge2.0-0t64 arm64 2.55.90-1 [66.7 kB]
1499s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-common-data arm64 0.8-16ubuntu1 [30.9 kB]
1499s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-common3 arm64 0.8-16ubuntu1 [22.9 kB]
1499s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-client3 arm64 0.8-16ubuntu1 [26.9 kB]
1499s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-python1.83.0 arm64 1.83.0-4.1ubuntu1 [323 kB]
1499s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 libboost-numpy1.83.0 arm64 1.83.0-4.1ubuntu1 [242 kB]
1499s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250222-0ubuntu1 [28.0 kB]
1499s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250222-0ubuntu1 [1319 kB]
1499s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250222-0ubuntu1 [2694 kB]
1499s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250222-0ubuntu1 [1178 kB]
1499s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250222-0ubuntu1 [1642 kB]
1499s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu3 [2593 kB]
1499s Get:87 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu3 [2499 kB]
1500s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost1.83-dev arm64 1.83.0-4.1ubuntu1 [10.7 MB]
1500s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 libexpat1-dev arm64 2.6.4-1 [129 kB]
1500s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB]
1500s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-dev arm64 3.13.2-1 [5399 kB]
1500s Get:92 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-dev arm64 3.13.2-2 [10.7 kB]
1500s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-dev arm64 3.13.2-1 [508 kB]
1500s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
1500s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
1500s Get:96 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 8.1.3-4 [30.9 kB]
1500s Get:97 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dev arm64 3.13.2-2 [26.7 kB]
1500s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 libboost-python1.83-dev arm64 1.83.0-4.1ubuntu1 [336 kB]
1500s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 libboost-python-dev arm64 1.83.0.2ubuntu1 [4516 B]
1500s Get:100 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-thread1.83.0 arm64 1.83.0-4.1ubuntu1 [276 kB]
1500s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 libboost-timer1.83.0 arm64 1.83.0-4.1ubuntu1 [242 kB]
1500s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB]
1501s Get:103 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB]
1501s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B]
1501s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB]
1501s Get:106 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo-gobject2 arm64 1.18.2-2 [127 kB]
1501s Get:107 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcbf1t64 arm64 0.9.7+dfsg1-5build1 [356 kB]
1501s Get:108 http://ftpmaster.internal/ubuntu plucky/universe arm64 libccp4-data all 8.0.0-4 [65.2 kB]
1501s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 libccp4c0t64 arm64 8.0.0-4 [93.5 kB]
1501s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmmdb2-0 arm64 2.0.22-1 [347 kB]
1501s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 libccp4f0t64 arm64 8.0.0-4 [202 kB]
1501s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 libccp4-dev arm64 8.0.0-4 [42.3 kB]
1501s Get:113 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 libcctbx0 arm64 2024.10+ds2+~3.22.1+ds1-4build2 [2016 kB]
1501s Get:114 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 libcctbx-dev arm64 2024.10+ds2+~3.22.1+ds1-4build2 [1192 kB]
1501s Get:115 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB]
1501s Get:116 http://ftpmaster.internal/ubuntu plucky/main arm64 libcolord2 arm64 1.4.7-3 [151 kB]
1501s Get:117 http://ftpmaster.internal/ubuntu plucky/main arm64 libcups2t64 arm64 2.4.11-0ubuntu2 [274 kB]
1501s Get:118 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB]
1501s Get:119 http://ftpmaster.internal/ubuntu plucky/universe arm64 libdouble-conversion3 arm64 3.3.1-1 [38.8 kB]
1501s Get:120 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-server0 arm64 1.23.1-3 [36.1 kB]
1501s Get:121 http://ftpmaster.internal/ubuntu plucky/main arm64 libx11-xcb1 arm64 2:1.8.10-2 [8020 B]
1501s Get:122 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-dri3-0 arm64 1.17.0-2 [7606 B]
1501s Get:123 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-present0 arm64 1.17.0-2 [6224 B]
1501s Get:124 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-randr0 arm64 1.17.0-2 [18.5 kB]
1501s Get:125 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-sync1 arm64 1.17.0-2 [9688 B]
1501s Get:126 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-xfixes0 arm64 1.17.0-2 [10.6 kB]
1501s Get:127 http://ftpmaster.internal/ubuntu plucky/main arm64 libxshmfence1 arm64 1.3-1build5 [4938 B]
1501s Get:128 http://ftpmaster.internal/ubuntu plucky/main arm64 mesa-libgallium arm64 25.0.1-2ubuntu1 [9450 kB]
1501s Get:129 http://ftpmaster.internal/ubuntu plucky/main arm64 libgbm1 arm64 25.0.1-2ubuntu1 [33.7 kB]
1501s Get:130 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-client0 arm64 1.23.1-3 [27.0 kB]
1501s Get:131 http://ftpmaster.internal/ubuntu plucky/main arm64 libegl-mesa0 arm64 25.0.1-2ubuntu1 [122 kB]
1501s Get:132 http://ftpmaster.internal/ubuntu plucky/main arm64 libepoxy0 arm64 1.5.10-2 [236 kB]
1501s Get:133 http://ftpmaster.internal/ubuntu plucky/main arm64 libvulkan1 arm64 1.4.304.0-1 [158 kB]
1501s Get:134 http://ftpmaster.internal/ubuntu plucky/main arm64 libgl1-mesa-dri arm64 25.0.1-2ubuntu1 [34.5 kB]
1501s Get:135 http://ftpmaster.internal/ubuntu plucky/main arm64 libglvnd0 arm64 1.7.0-1build1 [60.6 kB]
1501s Get:136 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-glx0 arm64 1.17.0-2 [25.5 kB]
1501s Get:137 http://ftpmaster.internal/ubuntu plucky/main arm64 libxxf86vm1 arm64 1:1.1.4-1build4 [9130 B]
1501s Get:138 http://ftpmaster.internal/ubuntu plucky/main arm64 libglx-mesa0 arm64 25.0.1-2ubuntu1 [151 kB]
1501s Get:139 http://ftpmaster.internal/ubuntu plucky/main arm64 libglx0 arm64 1.7.0-1build1 [33.2 kB]
1502s Get:140 http://ftpmaster.internal/ubuntu plucky/main arm64 libgl1 arm64 1.7.0-1build1 [106 kB]
1502s Get:141 http://ftpmaster.internal/ubuntu plucky/universe arm64 libglew2.2 arm64 2.2.0-4build1 [191 kB]
1502s Get:142 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB]
1502s Get:143 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB]
1502s Get:144 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB]
1502s Get:145 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB]
1502s Get:146 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.1-1 [238 kB]
1502s Get:147 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.1-1 [49.6 kB]
1502s Get:148 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.1-1 [27.6 kB]
1502s Get:149 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-cursor0 arm64 1.23.1-3 [10.8 kB]
1502s Get:150 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-egl1 arm64 1.23.1-3 [6180 B]
1502s Get:151 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcomposite1 arm64 1:0.4.6-1 [6626 B]
1502s Get:152 http://ftpmaster.internal/ubuntu plucky/main arm64 libxfixes3 arm64 1:6.0.0-2build1 [11.2 kB]
1502s Get:153 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcursor1 arm64 1:1.2.3-1 [22.2 kB]
1502s Get:154 http://ftpmaster.internal/ubuntu plucky/main arm64 libxdamage1 arm64 1:1.1.6-1build1 [6236 B]
1502s Get:155 http://ftpmaster.internal/ubuntu plucky/main arm64 libxinerama1 arm64 2:1.1.4-3build1 [6394 B]
1502s Get:156 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrandr2 arm64 2:1.5.4-1 [19.6 kB]
1502s Get:157 http://ftpmaster.internal/ubuntu plucky/main arm64 libgtk-3-common all 3.24.48-3ubuntu1 [1424 kB]
1502s Get:158 http://ftpmaster.internal/ubuntu plucky/main arm64 libgtk-3-0t64 arm64 3.24.48-3ubuntu1 [2916 kB]
1502s Get:159 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB]
1502s Get:160 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB]
1502s Get:161 http://ftpmaster.internal/ubuntu plucky/main arm64 libwacom-common all 2.14.0-1 [103 kB]
1502s Get:162 http://ftpmaster.internal/ubuntu plucky/main arm64 libwacom9 arm64 2.14.0-1 [26.7 kB]
1502s Get:163 http://ftpmaster.internal/ubuntu plucky/main arm64 libinput-bin arm64 1.27.1-1 [23.5 kB]
1502s Get:164 http://ftpmaster.internal/ubuntu plucky/main arm64 libmtdev1t64 arm64 1.1.7-1 [14.6 kB]
1502s Get:165 http://ftpmaster.internal/ubuntu plucky/main arm64 libinput10 arm64 1.27.1-1 [136 kB]
1502s Get:166 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
1502s Get:167 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB]
1502s Get:168 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmd4c0 arm64 0.5.2-2 [42.4 kB]
1502s Get:169 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnetcdf22 arm64 1:4.9.3-1 [504 kB]
1502s Get:170 http://ftpmaster.internal/ubuntu plucky/main arm64 libnotify4 arm64 0.8.4-1 [26.5 kB]
1502s Get:171 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-16-0 arm64 10.45-1 [222 kB]
1502s Get:172 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-32-0 arm64 10.45-1 [210 kB]
1502s Get:173 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB]
1502s Get:174 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5core5t64 arm64 5.15.15+dfsg-4ubuntu1 [1999 kB]
1502s Get:175 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5dbus5t64 arm64 5.15.15+dfsg-4ubuntu1 [222 kB]
1502s Get:176 http://ftpmaster.internal/ubuntu plucky/main arm64 libegl1 arm64 1.7.0-1build1 [29.5 kB]
1502s Get:177 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5network5t64 arm64 5.15.15+dfsg-4ubuntu1 [735 kB]
1502s Get:178 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB]
1502s Get:179 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-icccm4 arm64 0.4.2-1 [10.9 kB]
1502s Get:180 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-util1 arm64 0.4.1-1 [10.9 kB]
1502s Get:181 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-image0 arm64 0.4.0-2build1 [10.8 kB]
1502s Get:182 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-keysyms1 arm64 0.4.1-1 [8802 B]
1502s Get:183 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render-util0 arm64 0.3.10-1 [10.5 kB]
1502s Get:184 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shape0 arm64 1.17.0-2 [6246 B]
1502s Get:185 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-xinerama0 arm64 1.17.0-2 [5590 B]
1502s Get:186 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-xinput0 arm64 1.17.0-2 [34.2 kB]
1502s Get:187 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-xkb1 arm64 1.17.0-2 [32.5 kB]
1502s Get:188 http://ftpmaster.internal/ubuntu plucky/main arm64 libxkbcommon-x11-0 arm64 1.7.0-2 [13.8 kB]
1502s Get:189 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5gui5t64 arm64 5.15.15+dfsg-4ubuntu1 [3680 kB]
1502s Get:190 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5widgets5t64 arm64 5.15.15+dfsg-4ubuntu1 [2568 kB]
1502s Get:191 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5xml5t64 arm64 5.15.15+dfsg-4ubuntu1 [124 kB]
1502s Get:192 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5designer5 arm64 5.15.15-6build1 [2840 kB]
1502s Get:193 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5sql5t64 arm64 5.15.15+dfsg-4ubuntu1 [123 kB]
1502s Get:194 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5help5 arm64 5.15.15-6build1 [165 kB]
1502s Get:195 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5opengl5t64 arm64 5.15.15+dfsg-4ubuntu1 [149 kB]
1502s Get:196 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5printsupport5t64 arm64 5.15.15+dfsg-4ubuntu1 [209 kB]
1502s Get:197 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqt5test5t64 arm64 5.15.15+dfsg-4ubuntu1 [144 kB]
1502s Get:198 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB]
1502s Get:199 http://ftpmaster.internal/ubuntu plucky/universe arm64 libssm2 arm64 1.4.0-2build1 [83.8 kB]
1502s Get:200 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB]
1502s Get:201 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB]
1503s Get:202 http://ftpmaster.internal/ubuntu plucky/universe arm64 libwxbase3.2-1t64 arm64 3.2.6+dfsg-2ubuntu1 [870 kB]
1503s Get:203 http://ftpmaster.internal/ubuntu plucky/main arm64 libxtst6 arm64 2:1.2.5-1 [13.2 kB]
1503s Get:204 http://ftpmaster.internal/ubuntu plucky/universe arm64 libwxgtk3.2-1t64 arm64 3.2.6+dfsg-2ubuntu1 [4426 kB]
1504s Get:205 http://ftpmaster.internal/ubuntu plucky/universe arm64 libwxgtk-gl3.2-1t64 arm64 3.2.6+dfsg-2ubuntu1 [52.8 kB]
1504s Get:206 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu2 [168 kB]
1504s Get:207 http://ftpmaster.internal/ubuntu plucky/universe arm64 pymol-data all 3.0.0+dfsg-3build2 [1394 kB]
1504s Get:208 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-7build1 [2934 kB]
1505s Get:209 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.13.2-2 [886 B]
1505s Get:210 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build4 [342 kB]
1505s Get:211 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-legacy-cgi all 2.6.2-1 [16.6 kB]
1505s Get:212 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pycbf arm64 0.9.7+dfsg1-5build1 [152 kB]
1505s Get:213 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-hdf5plugin all 5.0.0-1 [23.1 kB]
1505s Get:214 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB]
1505s Get:215 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu3 [182 kB]
1505s Get:216 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 11.1.0-5build1 [463 kB]
1505s Get:217 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.9-1 [115 kB]
1505s Get:218 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.2-1 [106 kB]
1505s Get:219 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.13.1-1 [9770 B]
1505s Get:220 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 11.1.0-5build1 [9892 B]
1505s Get:221 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.1-1build1 [182 kB]
1505s Get:222 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B]
1505s Get:223 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB]
1505s Get:224 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-7 [90.8 kB]
1505s Get:225 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.1-1build1 [1258 kB]
1505s Get:226 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.4.0+dfsg-1build1 [27.1 kB]
1505s Get:227 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB]
1505s Get:228 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu2 [16.7 MB]
1509s Get:229 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB]
1509s Get:230 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-5 [4229 kB]
1510s Get:231 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB]
1510s Get:232 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB]
1511s Get:233 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.55.3-2build1 [1466 kB]
1512s Get:234 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-importlib-resources all 6.5.2-1 [24.5 kB]
1512s Get:235 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-3build1 [50.7 kB]
1512s Get:236 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB]
1512s Get:237 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-7build1 [17.3 MB]
1516s Get:238 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB]
1516s Get:239 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mrcfile all 1.5.4-2 [116 kB]
1517s Get:240 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-natsort all 8.0.2-2 [33.8 kB]
1517s Get:241 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-flexcache all 0.3-2 [13.4 kB]
1517s Get:242 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-flexparser all 0.4-1 [43.8 kB]
1517s Get:243 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pint all 0.24.4-1 [203 kB]
1517s Get:244 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-nxmx all 0.0.4-1 [16.4 kB]
1517s Get:245 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ordered-set all 4.1.0-1 [9778 B]
1517s Get:246 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-procrunner all 2.3.3-2 [12.0 kB]
1517s Get:247 http://ftpmaster.internal/ubuntu plucky/main arm64 libopengl0 arm64 1.7.0-1build1 [35.1 kB]
1517s Get:248 http://ftpmaster.internal/ubuntu plucky/main arm64 libglu1-mesa arm64 9.0.2-1.1build1 [139 kB]
1517s Get:249 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-opengl all 3.1.7+dfsg-1 [612 kB]
1517s Get:250 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyqt5.sip arm64 12.17.0-1build1 [67.6 kB]
1517s Get:251 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyqt5 arm64 5.15.11+dfsg-2 [2580 kB]
1518s Get:252 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyqt5.qtopengl arm64 5.15.11+dfsg-2 [119 kB]
1518s Get:253 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pymol arm64 3.0.0+dfsg-3build2 [3961 kB]
1519s Get:254 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.17.0-1 [13.2 kB]
1519s Get:255 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tqdm all 4.67.1-2 [92.5 kB]
1519s Get:256 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-wxgtk4.0 arm64 4.2.2+dfsg-3build1 [7689 kB]
1521s Get:257 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-cctbx arm64 2024.10+ds2+~3.22.1+ds1-4build2 [28.3 MB]
1530s Get:258 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B]
1530s Get:259 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB]
1530s Get:260 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.4-1 [252 kB]
1530s Get:261 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-dials-data all 2.4.0-2 [110 kB]
1530s Get:262 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-datadir all 1.4.1+ds-1 [5386 B]
1530s Get:263 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-mock all 3.14.0-2 [11.7 kB]
1530s Get:264 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-regressions all 2.5.0+ds-2 [39.2 kB]
1531s Fetched 255 MB in 35s (7342 kB/s)
1531s Selecting previously unselected package fonts-lato.
1531s (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 ... 117763 files and directories currently installed.)
1531s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ...
1531s Unpacking fonts-lato (2.015-1) ...
1531s Selecting previously unselected package python3-numpy-dev:arm64.
1531s Preparing to unpack .../001-python3-numpy-dev_1%3a2.2.3+ds-4_arm64.deb ...
1531s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-4) ...
1531s Selecting previously unselected package libblas3:arm64.
1531s Preparing to unpack .../002-libblas3_3.12.1-2_arm64.deb ...
1531s Unpacking libblas3:arm64 (3.12.1-2) ...
1531s Selecting previously unselected package libgfortran5:arm64.
1531s Preparing to unpack .../003-libgfortran5_15-20250222-0ubuntu1_arm64.deb ...
1531s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ...
1531s Selecting previously unselected package liblapack3:arm64.
1531s Preparing to unpack .../004-liblapack3_3.12.1-2_arm64.deb ...
1531s Unpacking liblapack3:arm64 (3.12.1-2) ...
1531s Selecting previously unselected package python3-numpy.
1531s Preparing to unpack .../005-python3-numpy_1%3a2.2.3+ds-4_arm64.deb ...
1531s Unpacking python3-numpy (1:2.2.3+ds-4) ...
1532s Selecting previously unselected package libgdk-pixbuf2.0-common.
1532s Preparing to unpack .../006-libgdk-pixbuf2.0-common_2.42.12+dfsg-2_all.deb ...
1532s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ...
1532s Selecting previously unselected package libjpeg-turbo8:arm64.
1532s Preparing to unpack .../007-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ...
1532s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ...
1532s Selecting previously unselected package libjpeg8:arm64.
1532s Preparing to unpack .../008-libjpeg8_8c-2ubuntu11_arm64.deb ...
1532s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
1532s Selecting previously unselected package libdeflate0:arm64.
1532s Preparing to unpack .../009-libdeflate0_1.23-1_arm64.deb ...
1532s Unpacking libdeflate0:arm64 (1.23-1) ...
1532s Selecting previously unselected package libjbig0:arm64.
1532s Preparing to unpack .../010-libjbig0_2.1-6.1ubuntu2_arm64.deb ...
1532s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ...
1532s Selecting previously unselected package liblerc4:arm64.
1532s Preparing to unpack .../011-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ...
1532s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ...
1532s Selecting previously unselected package libsharpyuv0:arm64.
1532s Preparing to unpack .../012-libsharpyuv0_1.5.0-0.1_arm64.deb ...
1532s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ...
1532s Selecting previously unselected package libwebp7:arm64.
1532s Preparing to unpack .../013-libwebp7_1.5.0-0.1_arm64.deb ...
1532s Unpacking libwebp7:arm64 (1.5.0-0.1) ...
1532s Selecting previously unselected package libtiff6:arm64.
1532s Preparing to unpack .../014-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ...
1532s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ...
1532s Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64.
1532s Preparing to unpack .../015-libgdk-pixbuf-2.0-0_2.42.12+dfsg-2_arm64.deb ...
1532s Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-2) ...
1532s Selecting previously unselected package gtk-update-icon-cache.
1532s Preparing to unpack .../016-gtk-update-icon-cache_4.17.5+ds-3ubuntu1_arm64.deb ...
1532s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed.
1532s 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.
1532s Unpacking gtk-update-icon-cache (4.17.5+ds-3ubuntu1) ...
1532s Selecting previously unselected package hicolor-icon-theme.
1532s Preparing to unpack .../017-hicolor-icon-theme_0.18-2_all.deb ...
1532s Unpacking hicolor-icon-theme (0.18-2) ...
1532s Selecting previously unselected package adwaita-icon-theme.
1532s Preparing to unpack .../018-adwaita-icon-theme_48~beta-3_all.deb ...
1532s Unpacking adwaita-icon-theme (48~beta-3) ...
1532s Selecting previously unselected package at-spi2-common.
1532s Preparing to unpack .../019-at-spi2-common_2.55.90-1_all.deb ...
1532s Unpacking at-spi2-common (2.55.90-1) ...
1532s Selecting previously unselected package libaec0:arm64.
1532s Preparing to unpack .../020-libaec0_1.1.3-1_arm64.deb ...
1532s Unpacking libaec0:arm64 (1.1.3-1) ...
1532s Selecting previously unselected package libsz2:arm64.
1532s Preparing to unpack .../021-libsz2_1.1.3-1_arm64.deb ...
1532s Unpacking libsz2:arm64 (1.1.3-1) ...
1532s Selecting previously unselected package libhdf5-310:arm64.
1532s Preparing to unpack .../022-libhdf5-310_1.14.5+repack-3_arm64.deb ...
1532s Unpacking libhdf5-310:arm64 (1.14.5+repack-3) ...
1532s Selecting previously unselected package libhdf5-hl-310:arm64.
1532s Preparing to unpack .../023-libhdf5-hl-310_1.14.5+repack-3_arm64.deb ...
1532s Unpacking libhdf5-hl-310:arm64 (1.14.5+repack-3) ...
1532s Selecting previously unselected package liblzf1:arm64.
1532s Preparing to unpack .../024-liblzf1_3.6-4_arm64.deb ...
1532s Unpacking liblzf1:arm64 (3.6-4) ...
1532s Selecting previously unselected package python3-h5py-serial.
1532s Preparing to unpack .../025-python3-h5py-serial_3.13.0-1_arm64.deb ...
1532s Unpacking python3-h5py-serial (3.13.0-1) ...
1533s Selecting previously unselected package python3-h5py.
1533s Preparing to unpack .../026-python3-h5py_3.13.0-1_all.deb ...
1533s Unpacking python3-h5py (3.13.0-1) ...
1533s Selecting previously unselected package libgomp1:arm64.
1533s Preparing to unpack .../027-libgomp1_15-20250222-0ubuntu1_arm64.deb ...
1533s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ...
1533s Selecting previously unselected package libevent-pthreads-2.1-7t64:arm64.
1533s Preparing to unpack .../028-libevent-pthreads-2.1-7t64_2.1.12-stable-10_arm64.deb ...
1533s Unpacking libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ...
1533s Selecting previously unselected package librdmacm1t64:arm64.
1533s Preparing to unpack .../029-librdmacm1t64_55.0-1ubuntu1_arm64.deb ...
1533s Unpacking librdmacm1t64:arm64 (55.0-1ubuntu1) ...
1533s Selecting previously unselected package libfabric1:arm64.
1533s Preparing to unpack .../030-libfabric1_1.17.0-3.1_arm64.deb ...
1533s Unpacking libfabric1:arm64 (1.17.0-3.1) ...
1533s Selecting previously unselected package libhwloc15:arm64.
1533s Preparing to unpack .../031-libhwloc15_2.12.0-1_arm64.deb ...
1533s Unpacking libhwloc15:arm64 (2.12.0-1) ...
1533s Selecting previously unselected package libmunge2:arm64.
1533s Preparing to unpack .../032-libmunge2_0.5.16-1_arm64.deb ...
1533s Unpacking libmunge2:arm64 (0.5.16-1) ...
1533s Selecting previously unselected package libpciaccess0:arm64.
1533s Preparing to unpack .../033-libpciaccess0_0.17-3build1_arm64.deb ...
1533s Unpacking libpciaccess0:arm64 (0.17-3build1) ...
1533s Selecting previously unselected package libxnvctrl0:arm64.
1533s Preparing to unpack .../034-libxnvctrl0_510.47.03-0ubuntu4_arm64.deb ...
1533s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu4) ...
1533s Selecting previously unselected package ocl-icd-libopencl1:arm64.
1533s Preparing to unpack .../035-ocl-icd-libopencl1_2.3.2-1build1_arm64.deb ...
1533s Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1build1) ...
1533s Selecting previously unselected package libhwloc-plugins:arm64.
1533s Preparing to unpack .../036-libhwloc-plugins_2.12.0-1_arm64.deb ...
1533s Unpacking libhwloc-plugins:arm64 (2.12.0-1) ...
1533s Selecting previously unselected package libpmix2t64:arm64.
1533s Preparing to unpack .../037-libpmix2t64_5.0.6-5_arm64.deb ...
1533s Unpacking libpmix2t64:arm64 (5.0.6-5) ...
1533s Selecting previously unselected package libllvm17t64:arm64.
1533s Preparing to unpack .../038-libllvm17t64_1%3a17.0.6-21_arm64.deb ...
1533s Unpacking libllvm17t64:arm64 (1:17.0.6-21) ...
1534s Selecting previously unselected package libamd-comgr2:arm64.
1534s Preparing to unpack .../039-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_arm64.deb ...
1534s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ...
1534s Selecting previously unselected package libhsakmt1:arm64.
1534s Preparing to unpack .../040-libhsakmt1_5.7.0-1build1_arm64.deb ...
1534s Unpacking libhsakmt1:arm64 (5.7.0-1build1) ...
1534s Selecting previously unselected package libhsa-runtime64-1.
1534s Preparing to unpack .../041-libhsa-runtime64-1_5.7.1-2build1_arm64.deb ...
1534s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ...
1534s Selecting previously unselected package libamdhip64-5.
1534s Preparing to unpack .../042-libamdhip64-5_5.7.1-5_arm64.deb ...
1534s Unpacking libamdhip64-5 (5.7.1-5) ...
1534s Selecting previously unselected package libibumad3:arm64.
1534s Preparing to unpack .../043-libibumad3_55.0-1ubuntu1_arm64.deb ...
1534s Unpacking libibumad3:arm64 (55.0-1ubuntu1) ...
1534s Selecting previously unselected package libibmad5:arm64.
1534s Preparing to unpack .../044-libibmad5_55.0-1ubuntu1_arm64.deb ...
1534s Unpacking libibmad5:arm64 (55.0-1ubuntu1) ...
1534s Selecting previously unselected package libucx0:arm64.
1534s Preparing to unpack .../045-libucx0_1.18.1+ds-2_arm64.deb ...
1534s Unpacking libucx0:arm64 (1.18.1+ds-2) ...
1534s Selecting previously unselected package libopenmpi40:arm64.
1534s Preparing to unpack .../046-libopenmpi40_5.0.7-1_arm64.deb ...
1534s Unpacking libopenmpi40:arm64 (5.0.7-1) ...
1534s Selecting previously unselected package libhdf5-openmpi-310:arm64.
1534s Preparing to unpack .../047-libhdf5-openmpi-310_1.14.5+repack-3_arm64.deb ...
1535s Unpacking libhdf5-openmpi-310:arm64 (1.14.5+repack-3) ...
1535s Selecting previously unselected package bitshuffle.
1535s Preparing to unpack .../048-bitshuffle_0.5.2-1build2_arm64.deb ...
1535s Unpacking bitshuffle (0.5.2-1build2) ...
1535s Selecting previously unselected package libtcl8.6:arm64.
1535s Preparing to unpack .../049-libtcl8.6_8.6.16+dfsg-1_arm64.deb ...
1535s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ...
1535s Selecting previously unselected package fonts-dejavu-mono.
1535s Preparing to unpack .../050-fonts-dejavu-mono_2.37-8_all.deb ...
1535s Unpacking fonts-dejavu-mono (2.37-8) ...
1535s Selecting previously unselected package fonts-dejavu-core.
1535s Preparing to unpack .../051-fonts-dejavu-core_2.37-8_all.deb ...
1535s Unpacking fonts-dejavu-core (2.37-8) ...
1535s Selecting previously unselected package fontconfig-config.
1535s Preparing to unpack .../052-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ...
1535s Unpacking fontconfig-config (2.15.0-2ubuntu1) ...
1535s Selecting previously unselected package libfontconfig1:arm64.
1535s Preparing to unpack .../053-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ...
1535s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ...
1535s Selecting previously unselected package libxrender1:arm64.
1535s Preparing to unpack .../054-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ...
1535s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ...
1535s Selecting previously unselected package libxft2:arm64.
1535s Preparing to unpack .../055-libxft2_2.3.6-1build1_arm64.deb ...
1535s Unpacking libxft2:arm64 (2.3.6-1build1) ...
1535s Selecting previously unselected package x11-common.
1535s Preparing to unpack .../056-x11-common_1%3a7.7+23ubuntu3_all.deb ...
1535s Unpacking x11-common (1:7.7+23ubuntu3) ...
1535s Selecting previously unselected package libxss1:arm64.
1535s Preparing to unpack .../057-libxss1_1%3a1.2.3-1build3_arm64.deb ...
1535s Unpacking libxss1:arm64 (1:1.2.3-1build3) ...
1535s Selecting previously unselected package libtk8.6:arm64.
1535s Preparing to unpack .../058-libtk8.6_8.6.16-1_arm64.deb ...
1535s Unpacking libtk8.6:arm64 (8.6.16-1) ...
1535s Selecting previously unselected package tk8.6-blt2.5.
1535s Preparing to unpack .../059-tk8.6-blt2.5_2.5.3+dfsg-8_arm64.deb ...
1535s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ...
1535s Selecting previously unselected package blt.
1536s Preparing to unpack .../060-blt_2.5.3+dfsg-8_arm64.deb ...
1536s Unpacking blt (2.5.3+dfsg-8) ...
1536s Selecting previously unselected package libdconf1:arm64.
1536s Preparing to unpack .../061-libdconf1_0.40.0-5_arm64.deb ...
1536s Unpacking libdconf1:arm64 (0.40.0-5) ...
1536s Selecting previously unselected package dconf-service.
1536s Preparing to unpack .../062-dconf-service_0.40.0-5_arm64.deb ...
1536s Unpacking dconf-service (0.40.0-5) ...
1536s Selecting previously unselected package dconf-gsettings-backend:arm64.
1536s Preparing to unpack .../063-dconf-gsettings-backend_0.40.0-5_arm64.deb ...
1536s Unpacking dconf-gsettings-backend:arm64 (0.40.0-5) ...
1536s Selecting previously unselected package fontconfig.
1536s Preparing to unpack .../064-fontconfig_2.15.0-2ubuntu1_arm64.deb ...
1536s Unpacking fontconfig (2.15.0-2ubuntu1) ...
1536s Selecting previously unselected package fonts-font-awesome.
1536s Preparing to unpack .../065-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ...
1536s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
1536s Selecting previously unselected package fonts-lyx.
1536s Preparing to unpack .../066-fonts-lyx_2.4.3-1_all.deb ...
1536s Unpacking fonts-lyx (2.4.3-1) ...
1536s Selecting previously unselected package libann-cctbx0.
1536s Preparing to unpack .../067-libann-cctbx0_1.1.2+doc-9build1_arm64.deb ...
1536s Unpacking libann-cctbx0 (1.1.2+doc-9build1) ...
1536s Selecting previously unselected package libann-cctbx-dev.
1536s Preparing to unpack .../068-libann-cctbx-dev_1.1.2+doc-9build1_arm64.deb ...
1536s Unpacking libann-cctbx-dev (1.1.2+doc-9build1) ...
1536s Selecting previously unselected package libantlr3c-3.4-0:arm64.
1536s Preparing to unpack .../069-libantlr3c-3.4-0_3.4+dfsg-4build2_arm64.deb ...
1536s Unpacking libantlr3c-3.4-0:arm64 (3.4+dfsg-4build2) ...
1536s Selecting previously unselected package libasan8:arm64.
1536s Preparing to unpack .../070-libasan8_15-20250222-0ubuntu1_arm64.deb ...
1536s Unpacking libasan8:arm64 (15-20250222-0ubuntu1) ...
1536s Selecting previously unselected package libatk1.0-0t64:arm64.
1536s Preparing to unpack .../071-libatk1.0-0t64_2.55.90-1_arm64.deb ...
1536s Unpacking libatk1.0-0t64:arm64 (2.55.90-1) ...
1536s Selecting previously unselected package libxi6:arm64.
1536s Preparing to unpack .../072-libxi6_2%3a1.8.2-1_arm64.deb ...
1536s Unpacking libxi6:arm64 (2:1.8.2-1) ...
1536s Selecting previously unselected package libatspi2.0-0t64:arm64.
1536s Preparing to unpack .../073-libatspi2.0-0t64_2.55.90-1_arm64.deb ...
1536s Unpacking libatspi2.0-0t64:arm64 (2.55.90-1) ...
1536s Selecting previously unselected package libatk-bridge2.0-0t64:arm64.
1536s Preparing to unpack .../074-libatk-bridge2.0-0t64_2.55.90-1_arm64.deb ...
1536s Unpacking libatk-bridge2.0-0t64:arm64 (2.55.90-1) ...
1536s Selecting previously unselected package libavahi-common-data:arm64.
1536s Preparing to unpack .../075-libavahi-common-data_0.8-16ubuntu1_arm64.deb ...
1536s Unpacking libavahi-common-data:arm64 (0.8-16ubuntu1) ...
1536s Selecting previously unselected package libavahi-common3:arm64.
1536s Preparing to unpack .../076-libavahi-common3_0.8-16ubuntu1_arm64.deb ...
1536s Unpacking libavahi-common3:arm64 (0.8-16ubuntu1) ...
1536s Selecting previously unselected package libavahi-client3:arm64.
1536s Preparing to unpack .../077-libavahi-client3_0.8-16ubuntu1_arm64.deb ...
1536s Unpacking libavahi-client3:arm64 (0.8-16ubuntu1) ...
1536s Selecting previously unselected package libboost-python1.83.0.
1536s Preparing to unpack .../078-libboost-python1.83.0_1.83.0-4.1ubuntu1_arm64.deb ...
1536s Unpacking libboost-python1.83.0 (1.83.0-4.1ubuntu1) ...
1537s Selecting previously unselected package libboost-numpy1.83.0.
1537s Preparing to unpack .../079-libboost-numpy1.83.0_1.83.0-4.1ubuntu1_arm64.deb ...
1537s Unpacking libboost-numpy1.83.0 (1.83.0-4.1ubuntu1) ...
1537s Selecting previously unselected package libitm1:arm64.
1537s Preparing to unpack .../080-libitm1_15-20250222-0ubuntu1_arm64.deb ...
1537s Unpacking libitm1:arm64 (15-20250222-0ubuntu1) ...
1537s Selecting previously unselected package liblsan0:arm64.
1537s Preparing to unpack .../081-liblsan0_15-20250222-0ubuntu1_arm64.deb ...
1537s Unpacking liblsan0:arm64 (15-20250222-0ubuntu1) ...
1537s Selecting previously unselected package libtsan2:arm64.
1537s Preparing to unpack .../082-libtsan2_15-20250222-0ubuntu1_arm64.deb ...
1537s Unpacking libtsan2:arm64 (15-20250222-0ubuntu1) ...
1537s Selecting previously unselected package libubsan1:arm64.
1537s Preparing to unpack .../083-libubsan1_15-20250222-0ubuntu1_arm64.deb ...
1537s Unpacking libubsan1:arm64 (15-20250222-0ubuntu1) ...
1537s Selecting previously unselected package libhwasan0:arm64.
1537s Preparing to unpack .../084-libhwasan0_15-20250222-0ubuntu1_arm64.deb ...
1537s Unpacking libhwasan0:arm64 (15-20250222-0ubuntu1) ...
1537s Selecting previously unselected package libgcc-14-dev:arm64.
1537s Preparing to unpack .../085-libgcc-14-dev_14.2.0-17ubuntu3_arm64.deb ...
1537s Unpacking libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ...
1537s Selecting previously unselected package libstdc++-14-dev:arm64.
1537s Preparing to unpack .../086-libstdc++-14-dev_14.2.0-17ubuntu3_arm64.deb ...
1537s Unpacking libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ...
1537s Selecting previously unselected package libboost1.83-dev:arm64.
1537s Preparing to unpack .../087-libboost1.83-dev_1.83.0-4.1ubuntu1_arm64.deb ...
1537s Unpacking libboost1.83-dev:arm64 (1.83.0-4.1ubuntu1) ...
1539s Selecting previously unselected package libexpat1-dev:arm64.
1539s Preparing to unpack .../088-libexpat1-dev_2.6.4-1_arm64.deb ...
1539s Unpacking libexpat1-dev:arm64 (2.6.4-1) ...
1539s Selecting previously unselected package zlib1g-dev:arm64.
1539s Preparing to unpack .../089-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ...
1539s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
1539s Selecting previously unselected package libpython3.13-dev:arm64.
1539s Preparing to unpack .../090-libpython3.13-dev_3.13.2-1_arm64.deb ...
1539s Unpacking libpython3.13-dev:arm64 (3.13.2-1) ...
1539s Selecting previously unselected package libpython3-dev:arm64.
1539s Preparing to unpack .../091-libpython3-dev_3.13.2-2_arm64.deb ...
1539s Unpacking libpython3-dev:arm64 (3.13.2-2) ...
1539s Selecting previously unselected package python3.13-dev.
1539s Preparing to unpack .../092-python3.13-dev_3.13.2-1_arm64.deb ...
1539s Unpacking python3.13-dev (3.13.2-1) ...
1539s Selecting previously unselected package libjs-jquery.
1539s Preparing to unpack .../093-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
1539s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
1539s Selecting previously unselected package libjs-underscore.
1539s Preparing to unpack .../094-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ...
1539s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
1539s Selecting previously unselected package libjs-sphinxdoc.
1539s Preparing to unpack .../095-libjs-sphinxdoc_8.1.3-4_all.deb ...
1539s Unpacking libjs-sphinxdoc (8.1.3-4) ...
1540s Selecting previously unselected package python3-dev.
1540s Preparing to unpack .../096-python3-dev_3.13.2-2_arm64.deb ...
1540s Unpacking python3-dev (3.13.2-2) ...
1540s Selecting previously unselected package libboost-python1.83-dev.
1540s Preparing to unpack .../097-libboost-python1.83-dev_1.83.0-4.1ubuntu1_arm64.deb ...
1540s Unpacking libboost-python1.83-dev (1.83.0-4.1ubuntu1) ...
1540s Selecting previously unselected package libboost-python-dev.
1540s Preparing to unpack .../098-libboost-python-dev_1.83.0.2ubuntu1_arm64.deb ...
1540s Unpacking libboost-python-dev (1.83.0.2ubuntu1) ...
1540s Selecting previously unselected package libboost-thread1.83.0:arm64.
1540s Preparing to unpack .../099-libboost-thread1.83.0_1.83.0-4.1ubuntu1_arm64.deb ...
1540s Unpacking libboost-thread1.83.0:arm64 (1.83.0-4.1ubuntu1) ...
1540s Selecting previously unselected package libboost-timer1.83.0:arm64.
1540s Preparing to unpack .../100-libboost-timer1.83.0_1.83.0-4.1ubuntu1_arm64.deb ...
1540s Unpacking libboost-timer1.83.0:arm64 (1.83.0-4.1ubuntu1) ...
1540s Selecting previously unselected package libpixman-1-0:arm64.
1540s Preparing to unpack .../101-libpixman-1-0_0.44.0-3_arm64.deb ...
1540s Unpacking libpixman-1-0:arm64 (0.44.0-3) ...
1540s Selecting previously unselected package libxcb-render0:arm64.
1540s Preparing to unpack .../102-libxcb-render0_1.17.0-2_arm64.deb ...
1540s Unpacking libxcb-render0:arm64 (1.17.0-2) ...
1540s Selecting previously unselected package libxcb-shm0:arm64.
1540s Preparing to unpack .../103-libxcb-shm0_1.17.0-2_arm64.deb ...
1540s Unpacking libxcb-shm0:arm64 (1.17.0-2) ...
1540s Selecting previously unselected package libcairo2:arm64.
1540s Preparing to unpack .../104-libcairo2_1.18.2-2_arm64.deb ...
1540s Unpacking libcairo2:arm64 (1.18.2-2) ...
1540s Selecting previously unselected package libcairo-gobject2:arm64.
1540s Preparing to unpack .../105-libcairo-gobject2_1.18.2-2_arm64.deb ...
1540s Unpacking libcairo-gobject2:arm64 (1.18.2-2) ...
1540s Selecting previously unselected package libcbf1t64:arm64.
1540s Preparing to unpack .../106-libcbf1t64_0.9.7+dfsg1-5build1_arm64.deb ...
1540s Unpacking libcbf1t64:arm64 (0.9.7+dfsg1-5build1) ...
1540s Selecting previously unselected package libccp4-data.
1540s Preparing to unpack .../107-libccp4-data_8.0.0-4_all.deb ...
1540s Unpacking libccp4-data (8.0.0-4) ...
1540s Selecting previously unselected package libccp4c0t64:arm64.
1540s Preparing to unpack .../108-libccp4c0t64_8.0.0-4_arm64.deb ...
1540s Unpacking libccp4c0t64:arm64 (8.0.0-4) ...
1540s Selecting previously unselected package libmmdb2-0:arm64.
1540s Preparing to unpack .../109-libmmdb2-0_2.0.22-1_arm64.deb ...
1540s Unpacking libmmdb2-0:arm64 (2.0.22-1) ...
1540s Selecting previously unselected package libccp4f0t64:arm64.
1540s Preparing to unpack .../110-libccp4f0t64_8.0.0-4_arm64.deb ...
1540s Unpacking libccp4f0t64:arm64 (8.0.0-4) ...
1540s Selecting previously unselected package libccp4-dev:arm64.
1540s Preparing to unpack .../111-libccp4-dev_8.0.0-4_arm64.deb ...
1540s Unpacking libccp4-dev:arm64 (8.0.0-4) ...
1540s Selecting previously unselected package libcctbx0.
1540s Preparing to unpack .../112-libcctbx0_2024.10+ds2+~3.22.1+ds1-4build2_arm64.deb ...
1540s Unpacking libcctbx0 (2024.10+ds2+~3.22.1+ds1-4build2) ...
1540s Selecting previously unselected package libcctbx-dev.
1540s Preparing to unpack .../113-libcctbx-dev_2024.10+ds2+~3.22.1+ds1-4build2_arm64.deb ...
1540s Unpacking libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4build2) ...
1541s Selecting previously unselected package liblcms2-2:arm64.
1541s Preparing to unpack .../114-liblcms2-2_2.16-2_arm64.deb ...
1541s Unpacking liblcms2-2:arm64 (2.16-2) ...
1541s Selecting previously unselected package libcolord2:arm64.
1541s Preparing to unpack .../115-libcolord2_1.4.7-3_arm64.deb ...
1541s Unpacking libcolord2:arm64 (1.4.7-3) ...
1541s Selecting previously unselected package libcups2t64:arm64.
1541s Preparing to unpack .../116-libcups2t64_2.4.11-0ubuntu2_arm64.deb ...
1541s Unpacking libcups2t64:arm64 (2.4.11-0ubuntu2) ...
1541s Selecting previously unselected package libdatrie1:arm64.
1541s Preparing to unpack .../117-libdatrie1_0.2.13-3build1_arm64.deb ...
1541s Unpacking libdatrie1:arm64 (0.2.13-3build1) ...
1541s Selecting previously unselected package libdouble-conversion3:arm64.
1541s Preparing to unpack .../118-libdouble-conversion3_3.3.1-1_arm64.deb ...
1541s Unpacking libdouble-conversion3:arm64 (3.3.1-1) ...
1541s Selecting previously unselected package libwayland-server0:arm64.
1541s Preparing to unpack .../119-libwayland-server0_1.23.1-3_arm64.deb ...
1541s Unpacking libwayland-server0:arm64 (1.23.1-3) ...
1541s Selecting previously unselected package libx11-xcb1:arm64.
1541s Preparing to unpack .../120-libx11-xcb1_2%3a1.8.10-2_arm64.deb ...
1541s Unpacking libx11-xcb1:arm64 (2:1.8.10-2) ...
1541s Selecting previously unselected package libxcb-dri3-0:arm64.
1541s Preparing to unpack .../121-libxcb-dri3-0_1.17.0-2_arm64.deb ...
1541s Unpacking libxcb-dri3-0:arm64 (1.17.0-2) ...
1541s Selecting previously unselected package libxcb-present0:arm64.
1541s Preparing to unpack .../122-libxcb-present0_1.17.0-2_arm64.deb ...
1541s Unpacking libxcb-present0:arm64 (1.17.0-2) ...
1541s Selecting previously unselected package libxcb-randr0:arm64.
1541s Preparing to unpack .../123-libxcb-randr0_1.17.0-2_arm64.deb ...
1541s Unpacking libxcb-randr0:arm64 (1.17.0-2) ...
1541s Selecting previously unselected package libxcb-sync1:arm64.
1541s Preparing to unpack .../124-libxcb-sync1_1.17.0-2_arm64.deb ...
1541s Unpacking libxcb-sync1:arm64 (1.17.0-2) ...
1541s Selecting previously unselected package libxcb-xfixes0:arm64.
1541s Preparing to unpack .../125-libxcb-xfixes0_1.17.0-2_arm64.deb ...
1541s Unpacking libxcb-xfixes0:arm64 (1.17.0-2) ...
1541s Selecting previously unselected package libxshmfence1:arm64.
1541s Preparing to unpack .../126-libxshmfence1_1.3-1build5_arm64.deb ...
1541s Unpacking libxshmfence1:arm64 (1.3-1build5) ...
1541s Selecting previously unselected package mesa-libgallium:arm64.
1541s Preparing to unpack .../127-mesa-libgallium_25.0.1-2ubuntu1_arm64.deb ...
1541s Unpacking mesa-libgallium:arm64 (25.0.1-2ubuntu1) ...
1541s Selecting previously unselected package libgbm1:arm64.
1541s Preparing to unpack .../128-libgbm1_25.0.1-2ubuntu1_arm64.deb ...
1541s Unpacking libgbm1:arm64 (25.0.1-2ubuntu1) ...
1541s Selecting previously unselected package libwayland-client0:arm64.
1542s Preparing to unpack .../129-libwayland-client0_1.23.1-3_arm64.deb ...
1542s Unpacking libwayland-client0:arm64 (1.23.1-3) ...
1542s Selecting previously unselected package libegl-mesa0:arm64.
1542s Preparing to unpack .../130-libegl-mesa0_25.0.1-2ubuntu1_arm64.deb ...
1542s Unpacking libegl-mesa0:arm64 (25.0.1-2ubuntu1) ...
1542s Selecting previously unselected package libepoxy0:arm64.
1542s Preparing to unpack .../131-libepoxy0_1.5.10-2_arm64.deb ...
1542s Unpacking libepoxy0:arm64 (1.5.10-2) ...
1542s Selecting previously unselected package libvulkan1:arm64.
1542s Preparing to unpack .../132-libvulkan1_1.4.304.0-1_arm64.deb ...
1542s Unpacking libvulkan1:arm64 (1.4.304.0-1) ...
1542s Selecting previously unselected package libgl1-mesa-dri:arm64.
1542s Preparing to unpack .../133-libgl1-mesa-dri_25.0.1-2ubuntu1_arm64.deb ...
1542s Unpacking libgl1-mesa-dri:arm64 (25.0.1-2ubuntu1) ...
1542s Selecting previously unselected package libglvnd0:arm64.
1542s Preparing to unpack .../134-libglvnd0_1.7.0-1build1_arm64.deb ...
1542s Unpacking libglvnd0:arm64 (1.7.0-1build1) ...
1542s Selecting previously unselected package libxcb-glx0:arm64.
1542s Preparing to unpack .../135-libxcb-glx0_1.17.0-2_arm64.deb ...
1542s Unpacking libxcb-glx0:arm64 (1.17.0-2) ...
1542s Selecting previously unselected package libxxf86vm1:arm64.
1542s Preparing to unpack .../136-libxxf86vm1_1%3a1.1.4-1build4_arm64.deb ...
1542s Unpacking libxxf86vm1:arm64 (1:1.1.4-1build4) ...
1542s Selecting previously unselected package libglx-mesa0:arm64.
1542s Preparing to unpack .../137-libglx-mesa0_25.0.1-2ubuntu1_arm64.deb ...
1542s Unpacking libglx-mesa0:arm64 (25.0.1-2ubuntu1) ...
1542s Selecting previously unselected package libglx0:arm64.
1542s Preparing to unpack .../138-libglx0_1.7.0-1build1_arm64.deb ...
1542s Unpacking libglx0:arm64 (1.7.0-1build1) ...
1542s Selecting previously unselected package libgl1:arm64.
1542s Preparing to unpack .../139-libgl1_1.7.0-1build1_arm64.deb ...
1542s Unpacking libgl1:arm64 (1.7.0-1build1) ...
1542s Selecting previously unselected package libglew2.2:arm64.
1542s Preparing to unpack .../140-libglew2.2_2.2.0-4build1_arm64.deb ...
1542s Unpacking libglew2.2:arm64 (2.2.0-4build1) ...
1542s Selecting previously unselected package libgraphite2-3:arm64.
1542s Preparing to unpack .../141-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ...
1542s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
1542s Selecting previously unselected package libharfbuzz0b:arm64.
1542s Preparing to unpack .../142-libharfbuzz0b_10.2.0-1_arm64.deb ...
1542s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ...
1542s Selecting previously unselected package libthai-data.
1542s Preparing to unpack .../143-libthai-data_0.1.29-2build1_all.deb ...
1542s Unpacking libthai-data (0.1.29-2build1) ...
1542s Selecting previously unselected package libthai0:arm64.
1542s Preparing to unpack .../144-libthai0_0.1.29-2build1_arm64.deb ...
1542s Unpacking libthai0:arm64 (0.1.29-2build1) ...
1542s Selecting previously unselected package libpango-1.0-0:arm64.
1542s Preparing to unpack .../145-libpango-1.0-0_1.56.1-1_arm64.deb ...
1542s Unpacking libpango-1.0-0:arm64 (1.56.1-1) ...
1542s Selecting previously unselected package libpangoft2-1.0-0:arm64.
1542s Preparing to unpack .../146-libpangoft2-1.0-0_1.56.1-1_arm64.deb ...
1542s Unpacking libpangoft2-1.0-0:arm64 (1.56.1-1) ...
1542s Selecting previously unselected package libpangocairo-1.0-0:arm64.
1542s Preparing to unpack .../147-libpangocairo-1.0-0_1.56.1-1_arm64.deb ...
1542s Unpacking libpangocairo-1.0-0:arm64 (1.56.1-1) ...
1542s Selecting previously unselected package libwayland-cursor0:arm64.
1542s Preparing to unpack .../148-libwayland-cursor0_1.23.1-3_arm64.deb ...
1542s Unpacking libwayland-cursor0:arm64 (1.23.1-3) ...
1543s Selecting previously unselected package libwayland-egl1:arm64.
1543s Preparing to unpack .../149-libwayland-egl1_1.23.1-3_arm64.deb ...
1543s Unpacking libwayland-egl1:arm64 (1.23.1-3) ...
1543s Selecting previously unselected package libxcomposite1:arm64.
1543s Preparing to unpack .../150-libxcomposite1_1%3a0.4.6-1_arm64.deb ...
1543s Unpacking libxcomposite1:arm64 (1:0.4.6-1) ...
1543s Selecting previously unselected package libxfixes3:arm64.
1543s Preparing to unpack .../151-libxfixes3_1%3a6.0.0-2build1_arm64.deb ...
1543s Unpacking libxfixes3:arm64 (1:6.0.0-2build1) ...
1543s Selecting previously unselected package libxcursor1:arm64.
1543s Preparing to unpack .../152-libxcursor1_1%3a1.2.3-1_arm64.deb ...
1543s Unpacking libxcursor1:arm64 (1:1.2.3-1) ...
1543s Selecting previously unselected package libxdamage1:arm64.
1543s Preparing to unpack .../153-libxdamage1_1%3a1.1.6-1build1_arm64.deb ...
1543s Unpacking libxdamage1:arm64 (1:1.1.6-1build1) ...
1543s Selecting previously unselected package libxinerama1:arm64.
1543s Preparing to unpack .../154-libxinerama1_2%3a1.1.4-3build1_arm64.deb ...
1543s Unpacking libxinerama1:arm64 (2:1.1.4-3build1) ...
1543s Selecting previously unselected package libxrandr2:arm64.
1543s Preparing to unpack .../155-libxrandr2_2%3a1.5.4-1_arm64.deb ...
1543s Unpacking libxrandr2:arm64 (2:1.5.4-1) ...
1543s Selecting previously unselected package libgtk-3-common.
1543s Preparing to unpack .../156-libgtk-3-common_3.24.48-3ubuntu1_all.deb ...
1543s Unpacking libgtk-3-common (3.24.48-3ubuntu1) ...
1543s Selecting previously unselected package libgtk-3-0t64:arm64.
1543s Preparing to unpack .../157-libgtk-3-0t64_3.24.48-3ubuntu1_arm64.deb ...
1543s Unpacking libgtk-3-0t64:arm64 (3.24.48-3ubuntu1) ...
1543s Selecting previously unselected package libice6:arm64.
1543s Preparing to unpack .../158-libice6_2%3a1.1.1-1_arm64.deb ...
1543s Unpacking libice6:arm64 (2:1.1.1-1) ...
1543s Selecting previously unselected package libimagequant0:arm64.
1543s Preparing to unpack .../159-libimagequant0_2.18.0-1build1_arm64.deb ...
1543s Unpacking libimagequant0:arm64 (2.18.0-1build1) ...
1543s Selecting previously unselected package libwacom-common.
1543s Preparing to unpack .../160-libwacom-common_2.14.0-1_all.deb ...
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1543s Selecting previously unselected package libwacom9:arm64.
1543s Preparing to unpack .../161-libwacom9_2.14.0-1_arm64.deb ...
1543s Unpacking libwacom9:arm64 (2.14.0-1) ...
1543s Selecting previously unselected package libinput-bin.
1543s Preparing to unpack .../162-libinput-bin_1.27.1-1_arm64.deb ...
1543s Unpacking libinput-bin (1.27.1-1) ...
1543s Selecting previously unselected package libmtdev1t64:arm64.
1543s Preparing to unpack .../163-libmtdev1t64_1.1.7-1_arm64.deb ...
1543s Unpacking libmtdev1t64:arm64 (1.1.7-1) ...
1543s Selecting previously unselected package libinput10:arm64.
1543s Preparing to unpack .../164-libinput10_1.27.1-1_arm64.deb ...
1543s Unpacking libinput10:arm64 (1.27.1-1) ...
1543s Selecting previously unselected package libjs-jquery-ui.
1543s Preparing to unpack .../165-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ...
1543s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ...
1543s Selecting previously unselected package liblbfgsb0:arm64.
1544s Preparing to unpack .../166-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ...
1544s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ...
1544s Selecting previously unselected package libmd4c0:arm64.
1544s Preparing to unpack .../167-libmd4c0_0.5.2-2_arm64.deb ...
1544s Unpacking libmd4c0:arm64 (0.5.2-2) ...
1544s Selecting previously unselected package libnetcdf22:arm64.
1544s Preparing to unpack .../168-libnetcdf22_1%3a4.9.3-1_arm64.deb ...
1544s Unpacking libnetcdf22:arm64 (1:4.9.3-1) ...
1544s Selecting previously unselected package libnotify4:arm64.
1544s Preparing to unpack .../169-libnotify4_0.8.4-1_arm64.deb ...
1544s Unpacking libnotify4:arm64 (0.8.4-1) ...
1544s Selecting previously unselected package libpcre2-16-0:arm64.
1544s Preparing to unpack .../170-libpcre2-16-0_10.45-1_arm64.deb ...
1544s Unpacking libpcre2-16-0:arm64 (10.45-1) ...
1544s Selecting previously unselected package libpcre2-32-0:arm64.
1544s Preparing to unpack .../171-libpcre2-32-0_10.45-1_arm64.deb ...
1544s Unpacking libpcre2-32-0:arm64 (10.45-1) ...
1544s Selecting previously unselected package libqhull-r8.0:arm64.
1544s Preparing to unpack .../172-libqhull-r8.0_2020.2-6build1_arm64.deb ...
1544s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ...
1544s Selecting previously unselected package libqt5core5t64:arm64.
1544s Preparing to unpack .../173-libqt5core5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ...
1544s Unpacking libqt5core5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
1544s Selecting previously unselected package libqt5dbus5t64:arm64.
1544s Preparing to unpack .../174-libqt5dbus5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ...
1544s Unpacking libqt5dbus5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
1544s Selecting previously unselected package libegl1:arm64.
1544s Preparing to unpack .../175-libegl1_1.7.0-1build1_arm64.deb ...
1544s Unpacking libegl1:arm64 (1.7.0-1build1) ...
1544s Selecting previously unselected package libqt5network5t64:arm64.
1544s Preparing to unpack .../176-libqt5network5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ...
1544s Unpacking libqt5network5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
1544s Selecting previously unselected package libsm6:arm64.
1544s Preparing to unpack .../177-libsm6_2%3a1.2.4-1_arm64.deb ...
1544s Unpacking libsm6:arm64 (2:1.2.4-1) ...
1544s Selecting previously unselected package libxcb-icccm4:arm64.
1544s Preparing to unpack .../178-libxcb-icccm4_0.4.2-1_arm64.deb ...
1544s Unpacking libxcb-icccm4:arm64 (0.4.2-1) ...
1544s Selecting previously unselected package libxcb-util1:arm64.
1544s Preparing to unpack .../179-libxcb-util1_0.4.1-1_arm64.deb ...
1544s Unpacking libxcb-util1:arm64 (0.4.1-1) ...
1544s Selecting previously unselected package libxcb-image0:arm64.
1544s Preparing to unpack .../180-libxcb-image0_0.4.0-2build1_arm64.deb ...
1544s Unpacking libxcb-image0:arm64 (0.4.0-2build1) ...
1544s Selecting previously unselected package libxcb-keysyms1:arm64.
1544s Preparing to unpack .../181-libxcb-keysyms1_0.4.1-1_arm64.deb ...
1544s Unpacking libxcb-keysyms1:arm64 (0.4.1-1) ...
1544s Selecting previously unselected package libxcb-render-util0:arm64.
1544s Preparing to unpack .../182-libxcb-render-util0_0.3.10-1_arm64.deb ...
1544s Unpacking libxcb-render-util0:arm64 (0.3.10-1) ...
1544s Selecting previously unselected package libxcb-shape0:arm64.
1544s Preparing to unpack .../183-libxcb-shape0_1.17.0-2_arm64.deb ...
1544s Unpacking libxcb-shape0:arm64 (1.17.0-2) ...
1544s Selecting previously unselected package libxcb-xinerama0:arm64.
1544s Preparing to unpack .../184-libxcb-xinerama0_1.17.0-2_arm64.deb ...
1544s Unpacking libxcb-xinerama0:arm64 (1.17.0-2) ...
1544s Selecting previously unselected package libxcb-xinput0:arm64.
1544s Preparing to unpack .../185-libxcb-xinput0_1.17.0-2_arm64.deb ...
1544s Unpacking libxcb-xinput0:arm64 (1.17.0-2) ...
1544s Selecting previously unselected package libxcb-xkb1:arm64.
1545s Preparing to unpack .../186-libxcb-xkb1_1.17.0-2_arm64.deb ...
1545s Unpacking libxcb-xkb1:arm64 (1.17.0-2) ...
1545s Selecting previously unselected package libxkbcommon-x11-0:arm64.
1545s Preparing to unpack .../187-libxkbcommon-x11-0_1.7.0-2_arm64.deb ...
1545s Unpacking libxkbcommon-x11-0:arm64 (1.7.0-2) ...
1545s Selecting previously unselected package libqt5gui5t64:arm64.
1545s Preparing to unpack .../188-libqt5gui5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ...
1545s Unpacking libqt5gui5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
1545s Selecting previously unselected package libqt5widgets5t64:arm64.
1545s Preparing to unpack .../189-libqt5widgets5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ...
1545s Unpacking libqt5widgets5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
1545s Selecting previously unselected package libqt5xml5t64:arm64.
1545s Preparing to unpack .../190-libqt5xml5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ...
1545s Unpacking libqt5xml5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
1545s Selecting previously unselected package libqt5designer5:arm64.
1545s Preparing to unpack .../191-libqt5designer5_5.15.15-6build1_arm64.deb ...
1545s Unpacking libqt5designer5:arm64 (5.15.15-6build1) ...
1545s Selecting previously unselected package libqt5sql5t64:arm64.
1545s Preparing to unpack .../192-libqt5sql5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ...
1545s Unpacking libqt5sql5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
1545s Selecting previously unselected package libqt5help5:arm64.
1545s Preparing to unpack .../193-libqt5help5_5.15.15-6build1_arm64.deb ...
1545s Unpacking libqt5help5:arm64 (5.15.15-6build1) ...
1545s Selecting previously unselected package libqt5opengl5t64:arm64.
1545s Preparing to unpack .../194-libqt5opengl5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ...
1545s Unpacking libqt5opengl5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
1545s Selecting previously unselected package libqt5printsupport5t64:arm64.
1545s Preparing to unpack .../195-libqt5printsupport5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ...
1545s Unpacking libqt5printsupport5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
1545s Selecting previously unselected package libqt5test5t64:arm64.
1545s Preparing to unpack .../196-libqt5test5t64_5.15.15+dfsg-4ubuntu1_arm64.deb ...
1545s Unpacking libqt5test5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
1545s Selecting previously unselected package libraqm0:arm64.
1545s Preparing to unpack .../197-libraqm0_0.10.2-1_arm64.deb ...
1545s Unpacking libraqm0:arm64 (0.10.2-1) ...
1545s Selecting previously unselected package libssm2:arm64.
1545s Preparing to unpack .../198-libssm2_1.4.0-2build1_arm64.deb ...
1545s Unpacking libssm2:arm64 (1.4.0-2build1) ...
1545s Selecting previously unselected package libwebpdemux2:arm64.
1545s Preparing to unpack .../199-libwebpdemux2_1.5.0-0.1_arm64.deb ...
1545s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ...
1545s Selecting previously unselected package libwebpmux3:arm64.
1545s Preparing to unpack .../200-libwebpmux3_1.5.0-0.1_arm64.deb ...
1545s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ...
1545s Selecting previously unselected package libwxbase3.2-1t64:arm64.
1545s Preparing to unpack .../201-libwxbase3.2-1t64_3.2.6+dfsg-2ubuntu1_arm64.deb ...
1545s Unpacking libwxbase3.2-1t64:arm64 (3.2.6+dfsg-2ubuntu1) ...
1545s Selecting previously unselected package libxtst6:arm64.
1545s Preparing to unpack .../202-libxtst6_2%3a1.2.5-1_arm64.deb ...
1545s Unpacking libxtst6:arm64 (2:1.2.5-1) ...
1545s Selecting previously unselected package libwxgtk3.2-1t64:arm64.
1546s Preparing to unpack .../203-libwxgtk3.2-1t64_3.2.6+dfsg-2ubuntu1_arm64.deb ...
1546s Unpacking libwxgtk3.2-1t64:arm64 (3.2.6+dfsg-2ubuntu1) ...
1546s Selecting previously unselected package libwxgtk-gl3.2-1t64:arm64.
1546s Preparing to unpack .../204-libwxgtk-gl3.2-1t64_3.2.6+dfsg-2ubuntu1_arm64.deb ...
1546s Unpacking libwxgtk-gl3.2-1t64:arm64 (3.2.6+dfsg-2ubuntu1) ...
1546s Selecting previously unselected package libxslt1.1:arm64.
1546s Preparing to unpack .../205-libxslt1.1_1.1.39-0exp1ubuntu2_arm64.deb ...
1546s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ...
1546s Selecting previously unselected package pymol-data.
1546s Preparing to unpack .../206-pymol-data_3.0.0+dfsg-3build2_all.deb ...
1546s Unpacking pymol-data (3.0.0+dfsg-3build2) ...
1546s Selecting previously unselected package python-matplotlib-data.
1546s Preparing to unpack .../207-python-matplotlib-data_3.8.3-7build1_all.deb ...
1546s Unpacking python-matplotlib-data (3.8.3-7build1) ...
1546s Selecting previously unselected package python3-all.
1546s Preparing to unpack .../208-python3-all_3.13.2-2_arm64.deb ...
1546s Unpacking python3-all (3.13.2-2) ...
1546s Selecting previously unselected package python3-brotli.
1546s Preparing to unpack .../209-python3-brotli_1.1.0-2build4_arm64.deb ...
1546s Unpacking python3-brotli (1.1.0-2build4) ...
1546s Selecting previously unselected package python3-legacy-cgi.
1546s Preparing to unpack .../210-python3-legacy-cgi_2.6.2-1_all.deb ...
1546s Unpacking python3-legacy-cgi (2.6.2-1) ...
1546s Selecting previously unselected package python3-pycbf.
1546s Preparing to unpack .../211-python3-pycbf_0.9.7+dfsg1-5build1_arm64.deb ...
1546s Unpacking python3-pycbf (0.9.7+dfsg1-5build1) ...
1546s Selecting previously unselected package python3-hdf5plugin.
1546s Preparing to unpack .../212-python3-hdf5plugin_5.0.0-1_all.deb ...
1546s Unpacking python3-hdf5plugin (5.0.0-1) ...
1546s Selecting previously unselected package python3-dateutil.
1546s Preparing to unpack .../213-python3-dateutil_2.9.0-3_all.deb ...
1546s Unpacking python3-dateutil (2.9.0-3) ...
1546s Selecting previously unselected package libopenjp2-7:arm64.
1546s Preparing to unpack .../214-libopenjp2-7_2.5.0-2ubuntu3_arm64.deb ...
1546s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu3) ...
1546s Selecting previously unselected package python3-pil:arm64.
1546s Preparing to unpack .../215-python3-pil_11.1.0-5build1_arm64.deb ...
1546s Unpacking python3-pil:arm64 (11.1.0-5build1) ...
1546s Selecting previously unselected package python3.12-tk.
1546s Preparing to unpack .../216-python3.12-tk_3.12.9-1_arm64.deb ...
1546s Unpacking python3.12-tk (3.12.9-1) ...
1546s Selecting previously unselected package python3.13-tk.
1546s Preparing to unpack .../217-python3.13-tk_3.13.2-1_arm64.deb ...
1546s Unpacking python3.13-tk (3.13.2-1) ...
1546s Selecting previously unselected package python3-tk:arm64.
1546s Preparing to unpack .../218-python3-tk_3.13.1-1_arm64.deb ...
1546s Unpacking python3-tk:arm64 (3.13.1-1) ...
1547s Selecting previously unselected package python3-pil.imagetk:arm64.
1547s Preparing to unpack .../219-python3-pil.imagetk_11.1.0-5build1_arm64.deb ...
1547s Unpacking python3-pil.imagetk:arm64 (11.1.0-5build1) ...
1547s Selecting previously unselected package python3-contourpy.
1547s Preparing to unpack .../220-python3-contourpy_1.3.1-1build1_arm64.deb ...
1547s Unpacking python3-contourpy (1.3.1-1build1) ...
1547s Selecting previously unselected package python3-cycler.
1547s Preparing to unpack .../221-python3-cycler_0.12.1-1_all.deb ...
1547s Unpacking python3-cycler (0.12.1-1) ...
1547s Selecting previously unselected package python3-platformdirs.
1547s Preparing to unpack .../222-python3-platformdirs_4.3.6-1_all.deb ...
1547s Unpacking python3-platformdirs (4.3.6-1) ...
1547s Selecting previously unselected package python3-fs.
1547s Preparing to unpack .../223-python3-fs_2.4.16-7_all.deb ...
1547s Unpacking python3-fs (2.4.16-7) ...
1547s Selecting previously unselected package python3-lxml:arm64.
1547s Preparing to unpack .../224-python3-lxml_5.3.1-1build1_arm64.deb ...
1547s Unpacking python3-lxml:arm64 (5.3.1-1build1) ...
1547s Selecting previously unselected package python3-lz4.
1547s Preparing to unpack .../225-python3-lz4_4.4.0+dfsg-1build1_arm64.deb ...
1547s Unpacking python3-lz4 (4.4.0+dfsg-1build1) ...
1547s Selecting previously unselected package python3-decorator.
1547s Preparing to unpack .../226-python3-decorator_5.1.1-5_all.deb ...
1547s Unpacking python3-decorator (5.1.1-5) ...
1547s Selecting previously unselected package python3-scipy.
1547s Preparing to unpack .../227-python3-scipy_1.14.1-4ubuntu2_arm64.deb ...
1547s Unpacking python3-scipy (1.14.1-4ubuntu2) ...
1547s Selecting previously unselected package python3-mpmath.
1547s Preparing to unpack .../228-python3-mpmath_1.3.0-1_all.deb ...
1547s Unpacking python3-mpmath (1.3.0-1) ...
1547s Selecting previously unselected package python3-sympy.
1547s Preparing to unpack .../229-python3-sympy_1.13.3-5_all.deb ...
1547s Unpacking python3-sympy (1.13.3-5) ...
1548s Selecting previously unselected package python3-ufolib2.
1548s Preparing to unpack .../230-python3-ufolib2_0.17.0+dfsg1-1_all.deb ...
1548s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ...
1548s Selecting previously unselected package unicode-data.
1548s Preparing to unpack .../231-unicode-data_15.1.0-1_all.deb ...
1548s Unpacking unicode-data (15.1.0-1) ...
1548s Selecting previously unselected package python3-fonttools.
1548s Preparing to unpack .../232-python3-fonttools_4.55.3-2build1_arm64.deb ...
1548s Unpacking python3-fonttools (4.55.3-2build1) ...
1548s Selecting previously unselected package python3-importlib-resources.
1548s Preparing to unpack .../233-python3-importlib-resources_6.5.2-1_all.deb ...
1548s Unpacking python3-importlib-resources (6.5.2-1) ...
1548s Selecting previously unselected package python3-kiwisolver.
1548s Preparing to unpack .../234-python3-kiwisolver_1.4.7-3build1_arm64.deb ...
1548s Unpacking python3-kiwisolver (1.4.7-3build1) ...
1548s Selecting previously unselected package python3-packaging.
1548s Preparing to unpack .../235-python3-packaging_24.2-1_all.deb ...
1548s Unpacking python3-packaging (24.2-1) ...
1548s Selecting previously unselected package python3-matplotlib.
1548s Preparing to unpack .../236-python3-matplotlib_3.8.3-7build1_arm64.deb ...
1548s Unpacking python3-matplotlib (3.8.3-7build1) ...
1549s Selecting previously unselected package sphinx-rtd-theme-common.
1549s Preparing to unpack .../237-sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb ...
1549s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-2) ...
1549s Selecting previously unselected package python3-mrcfile.
1549s Preparing to unpack .../238-python3-mrcfile_1.5.4-2_all.deb ...
1549s Unpacking python3-mrcfile (1.5.4-2) ...
1549s Selecting previously unselected package python3-natsort.
1549s Preparing to unpack .../239-python3-natsort_8.0.2-2_all.deb ...
1549s Unpacking python3-natsort (8.0.2-2) ...
1549s Selecting previously unselected package python3-flexcache.
1549s Preparing to unpack .../240-python3-flexcache_0.3-2_all.deb ...
1549s Unpacking python3-flexcache (0.3-2) ...
1549s Selecting previously unselected package python3-flexparser.
1549s Preparing to unpack .../241-python3-flexparser_0.4-1_all.deb ...
1549s Unpacking python3-flexparser (0.4-1) ...
1549s Selecting previously unselected package python3-pint.
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1549s Selecting previously unselected package python3-nxmx.
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1549s Unpacking python3-nxmx (0.0.4-1) ...
1549s Selecting previously unselected package python3-ordered-set.
1549s Preparing to unpack .../244-python3-ordered-set_4.1.0-1_all.deb ...
1549s Unpacking python3-ordered-set (4.1.0-1) ...
1549s Selecting previously unselected package python3-procrunner.
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1549s Unpacking python3-procrunner (2.3.3-2) ...
1549s Selecting previously unselected package libopengl0:arm64.
1549s Preparing to unpack .../246-libopengl0_1.7.0-1build1_arm64.deb ...
1549s Unpacking libopengl0:arm64 (1.7.0-1build1) ...
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1549s Preparing to unpack .../247-libglu1-mesa_9.0.2-1.1build1_arm64.deb ...
1549s Unpacking libglu1-mesa:arm64 (9.0.2-1.1build1) ...
1549s Selecting previously unselected package python3-opengl.
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1549s Unpacking python3-opengl (3.1.7+dfsg-1) ...
1550s Selecting previously unselected package python3-pyqt5.sip.
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1550s Unpacking python3-pyqt5.sip (12.17.0-1build1) ...
1550s Selecting previously unselected package python3-pyqt5.
1550s Preparing to unpack .../250-python3-pyqt5_5.15.11+dfsg-2_arm64.deb ...
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1550s Selecting previously unselected package python3-pymol.
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1550s Selecting previously unselected package python3-six.
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1550s Unpacking python3-six (1.17.0-1) ...
1550s Selecting previously unselected package python3-tqdm.
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1550s Unpacking python3-tqdm (4.67.1-2) ...
1550s Selecting previously unselected package python3-wxgtk4.0.
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1550s Unpacking python3-wxgtk4.0 (4.2.2+dfsg-3build1) ...
1550s Selecting previously unselected package python3-cctbx.
1550s Preparing to unpack .../256-python3-cctbx_2024.10+ds2+~3.22.1+ds1-4build2_arm64.deb ...
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1552s Selecting previously unselected package python3-iniconfig.
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1552s Unpacking python3-iniconfig (1.1.1-2) ...
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1552s Unpacking python3-pluggy (1.5.0-1) ...
1552s Selecting previously unselected package python3-pytest.
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1552s Unpacking python3-pytest (8.3.4-1) ...
1552s Selecting previously unselected package python3-dials-data.
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1552s Unpacking python3-dials-data (2.4.0-2) ...
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1552s Selecting previously unselected package python3-pytest-mock.
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1552s Unpacking python3-pytest-mock (3.14.0-2) ...
1552s Selecting previously unselected package python3-pytest-regressions.
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1552s Unpacking python3-pytest-regressions (2.5.0+ds-2) ...
1552s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
1552s Setting up libboost-python1.83.0 (1.83.0-4.1ubuntu1) ...
1552s Setting up libxcb-dri3-0:arm64 (1.17.0-2) ...
1552s Setting up liblcms2-2:arm64 (2.16-2) ...
1552s Setting up python3-iniconfig (1.1.1-2) ...
1552s Setting up libpixman-1-0:arm64 (0.44.0-3) ...
1552s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ...
1552s Setting up libwayland-server0:arm64 (1.23.1-3) ...
1552s Setting up libx11-xcb1:arm64 (2:1.8.10-2) ...
1552s Setting up libpciaccess0:arm64 (0.17-3build1) ...
1552s Setting up libdouble-conversion3:arm64 (3.3.1-1) ...
1552s Setting up fonts-lato (2.015-1) ...
1552s Setting up libxdamage1:arm64 (1:1.1.6-1build1) ...
1552s Setting up libxcb-xfixes0:arm64 (1.17.0-2) ...
1552s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ...
1552s Setting up libantlr3c-3.4-0:arm64 (3.4+dfsg-4build2) ...
1552s Setting up hicolor-icon-theme (0.18-2) ...
1552s Setting up libxi6:arm64 (2:1.8.2-1) ...
1552s Setting up libxcb-xinput0:arm64 (1.17.0-2) ...
1552s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ...
1552s Setting up libdatrie1:arm64 (0.2.13-3build1) ...
1552s Setting up python3-importlib-resources (6.5.2-1) ...
1552s Setting up libmmdb2-0:arm64 (2.0.22-1) ...
1552s Setting up libboost-timer1.83.0:arm64 (1.83.0-4.1ubuntu1) ...
1552s Setting up python3-lz4 (4.4.0+dfsg-1build1) ...
1552s Setting up libxcb-render0:arm64 (1.17.0-2) ...
1552s Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ...
1552s Setting up libglvnd0:arm64 (1.7.0-1build1) ...
1552s Setting up fonts-lyx (2.4.3-1) ...
1552s Setting up libxcb-glx0:arm64 (1.17.0-2) ...
1552s Setting up python3-tqdm (4.67.1-2) ...
1553s Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ...
1553s Setting up libxcb-keysyms1:arm64 (0.4.1-1) ...
1553s Setting up libxcb-shape0:arm64 (1.17.0-2) ...
1553s Setting up x11-common (1:7.7+23ubuntu3) ...
1553s Setting up libibumad3:arm64 (55.0-1ubuntu1) ...
1553s Setting up libdeflate0:arm64 (1.23-1) ...
1553s Setting up libboost-thread1.83.0:arm64 (1.83.0-4.1ubuntu1) ...
1553s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ...
1553s Setting up libxcb-render-util0:arm64 (0.3.10-1) ...
1553s Setting up python3-all (3.13.2-2) ...
1553s Setting up python3-ordered-set (4.1.0-1) ...
1553s Setting up libxcb-shm0:arm64 (1.17.0-2) ...
1553s Setting up libibmad5:arm64 (55.0-1ubuntu1) ...
1553s Setting up libxcb-icccm4:arm64 (0.4.2-1) ...
1553s Setting up libccp4-data (8.0.0-4) ...
1553s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ...
1553s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ...
1553s Setting up libpcre2-16-0:arm64 (10.45-1) ...
1553s Setting up libaec0:arm64 (1.1.3-1) ...
1553s Setting up libcolord2:arm64 (1.4.7-3) ...
1553s Setting up python3-platformdirs (4.3.6-1) ...
1553s Setting up libopengl0:arm64 (1.7.0-1build1) ...
1553s Setting up python3-natsort (8.0.2-2) ...
1553s Setting up libxcb-util1:arm64 (0.4.1-1) ...
1553s Setting up libxxf86vm1:arm64 (1:1.1.4-1build4) ...
1553s Setting up libxcb-xkb1:arm64 (1.17.0-2) ...
1553s Setting up libxcb-image0:arm64 (0.4.0-2build1) ...
1553s Setting up python3-fs (2.4.16-7) ...
1554s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu4) ...
1554s Setting up libxcb-present0:arm64 (1.17.0-2) ...
1554s Setting up libdconf1:arm64 (0.40.0-5) ...
1554s Setting up unicode-data (15.1.0-1) ...
1554s Setting up python3-six (1.17.0-1) ...
1554s Setting up libqt5core5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
1554s Setting up python3-decorator (5.1.1-5) ...
1554s Setting up libboost-numpy1.83.0 (1.83.0-4.1ubuntu1) ...
1554s Setting up libpcre2-32-0:arm64 (10.45-1) ...
1554s Setting up libblas3:arm64 (3.12.1-2) ...
1554s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
1554s Setting up python3-packaging (24.2-1) ...
1554s Setting up libxcb-xinerama0:arm64 (1.17.0-2) ...
1554s Setting up python3-flexparser (0.4-1) ...
1554s Setting up libmunge2:arm64 (0.5.16-1) ...
1554s Setting up libllvm17t64:arm64 (1:17.0.6-21) ...
1554s Setting up libexpat1-dev:arm64 (2.6.4-1) ...
1554s Setting up libann-cctbx0 (1.1.2+doc-9build1) ...
1554s Setting up libepoxy0:arm64 (1.5.10-2) ...
1554s Setting up libxfixes3:arm64 (1:6.0.0-2build1) ...
1554s Setting up libxcb-sync1:arm64 (1.17.0-2) ...
1554s Setting up python3-brotli (1.1.0-2build4) ...
1554s Setting up libavahi-common-data:arm64 (0.8-16ubuntu1) ...
1554s Setting up libatspi2.0-0t64:arm64 (2.55.90-1) ...
1554s Setting up liblzf1:arm64 (3.6-4) ...
1554s Setting up python3-cycler (0.12.1-1) ...
1555s Setting up libxinerama1:arm64 (2:1.1.4-3build1) ...
1555s Setting up libimagequant0:arm64 (2.18.0-1build1) ...
1555s Setting up pymol-data (3.0.0+dfsg-3build2) ...
1555s Setting up libxkbcommon-x11-0:arm64 (1.7.0-2) ...
1555s Setting up fonts-dejavu-mono (2.37-8) ...
1555s Setting up python3-kiwisolver (1.4.7-3build1) ...
1555s Setting up libhwloc15:arm64 (2.12.0-1) ...
1555s Setting up python3-numpy-dev:arm64 (1:2.2.3+ds-4) ...
1555s Setting up libxrandr2:arm64 (2:1.5.4-1) ...
1555s Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ...
1555s Setting up fonts-dejavu-core (2.37-8) ...
1555s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ...
1555s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ...
1555s Setting up libvulkan1:arm64 (1.4.304.0-1) ...
1555s Setting up python3-pluggy (1.5.0-1) ...
1555s Setting up libwebp7:arm64 (1.5.0-0.1) ...
1555s Setting up libubsan1:arm64 (15-20250222-0ubuntu1) ...
1555s Setting up python3-legacy-cgi (2.6.2-1) ...
1555s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
1555s Setting up python3-pyqt5.sip (12.17.0-1build1) ...
1555s Setting up libmtdev1t64:arm64 (1.1.7-1) ...
1555s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1build1) ...
1555s Setting up libxshmfence1:arm64 (1.3-1build5) ...
1555s Setting up libhwasan0:arm64 (15-20250222-0ubuntu1) ...
1555s Setting up at-spi2-common (2.55.90-1) ...
1555s Setting up libccp4c0t64:arm64 (8.0.0-4) ...
1555s Setting up libxcb-randr0:arm64 (1.17.0-2) ...
1555s Setting up libasan8:arm64 (15-20250222-0ubuntu1) ...
1555s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ...
1555s Setting up libqt5sql5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
1555s Setting up libmd4c0:arm64 (0.5.2-2) ...
1555s Setting up librdmacm1t64:arm64 (55.0-1ubuntu1) ...
1555s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu3) ...
1555s Setting up libharfbuzz0b:arm64 (10.2.0-1) ...
1555s Setting up libthai-data (0.1.29-2build1) ...
1555s Setting up python3-dateutil (2.9.0-3) ...
1555s Setting up python3-flexcache (0.3-2) ...
1555s Setting up libglu1-mesa:arm64 (9.0.2-1.1build1) ...
1555s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ...
1555s Setting up libwayland-egl1:arm64 (1.23.1-3) ...
1555s Setting up libxss1:arm64 (1:1.2.3-1build3) ...
1555s Setting up libtsan2:arm64 (15-20250222-0ubuntu1) ...
1555s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
1555s Setting up libwxbase3.2-1t64:arm64 (3.2.6+dfsg-2ubuntu1) ...
1555s Setting up python3-mpmath (1.3.0-1) ...
1556s Setting up python-matplotlib-data (3.8.3-7build1) ...
1556s Setting up libwebpmux3:arm64 (1.5.0-0.1) ...
1556s Setting up libxcomposite1:arm64 (1:0.4.6-1) ...
1556s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
1556s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-2) ...
1556s Setting up python3-procrunner (2.3.3-2) ...
1556s Setting up liblsan0:arm64 (15-20250222-0ubuntu1) ...
1556s Setting up libhsakmt1:arm64 (5.7.0-1build1) ...
1556s Setting up libsz2:arm64 (1.1.3-1) ...
1556s Setting up libitm1:arm64 (15-20250222-0ubuntu1) ...
1556s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
1556s Setting up libann-cctbx-dev (1.1.2+doc-9build1) ...
1556s Setting up libwacom-common (2.14.0-1) ...
1556s Setting up libwayland-client0:arm64 (1.23.1-3) ...
1556s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
1556s Setting up libfabric1:arm64 (1.17.0-3.1) ...
1556s Setting up python3-sympy (1.13.3-5) ...
1562s Setting up libice6:arm64 (2:1.1.1-1) ...
1562s Setting up mesa-libgallium:arm64 (25.0.1-2ubuntu1) ...
1562s Setting up liblapack3:arm64 (3.12.1-2) ...
1562s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
1562s Setting up libqt5dbus5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
1562s Setting up libssm2:arm64 (1.4.0-2build1) ...
1562s Setting up libatk1.0-0t64:arm64 (2.55.90-1) ...
1562s Setting up libgbm1:arm64 (25.0.1-2ubuntu1) ...
1562s Setting up libwacom9:arm64 (2.14.0-1) ...
1562s Setting up fontconfig-config (2.15.0-2ubuntu1) ...
1562s Setting up python3-pytest (8.3.4-1) ...
1562s Setting up libxtst6:arm64 (2:1.2.5-1) ...
1562s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ...
1562s Setting up python3-pytest-datadir (1.4.1+ds-1) ...
1563s Setting up libxcursor1:arm64 (1:1.2.3-1) ...
1563s Setting up libgl1-mesa-dri:arm64 (25.0.1-2ubuntu1) ...
1563s Setting up libqt5network5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
1563s Setting up libavahi-common3:arm64 (0.8-16ubuntu1) ...
1563s Setting up libqt5xml5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
1563s Setting up dconf-service (0.40.0-5) ...
1563s Setting up libqt5test5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
1563s Setting up libhwloc-plugins:arm64 (2.12.0-1) ...
1563s Setting up libccp4f0t64:arm64 (8.0.0-4) ...
1563s Setting up libinput-bin (1.27.1-1) ...
1563s Setting up python3-pint (0.24.4-1) ...
1563s Setting up libthai0:arm64 (0.1.29-2build1) ...
1563s Setting up libegl-mesa0:arm64 (25.0.1-2ubuntu1) ...
1563s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
1563s Setting up libraqm0:arm64 (0.10.2-1) ...
1563s Setting up libpython3.13-dev:arm64 (3.13.2-1) ...
1563s Setting up libpmix2t64:arm64 (5.0.6-5) ...
1563s Setting up python3-numpy (1:2.2.3+ds-4) ...
1565s Setting up libjs-sphinxdoc (8.1.3-4) ...
1565s Setting up libhdf5-310:arm64 (1.14.5+repack-3) ...
1565s Setting up python3-pytest-mock (3.14.0-2) ...
1565s Setting up python3-lxml:arm64 (5.3.1-1build1) ...
1565s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ...
1565s Setting up libwayland-cursor0:arm64 (1.23.1-3) ...
1565s Setting up libhsa-runtime64-1 (5.7.1-2build1) ...
1565s Setting up libegl1:arm64 (1.7.0-1build1) ...
1565s Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-2) ...
1565s Setting up python3-contourpy (1.3.1-1build1) ...
1565s Setting up libfontconfig1:arm64 (2.15.0-2ubuntu1) ...
1565s Setting up libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ...
1565s Setting up python3-dials-data (2.4.0-2) ...
1565s Setting up libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ...
1565s Setting up libsm6:arm64 (2:1.2.4-1) ...
1565s Setting up libavahi-client3:arm64 (0.8-16ubuntu1) ...
1565s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ...
1565s Setting up python3-mrcfile (1.5.4-2) ...
1565s Setting up libatk-bridge2.0-0t64:arm64 (2.55.90-1) ...
1565s Setting up libinput10:arm64 (1.27.1-1) ...
1565s Setting up gtk-update-icon-cache (4.17.5+ds-3ubuntu1) ...
1565s Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3) ...
1565s Setting up fontconfig (2.15.0-2ubuntu1) ...
1567s Regenerating fonts cache... done.
1567s Setting up libxft2:arm64 (2.3.6-1build1) ...
1567s Setting up libboost1.83-dev:arm64 (1.83.0-4.1ubuntu1) ...
1567s Setting up libglx-mesa0:arm64 (25.0.1-2ubuntu1) ...
1567s Setting up python3-scipy (1.14.1-4ubuntu2) ...
1571s Setting up libpython3-dev:arm64 (3.13.2-2) ...
1571s Setting up libcbf1t64:arm64 (0.9.7+dfsg1-5build1) ...
1571s Setting up libglx0:arm64 (1.7.0-1build1) ...
1571s Setting up dconf-gsettings-backend:arm64 (0.40.0-5) ...
1571s Setting up libccp4-dev:arm64 (8.0.0-4) ...
1571s Setting up python3.13-dev (3.13.2-1) ...
1571s Setting up libtk8.6:arm64 (8.6.16-1) ...
1571s Setting up libpango-1.0-0:arm64 (1.56.1-1) ...
1571s Setting up python3.12-tk (3.12.9-1) ...
1571s Setting up libnetcdf22:arm64 (1:4.9.3-1) ...
1571s Setting up python3-h5py-serial (3.13.0-1) ...
1571s Setting up libcairo2:arm64 (1.18.2-2) ...
1571s Setting up python3.13-tk (3.13.2-1) ...
1571s Setting up python3-pil:arm64 (11.1.0-5build1) ...
1571s Setting up libgl1:arm64 (1.7.0-1build1) ...
1571s Setting up libamdhip64-5 (5.7.1-5) ...
1571s Setting up python3-pytest-regressions (2.5.0+ds-2) ...
1571s Setting up adwaita-icon-theme (48~beta-3) ...
1571s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
1571s Setting up libnotify4:arm64 (0.8.4-1) ...
1571s Setting up python3-dev (3.13.2-2) ...
1571s Setting up libboost-python1.83-dev (1.83.0-4.1ubuntu1) ...
1571s Setting up python3-pycbf (0.9.7+dfsg1-5build1) ...
1572s Setting up python3-h5py (3.13.0-1) ...
1572s Setting up libglew2.2:arm64 (2.2.0-4build1) ...
1572s Setting up python3-hdf5plugin (5.0.0-1) ...
1572s Setting up libcairo-gobject2:arm64 (1.18.2-2) ...
1572s Setting up libpangoft2-1.0-0:arm64 (1.56.1-1) ...
1572s Setting up python3-nxmx (0.0.4-1) ...
1572s Setting up libcups2t64:arm64 (2.4.11-0ubuntu2) ...
1572s Setting up libgtk-3-common (3.24.48-3ubuntu1) ...
1572s Setting up libpangocairo-1.0-0:arm64 (1.56.1-1) ...
1572s Setting up libcctbx0 (2024.10+ds2+~3.22.1+ds1-4build2) ...
1572s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ...
1572s Setting up libucx0:arm64 (1.18.1+ds-2) ...
1572s Setting up blt (2.5.3+dfsg-8) ...
1572s Setting up python3-tk:arm64 (3.13.1-1) ...
1572s Setting up python3-opengl (3.1.7+dfsg-1) ...
1572s /usr/lib/python3/dist-packages/OpenGL/GL/AMD/vertex_shader_tessellator.py:1: SyntaxWarning: invalid escape sequence '\ '
1572s   '''OpenGL extension AMD.vertex_shader_tessellator
1574s Setting up libboost-python-dev (1.83.0.2ubuntu1) ...
1574s Setting up libqt5gui5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
1574s Setting up python3-pil.imagetk:arm64 (11.1.0-5build1) ...
1574s Setting up libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4build2) ...
1574s Setting up libopenmpi40:arm64 (5.0.7-1) ...
1574s Setting up libqt5widgets5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
1574s Setting up libhdf5-openmpi-310:arm64 (1.14.5+repack-3) ...
1574s Setting up libqt5help5:arm64 (5.15.15-6build1) ...
1574s Setting up libqt5opengl5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
1574s Setting up libqt5printsupport5t64:arm64 (5.15.15+dfsg-4ubuntu1) ...
1574s Setting up bitshuffle (0.5.2-1build2) ...
1574s Setting up libqt5designer5:arm64 (5.15.15-6build1) ...
1574s Setting up python3-pyqt5 (5.15.11+dfsg-2) ...
1574s Setting up python3-pyqt5.qtopengl (5.15.11+dfsg-2) ...
1574s Setting up python3-pymol (3.0.0+dfsg-3build2) ...
1575s Setting up python3-fonttools (4.55.3-2build1) ...
1576s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ...
1576s Setting up python3-matplotlib (3.8.3-7build1) ...
1577s Processing triggers for libc-bin (2.41-1ubuntu1) ...
1577s Processing triggers for man-db (2.13.0-1) ...
1578s Processing triggers for libglib2.0-0t64:arm64 (2.84.0-1) ...
1578s Setting up libgtk-3-0t64:arm64 (3.24.48-3ubuntu1) ...
1579s Processing triggers for udev (257.3-1ubuntu3) ...
1579s Setting up libwxgtk3.2-1t64:arm64 (3.2.6+dfsg-2ubuntu1) ...
1579s Setting up libwxgtk-gl3.2-1t64:arm64 (3.2.6+dfsg-2ubuntu1) ...
1579s Setting up python3-wxgtk4.0 (4.2.2+dfsg-3build1) ...
1580s Setting up python3-cctbx (2024.10+ds2+~3.22.1+ds1-4build2) ...
1583s /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:8: SyntaxWarning: invalid escape sequence '\{'
1583s   """ Iterator to generate strings of length n_chars, using upper-case,
1583s /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:46: SyntaxWarning: invalid escape sequence '\/'
1583s   special_characters = """[]_,.;:"&<>()\/\{}'`~!@#$%*|+-"""
1592s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:724: SyntaxWarning: invalid escape sequence '\o'
1592s   width=pairwise_differences_db, label='$\omega_{hkl}$'
1592s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:739: SyntaxWarning: invalid escape sequence '\o'
1592s   axes[0].set_ylabel('Distribution of $\omega_{hbk}$')
1592s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:740: SyntaxWarning: invalid escape sequence '\o'
1592s   axes[0].set_xlabel('Normalized PD ($\omega_{hbk}$)')
1592s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:759: SyntaxWarning: invalid escape sequence '\o'
1592s   axes[1].set_xlabel('Sorted Normalized PD ($\omega_{hbk}$)')
1592s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:778: SyntaxWarning: invalid escape sequence '\s'
1592s   axes[2].set_ylabel('Standard Deviation of $I_{hbk}/\sigma_{hbk}$')
1592s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:807: SyntaxWarning: invalid escape sequence '\m'
1592s   axes_sadd.set_ylabel('$s_{\mathrm{fac}}^2 \\times s_{\mathrm{add}}^2$')
1593s Processing triggers for libc-bin (2.41-1ubuntu1) ...
1616s autopkgtest [11:11:05]: test dxtbx: [-----------------------
1616s Testing dxtbx with python3.13:
1619s Fatal Python error: Segmentation fault
1619s 
1619s Current thread 0x0000ff2480327760 (most recent call first):
1619s   File "/usr/lib/python3/dist-packages/cctbx/sgtbx/__init__.py", line 102 in __init__
1619s   File "/usr/lib/python3/dist-packages/cctbx/crystal/__init__.py", line 75 in __init__
1619s   File "/tmp/autopkgtest.r32aCk/autopkgtest_tmp/tests/test_crystal_model_equivalence.py", line 28 in <module>
1619s   File "/usr/lib/python3/dist-packages/_pytest/assertion/rewrite.py", line 184 in exec_module
1619s   File "<frozen importlib._bootstrap>", line 935 in _load_unlocked
1619s   File "<frozen importlib._bootstrap>", line 1331 in _find_and_load_unlocked
1619s   File "<frozen importlib._bootstrap>", line 1360 in _find_and_load
1619s   File "<frozen importlib._bootstrap>", line 1387 in _gcd_import
1619s   File "/usr/lib/python3.13/importlib/__init__.py", line 88 in import_module
1619s   File "/usr/lib/python3/dist-packages/_pytest/pathlib.py", line 587 in import_path
1619s   File "/usr/lib/python3/dist-packages/_pytest/python.py", line 493 in importtestmodule
1619s   File "/usr/lib/python3/dist-packages/_pytest/python.py", line 546 in _getobj
1619s   File "/usr/lib/python3/dist-packages/_pytest/python.py", line 284 in obj
1619s   File "/usr/lib/python3/dist-packages/_pytest/python.py", line 562 in _register_setup_module_fixture
1619s   File "/usr/lib/python3/dist-packages/_pytest/python.py", line 549 in collect
1619s   File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389 in collect
1619s   File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341 in from_call
1619s   File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 391 in pytest_make_collect_report
1619s   File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall
1619s   File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
1619s   File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__
1619s   File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 567 in collect_one_node
1619s   File "/usr/lib/python3/dist-packages/_pytest/main.py", line 835 in _collect_one_node
1619s   File "/usr/lib/python3/dist-packages/_pytest/main.py", line 970 in genitems
1619s   File "/usr/lib/python3/dist-packages/_pytest/main.py", line 975 in genitems
1619s   File "/usr/lib/python3/dist-packages/_pytest/main.py", line 975 in genitems
1619s   File "/usr/lib/python3/dist-packages/_pytest/main.py", line 809 in perform_collect
1619s   File "/usr/lib/python3/dist-packages/_pytest/main.py", line 347 in pytest_collection
1619s   File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall
1619s   File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
1619s   File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__
1619s   File "/usr/lib/python3/dist-packages/_pytest/main.py", line 336 in _main
1619s   File "/usr/lib/python3/dist-packages/_pytest/main.py", line 283 in wrap_session
1619s   File "/usr/lib/python3/dist-packages/_pytest/main.py", line 330 in pytest_cmdline_main
1619s   File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall
1619s   File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
1619s   File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__
1619s   File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 175 in main
1619s   File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 201 in console_main
1619s   File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 9 in <module>
1619s   File "<frozen runpy>", line 88 in _run_code
1619s   File "<frozen runpy>", line 198 in _run_module_as_main
1619s 
1619s 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)
1623s Segmentation fault (core dumped)
1623s autopkgtest [11:11:12]: test dxtbx: -----------------------]
1623s autopkgtest [11:11:12]: test dxtbx:  - - - - - - - - - - results - - - - - - - - - -
1623s dxtbx                FAIL non-zero exit status 139
1624s autopkgtest [11:11:13]: @@@@@@@@@@@@@@@@@@@@ summary
1624s cctbx                FAIL non-zero exit status 1
1624s dxtbx                FAIL non-zero exit status 139
1642s nova [W] Using flock in prodstack6-arm64
1642s flock: timeout while waiting to get lock
1642s Creating nova instance adt-plucky-arm64-cctbx-20250313-104406-juju-7f2275-prod-proposed-migration-environment-2-d8421dd8-b1a3-4f83-8167-0b94862dad3b from image adt/ubuntu-plucky-arm64-server-20250313.img (UUID 1e0d5b46-827c-482e-8813-f0c13efee277)...
1642s nova [W] Timed out waiting for ffa698ea-223c-4f58-8cd2-2b395989a7d8 to get deleted.
1642s nova [W] Using flock in prodstack6-arm64
1642s Creating nova instance adt-plucky-arm64-cctbx-20250313-104406-juju-7f2275-prod-proposed-migration-environment-2-d8421dd8-b1a3-4f83-8167-0b94862dad3b from image adt/ubuntu-plucky-arm64-server-20250313.img (UUID 1e0d5b46-827c-482e-8813-f0c13efee277)...
1642s nova [W] Timed out waiting for 0a83da19-fed2-4150-a12a-d69eac6967f5 to get deleted.