0s autopkgtest [10:48:27]: starting date and time: 2025-03-13 10:48:27+0000 0s autopkgtest [10:48:27]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [10:48:27]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.40j2z9ju/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-20.secgroup --name adt-plucky-amd64-cctbx-20250313-104827-juju-7f2275-prod-proposed-migration-environment-2-314e3a55-3596-445d-bddb-4b6ab1470d91 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -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/ 52s autopkgtest [10:49:19]: testbed dpkg architecture: amd64 52s autopkgtest [10:49:19]: testbed apt version: 2.9.31ubuntu1 53s autopkgtest [10:49:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup 53s autopkgtest [10:49:20]: testbed release detected to be: None 54s autopkgtest [10:49:21]: updating testbed package index (apt update) 54s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 54s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 54s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 54s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 55s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [396 kB] 55s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [11.5 kB] 55s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [43.9 kB] 55s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [61.3 kB] 55s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [47.7 kB] 55s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [162 kB] 55s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [348 kB] 55s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [3536 B] 55s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [7592 B] 55s Fetched 1192 kB in 1s (1282 kB/s) 56s Reading package lists... 56s Reading package lists... 57s Building dependency tree... 57s Reading state information... 57s Calculating upgrade... 57s Calculating upgrade... 57s The following package was automatically installed and is no longer required: 57s libnl-genl-3-200 57s Use 'sudo apt autoremove' to remove it. 58s The following NEW packages will be installed: 58s libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-7 58s linux-headers-6.14.0-7-generic linux-image-6.14.0-7-generic 58s linux-modules-6.14.0-7-generic linux-modules-extra-6.14.0-7-generic 58s linux-tools-6.14.0-7 linux-tools-6.14.0-7-generic pnp.ids 58s The following packages will be upgraded: 58s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 58s curl dosfstools exfatprogs fwupd gcc-15-base gir1.2-girepository-2.0 58s gir1.2-glib-2.0 htop hwdata initramfs-tools initramfs-tools-bin 58s initramfs-tools-core libapparmor1 libapt-pkg7.0 libassuan9 libatomic1 58s libaudit-common libaudit1 libbinutils libbrotli1 libc-bin libc-dev-bin libc6 58s libc6-dev libcap-ng0 libctf-nobfd0 libctf0 libcurl3t64-gnutls libcurl4t64 58s libestr0 libftdi1-2 libfwupd3 libgcc-s1 libgirepository-1.0-1 58s libglib2.0-0t64 libglib2.0-data libgpgme11t64 libgprofng0 libjemalloc2 58s liblz4-1 liblzma5 libncurses6 libncursesw6 libnewt0.52 libnl-3-200 58s libnl-genl-3-200 libnl-route-3-200 libnss-systemd libpam-systemd 58s libparted2t64 libpci3 libpython3-stdlib libseccomp2 libselinux1 58s libsemanage-common libsemanage2 libsframe1 libsqlite3-0 libstdc++6 58s libsystemd-shared libsystemd0 libtinfo6 libudev1 libxml2 linux-firmware 58s linux-generic linux-headers-generic linux-headers-virtual 58s linux-image-generic linux-image-virtual linux-libc-dev linux-tools-common 58s linux-virtual locales media-types ncurses-base ncurses-bin ncurses-term 58s parted pci.ids pciutils python-apt-common python3 python3-apt python3-bcrypt 58s python3-cffi-backend python3-dbus python3-gi python3-lazr.uri 58s python3-markupsafe python3-minimal python3-newt python3-rpds-py 58s python3-systemd python3-yaml rsync rsyslog systemd systemd-cryptsetup 58s systemd-resolved systemd-sysv systemd-timesyncd ubuntu-kernel-accessories 58s ubuntu-minimal ubuntu-standard udev whiptail xz-utils 58s 114 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 58s Need to get 818 MB of archives. 58s After this operation, 325 MB of additional disk space will be used. 58s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 58s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 58s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 58s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 58s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 59s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 59s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-7.7 [1723 kB] 59s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250222-0ubuntu1 [10.4 kB] 59s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250222-0ubuntu1 [53.4 kB] 59s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250222-0ubuntu1 [77.8 kB] 59s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250222-0ubuntu1 [798 kB] 59s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 59s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 59s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 59s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 59s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.3-1ubuntu3 [595 kB] 59s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.3-1ubuntu3 [199 kB] 59s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.3-1ubuntu3 [11.9 kB] 59s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.3-1ubuntu3 [345 kB] 59s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.3-1ubuntu3 [302 kB] 59s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.3-1ubuntu3 [2371 kB] 59s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.3-1ubuntu3 [3052 kB] 59s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.3-1ubuntu3 [42.1 kB] 59s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.3-1ubuntu3 [124 kB] 59s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.3-1ubuntu3 [1404 kB] 59s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.3-1ubuntu3 [215 kB] 59s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 59s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 59s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 59s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu6 [53.5 kB] 59s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 59s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 59s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.32ubuntu1 [1138 kB] 59s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.32ubuntu1 [1439 kB] 59s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.32ubuntu1 [222 kB] 59s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 59s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 59s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 59s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 59s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 59s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2.1build1 [7268 B] 59s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2.1build1 [106 kB] 59s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 59s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 59s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 59s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.2-2 [43.1 kB] 59s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 59s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 59s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 59s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 59s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 59s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 59s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-newt amd64 0.52.24-4ubuntu2 [21.1 kB] 59s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libnewt0.52 amd64 0.52.24-4ubuntu2 [55.7 kB] 59s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 59s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 59s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 59s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 59s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 59s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 59s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 59s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 59s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 59s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 59s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 whiptail amd64 0.52.24-4ubuntu2 [19.1 kB] 59s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-minimal amd64 1.549 [11.5 kB] 59s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 59s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 59s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 59s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 59s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 59s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 parted amd64 3.6-5 [53.9 kB] 59s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libparted2t64 amd64 3.6-5 [158 kB] 59s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 59s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 59s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 59s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 59s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-standard amd64 1.549 [11.5 kB] 60s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 60s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 60s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 60s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 60s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 60s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 60s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 60s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 60s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 60s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 60s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 60s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 exfatprogs amd64 1.2.8-1 [76.3 kB] 60s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 60s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 60s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 60s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 60s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 60s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 60s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 76s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools all 0.146ubuntu1 [7920 B] 76s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-core all 0.146ubuntu1 [51.9 kB] 76s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-bin amd64 0.146ubuntu1 [26.2 kB] 76s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 76s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libftdi1-2 amd64 1.5-8build1 [30.2 kB] 76s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu2 [155 kB] 76s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 77s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-7-generic amd64 6.14.0-7.7 [41.2 MB] 78s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-7-generic amd64 6.14.0-7.7 [15.3 MB] 78s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-7-generic amd64 6.14.0-7.7 [120 MB] 82s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-7.7+1 [1736 B] 82s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-7.7+1 [11.1 kB] 82s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-7.7+1 [1724 B] 82s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-7.7+1 [11.1 kB] 82s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-7.7+1 [1648 B] 82s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-7 all 6.14.0-7.7 [14.2 MB] 82s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-7-generic amd64 6.14.0-7.7 [3859 kB] 82s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-7.7+1 [11.0 kB] 82s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-7.7 [521 kB] 82s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-7 amd64 6.14.0-7.7 [6147 kB] 83s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-7-generic amd64 6.14.0-7.7 [1612 B] 83s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 83s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 83s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu2 [278 kB] 83s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 83s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-kernel-accessories amd64 1.549 [11.2 kB] 83s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bcrypt amd64 4.2.0-2.1build1 [221 kB] 83s Preconfiguring packages ... 83s Fetched 818 MB in 25s (32.8 MB/s) 83s (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 ... 109140 files and directories currently installed.) 83s Preparing to unpack .../ncurses-bin_6.5+20250216-2_amd64.deb ... 83s Unpacking ncurses-bin (6.5+20250216-2) over (6.5+20250216-1) ... 84s Setting up ncurses-bin (6.5+20250216-2) ... 84s (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 ... 109140 files and directories currently installed.) 84s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_amd64.deb ... 84s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 84s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_amd64.deb ... 84s Unpacking libc6-dev:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 84s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 84s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 84s Preparing to unpack .../libc6_2.41-1ubuntu1_amd64.deb ... 84s Checking for services that may need to be restarted... 84s Checking init scripts... 84s Checking for services that may need to be restarted... 84s Checking init scripts... 84s Stopping some services possibly affected by the upgrade (will be restarted later): 84s cron: stopping...done. 84s 85s Unpacking libc6:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 85s Setting up libc6:amd64 (2.41-1ubuntu1) ... 85s Checking for services that may need to be restarted... 85s Checking init scripts... 85s Restarting services possibly affected by the upgrade: 85s cron: restarting...done. 85s 85s Services restarted successfully. 85s (Reading database ... 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106s Unpacking python3-rpds-py (0.21.0-2ubuntu2) over (0.21.0-2ubuntu1) ... 106s Preparing to unpack .../75-python3-systemd_235-1build6_amd64.deb ... 106s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 106s Preparing to unpack .../76-ubuntu-kernel-accessories_1.549_amd64.deb ... 106s Unpacking ubuntu-kernel-accessories (1.549) over (1.548) ... 106s Preparing to unpack .../77-python3-bcrypt_4.2.0-2.1build1_amd64.deb ... 106s Unpacking python3-bcrypt (4.2.0-2.1build1) over (4.2.0-2.1) ... 106s Setting up media-types (13.0.0) ... 106s Installing new version of config file /etc/mime.types ... 106s Setting up linux-modules-6.14.0-7-generic (6.14.0-7.7) ... 108s Setting up ubuntu-kernel-accessories (1.549) ... 108s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 108s Setting up pci.ids (0.0~2025.03.09-1) ... 108s Setting up libnewt0.52:amd64 (0.52.24-4ubuntu2) ... 108s Setting up apt-utils (2.9.32ubuntu1) ... 108s Setting up libdebuginfod-common (0.192-4) ... 108s Setting up exfatprogs (1.2.8-1) ... 108s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 108s Setting up libestr0:amd64 (0.1.11-2) ... 108s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 108s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 108s Setting up dosfstools (4.2-1.2) ... 108s Setting up rsyslog (8.2412.0-2ubuntu2) ... 108s info: The user `syslog' is already a member of `adm'. 109s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 109s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 109s Setting up linux-libc-dev:amd64 (6.14.0-7.7) ... 109s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 109s Setting up systemd (257.3-1ubuntu3) ... 109s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 109s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 110s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 110s Setting up libparted2t64:amd64 (3.6-5) ... 110s Removing 'diversion of 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Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 122s Setting up curl (8.12.1-3ubuntu1) ... 122s Setting up initramfs-tools-core (0.146ubuntu1) ... 122s Setting up linux-tools-common (6.14.0-7.7) ... 122s Setting up python3-systemd (235-1build6) ... 123s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 123s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 123s Setting up python3-dbus (1.3.2-5build5) ... 123s Setting up initramfs-tools (0.146ubuntu1) ... 123s Installing new version of config file /etc/kernel/postinst.d/initramfs-tools ... 123s Installing new version of config file /etc/kernel/postrm.d/initramfs-tools ... 123s update-initramfs: deferring update (trigger activated) 123s Setting up linux-headers-virtual (6.14.0-7.7+1) ... 123s Setting up linux-generic (6.14.0-7.7+1) ... 123s Setting up ubuntu-minimal (1.549) ... 123s Setting up python3-apt (2.9.9build1) ... 123s Setting up python3-bcrypt (4.2.0-2.1build1) ... 123s Setting up python3-yaml (6.0.2-1build2) ... 123s Setting up libfwupd3:amd64 (2.0.6-4) ... 123s Setting up python3-lazr.uri (1.0.6-6) ... 123s Setting up binutils (2.44-3ubuntu1) ... 123s Setting up ubuntu-standard (1.549) ... 123s Setting up linux-virtual (6.14.0-7.7+1) ... 123s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 123s Setting up python3-gi (3.50.0-4build1) ... 123s Setting up linux-tools-6.14.0-7 (6.14.0-7.7) ... 123s Setting up linux-tools-6.14.0-7-generic (6.14.0-7.7) ... 123s Setting up fwupd (2.0.6-4) ... 124s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 124s fwupd.service is a disabled or a static unit not running, not starting it. 124s Processing triggers for man-db (2.13.0-1) ... 126s Processing triggers for dbus (1.16.2-1ubuntu1) ... 126s Processing triggers for shared-mime-info (2.4-5) ... 126s Warning: program compiled against libxml 212 using older 209 126s Processing triggers for libc-bin (2.41-1ubuntu1) ... 126s Processing triggers for linux-image-6.14.0-7-generic (6.14.0-7.7) ... 126s /etc/kernel/postinst.d/initramfs-tools: 126s update-initramfs: Generating /boot/initrd.img-6.14.0-7-generic 126s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 137s /etc/kernel/postinst.d/zz-update-grub: 137s Sourcing file `/etc/default/grub' 137s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 137s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 137s Generating grub configuration file ... 137s Found linux image: /boot/vmlinuz-6.14.0-7-generic 137s Found initrd image: /boot/initrd.img-6.14.0-7-generic 137s Found linux image: /boot/vmlinuz-6.12.0-16-generic 137s Found initrd image: /boot/initrd.img-6.12.0-16-generic 137s Found linux image: /boot/vmlinuz-6.11.0-8-generic 137s Found initrd image: /boot/initrd.img-6.11.0-8-generic 137s Warning: os-prober will not be executed to detect other bootable partitions. 137s Systems on them will not be added to the GRUB boot configuration. 137s Check GRUB_DISABLE_OS_PROBER documentation entry. 137s Adding boot menu entry for UEFI Firmware Settings ... 137s done 137s Processing triggers for initramfs-tools (0.146ubuntu1) ... 137s update-initramfs: Generating /boot/initrd.img-6.14.0-7-generic 137s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s Solving dependencies... 149s The following packages will be REMOVED: 149s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 149s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 149s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 149s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 150s 0 upgraded, 0 newly installed, 11 to remove and 0 not upgraded. 150s After this operation, 225 MB disk space will be freed. 150s (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 ... 148650 files and directories currently installed.) 150s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 150s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 150s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 150s Removing libpython3.12t64:amd64 (3.12.9-1) ... 150s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 150s Removing libnsl2:amd64 (1.3.0-3build3) ... 150s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 150s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 151s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 153s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 153s /etc/kernel/postrm.d/initramfs-tools: 153s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 154s /etc/kernel/postrm.d/zz-update-grub: 154s Sourcing file `/etc/default/grub' 154s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 154s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 154s Generating grub configuration file ... 154s Found linux image: /boot/vmlinuz-6.14.0-7-generic 154s Found initrd image: /boot/initrd.img-6.14.0-7-generic 154s Found linux image: /boot/vmlinuz-6.12.0-16-generic 154s Found initrd image: /boot/initrd.img-6.12.0-16-generic 154s Warning: os-prober will not be executed to detect other bootable partitions. 154s Systems on them will not be added to the GRUB boot configuration. 154s Check GRUB_DISABLE_OS_PROBER documentation entry. 154s Adding boot menu entry for UEFI Firmware Settings ... 154s done 154s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 154s Processing triggers for libc-bin (2.41-1ubuntu1) ... 154s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 115819 files and directories currently installed.) 154s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 154s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 154s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 155s autopkgtest [10:51:02]: upgrading testbed (apt dist-upgrade and autopurge) 155s Reading package lists... 155s Building dependency tree... 155s Reading state information... 156s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 156s Starting 2 pkgProblemResolver with broken count: 0 156s Done 156s Entering ResolveByKeep 156s 156s Calculating upgrade... 157s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 157s Starting pkgProblemResolver with broken count: 0 157s Starting 2 pkgProblemResolver with broken count: 0 157s Done 158s Solving dependencies... 158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 158s autopkgtest [10:51:05]: rebooting testbed after setup commands that affected boot 182s autopkgtest [10:51:29]: testbed running kernel: Linux 6.14.0-7-generic #7-Ubuntu SMP PREEMPT_DYNAMIC Fri Feb 28 12:14:20 UTC 2025 185s autopkgtest [10:51:32]: @@@@@@@@@@@@@@@@@@@@ apt-source cctbx 206s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe cctbx 2024.10+ds2+~3.22.1+ds1-4build2 (dsc) [4106 B] 206s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe cctbx 2024.10+ds2+~3.22.1+ds1-4build2 (tar) [378 kB] 206s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe cctbx 2024.10+ds2+~3.22.1+ds1-4build2 (tar) [23.9 MB] 206s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe cctbx 2024.10+ds2+~3.22.1+ds1-4build2 (diff) [418 kB] 206s gpgv: Signature made Tue Mar 4 14:45:06 2025 UTC 206s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 206s gpgv: Can't check signature: No public key 206s dpkg-source: warning: cannot verify inline signature for ./cctbx_2024.10+ds2+~3.22.1+ds1-4build2.dsc: no acceptable signature found 208s autopkgtest [10:51:55]: testing package cctbx version 2024.10+ds2+~3.22.1+ds1-4build2 210s autopkgtest [10:51:57]: build not needed 219s autopkgtest [10:52:06]: test cctbx: preparing testbed 219s Reading package lists... 219s Building dependency tree... 219s Reading state information... 219s Starting pkgProblemResolver with broken count: 0 219s Starting 2 pkgProblemResolver with broken count: 0 219s Done 220s The following NEW packages will be installed: 220s adwaita-icon-theme at-spi2-common blt cpp cpp-14 cpp-14-x86-64-linux-gnu 220s cpp-x86-64-linux-gnu dconf-gsettings-backend dconf-service fontconfig 220s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 220s fonts-lato fonts-lyx g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu 220s gcc gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu 220s gtk-update-icon-cache hicolor-icon-theme libaec0 libann-cctbx-dev 220s libann-cctbx0 libantlr3c-3.4-0 libasan8 libatk-bridge2.0-0t64 libatk1.0-0t64 220s libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 220s libblas3 libboost-numpy1.83.0 libboost-python-dev libboost-python1.83-dev 220s libboost-python1.83.0 libboost-thread1.83.0 libboost-timer1.83.0 220s libboost1.83-dev libcairo-gobject2 libcairo2 libcbf1t64 libcc1-0 220s libccp4-data libccp4-dev libccp4c0t64 libccp4f0t64 libcctbx-dev libcctbx0 220s libcolord2 libcups2t64 libdatrie1 libdconf1 libdeflate0 220s libdouble-conversion3 libdrm-intel1 libegl-mesa0 libegl1 libepoxy0 220s libexpat1-dev libfontconfig1 libgbm1 libgcc-14-dev libgdk-pixbuf-2.0-0 220s libgdk-pixbuf2.0-common libgfortran5 libgl1 libgl1-mesa-dri libglew2.2 220s libglu1-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 220s libgtk-3-0t64 libgtk-3-common libharfbuzz0b libhdf5-310 libhdf5-hl-310 220s libhwasan0 libice6 libimagequant0 libinput-bin libinput10 libisl23 libitm1 220s libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 220s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 liblerc4 220s liblsan0 liblzf1 libmd4c0 libmmdb2-0 libmpc3 libmtdev1t64 libnetcdf22 220s libnotify4 libopengl0 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 220s libpangoft2-1.0-0 libpciaccess0 libpcre2-16-0 libpcre2-32-0 libpixman-1-0 220s libpython3-dev libpython3.13-dev libqhull-r8.0 libqt5core5t64 libqt5dbus5t64 220s libqt5designer5 libqt5gui5t64 libqt5help5 libqt5network5t64 libqt5opengl5t64 220s libqt5printsupport5t64 libqt5sql5t64 libqt5test5t64 libqt5widgets5t64 220s libqt5xml5t64 libquadmath0 libraqm0 libsharpyuv0 libsm6 libssm2 220s libstdc++-14-dev libsz2 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 220s libtsan2 libubsan1 libvulkan1 libwacom-common libwacom9 libwayland-client0 220s libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 220s libwebpmux3 libwxbase3.2-1t64 libwxgtk-gl3.2-1t64 libwxgtk3.2-1t64 220s libx11-xcb1 libxcb-dri3-0 libxcb-glx0 libxcb-icccm4 libxcb-image0 220s libxcb-keysyms1 libxcb-present0 libxcb-randr0 libxcb-render-util0 220s libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-util1 220s libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxcomposite1 220s libxcursor1 libxdamage1 libxfixes3 libxft2 libxi6 libxinerama1 220s libxkbcommon-x11-0 libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1 220s libxtst6 libxxf86vm1 mesa-libgallium pymol-data python-matplotlib-data 220s python3-all python3-brotli python3-cctbx python3-contourpy python3-cycler 220s python3-dateutil python3-decorator python3-dev python3-flexcache 220s python3-flexparser python3-fonttools python3-fs python3-h5py 220s python3-h5py-serial python3-hdf5plugin python3-iniconfig python3-kiwisolver 220s python3-legacy-cgi python3-lxml python3-lz4 python3-matplotlib 220s python3-mpmath python3-mrcfile python3-natsort python3-numpy 220s python3-numpy-dev python3-nxmx python3-opengl python3-ordered-set 220s python3-packaging python3-pil python3-pil.imagetk python3-pint 220s python3-platformdirs python3-pluggy python3-procrunner python3-pycbf 220s python3-pymol python3-pyqt5 python3-pyqt5.qtopengl python3-pyqt5.sip 220s python3-pytest python3-scipy python3-six python3-sympy python3-tk 220s python3-tqdm python3-ufolib2 python3-wxgtk4.0 python3.12-tk python3.13-dev 220s python3.13-tk sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data x11-common 220s zlib1g-dev 220s 0 upgraded, 256 newly installed, 0 to remove and 0 not upgraded. 220s Need to get 262 MB of archives. 220s After this operation, 1200 MB of additional disk space will be used. 220s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-lato all 2.015-1 [2781 kB] 223s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-4 [148 kB] 223s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 223s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB] 224s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 226s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:2.2.3+ds-4 [5702 kB] 229s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [8004 B] 229s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 229s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 229s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 229s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 229s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 229s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 229s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 229s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 229s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [161 kB] 229s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 gtk-update-icon-cache amd64 4.17.5+ds-3ubuntu1 [54.0 kB] 229s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 hicolor-icon-theme all 0.18-2 [13.3 kB] 229s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 adwaita-icon-theme all 48~beta-3 [578 kB] 229s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 at-spi2-common all 2.55.90-1 [9072 B] 229s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 230s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 230s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 230s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 230s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 230s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 230s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 230s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 230s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 230s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 231s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [694 kB] 231s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-8 [4824 B] 231s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 231s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 231s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [11.9 MB] 233s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-17ubuntu3 [1030 B] 233s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B] 233s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB] 233s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libdconf1 amd64 0.40.0-5 [39.8 kB] 233s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 dconf-service amd64 0.40.0-5 [28.4 kB] 233s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [22.7 kB] 233s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB] 233s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 233s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.3-1 [171 kB] 233s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 15-20250222-0ubuntu1 [47.0 kB] 233s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 233s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 15-20250222-0ubuntu1 [28.6 kB] 233s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 15-20250222-0ubuntu1 [3055 kB] 234s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 15-20250222-0ubuntu1 [1355 kB] 234s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 15-20250222-0ubuntu1 [2756 kB] 234s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 15-20250222-0ubuntu1 [1205 kB] 234s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 15-20250222-0ubuntu1 [1677 kB] 234s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 15-20250222-0ubuntu1 [152 kB] 234s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-17ubuntu3 [2816 kB] 235s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [23.3 MB] 236s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-17ubuntu3 [536 kB] 236s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B] 236s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B] 236s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-17ubuntu3 [2486 kB] 236s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [13.4 MB] 237s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-17ubuntu3 [21.8 kB] 237s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B] 237s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B] 237s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 237s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 libann-cctbx0 amd64 1.1.2+doc-9build1 [32.7 kB] 237s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 libann-cctbx-dev amd64 1.1.2+doc-9build1 [45.1 kB] 237s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 libantlr3c-3.4-0 amd64 3.4+dfsg-4build2 [44.9 kB] 237s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libatk1.0-0t64 amd64 2.55.90-1 [55.3 kB] 237s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libxi6 amd64 2:1.8.2-1 [32.4 kB] 237s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libatspi2.0-0t64 amd64 2.55.90-1 [91.1 kB] 237s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libatk-bridge2.0-0t64 amd64 2.55.90-1 [69.0 kB] 237s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common-data amd64 0.8-16ubuntu1 [30.9 kB] 237s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common3 amd64 0.8-16ubuntu1 [23.6 kB] 237s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-client3 amd64 0.8-16ubuntu1 [27.5 kB] 237s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-python1.83.0 amd64 1.83.0-4.1ubuntu1 [325 kB] 237s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 libboost-numpy1.83.0 amd64 1.83.0-4.1ubuntu1 [242 kB] 237s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost1.83-dev amd64 1.83.0-4.1ubuntu1 [10.7 MB] 238s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1-dev amd64 2.6.4-1 [148 kB] 238s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 238s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-dev amd64 3.13.2-1 [5501 kB] 238s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-dev amd64 3.13.2-2 [10.7 kB] 238s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-dev amd64 3.13.2-1 [508 kB] 238s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 239s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 239s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 8.1.3-4 [30.9 kB] 239s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dev amd64 3.13.2-2 [26.7 kB] 239s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 libboost-python1.83-dev amd64 1.83.0-4.1ubuntu1 [338 kB] 239s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 libboost-python-dev amd64 1.83.0.2ubuntu1 [4516 B] 239s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-thread1.83.0 amd64 1.83.0-4.1ubuntu1 [278 kB] 239s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 libboost-timer1.83.0 amd64 1.83.0-4.1ubuntu1 [241 kB] 239s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 239s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 239s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 239s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 239s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo-gobject2 amd64 1.18.2-2 [127 kB] 239s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 239s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-310 amd64 1.14.5+repack-3 [1519 kB] 239s Get:98 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcbf1t64 amd64 0.9.7+dfsg1-5build1 [361 kB] 239s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccp4-data all 8.0.0-4 [65.2 kB] 239s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccp4c0t64 amd64 8.0.0-4 [104 kB] 239s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmmdb2-0 amd64 2.0.22-1 [363 kB] 239s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccp4f0t64 amd64 8.0.0-4 [228 kB] 239s Get:103 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccp4-dev amd64 8.0.0-4 [42.4 kB] 239s Get:104 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libcctbx0 amd64 2024.10+ds2+~3.22.1+ds1-4build2 [2077 kB] 240s Get:105 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libcctbx-dev amd64 2024.10+ds2+~3.22.1+ds1-4build2 [1192 kB] 240s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 240s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libcolord2 amd64 1.4.7-3 [155 kB] 240s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 libcups2t64 amd64 2.4.11-0ubuntu2 [292 kB] 240s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 240s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 libdouble-conversion3 amd64 3.3.1-1 [41.7 kB] 240s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 240s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 libdrm-intel1 amd64 2.4.123-1 [68.8 kB] 240s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-server0 amd64 1.23.1-3 [37.2 kB] 240s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [7944 B] 240s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-dri3-0 amd64 1.17.0-2 [7508 B] 240s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-present0 amd64 1.17.0-2 [6064 B] 240s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-randr0 amd64 1.17.0-2 [17.9 kB] 240s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-sync1 amd64 1.17.0-2 [9312 B] 240s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xfixes0 amd64 1.17.0-2 [10.2 kB] 240s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 libxshmfence1 amd64 1.3-1build5 [4764 B] 240s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 mesa-libgallium amd64 25.0.1-2ubuntu1 [12.1 MB] 241s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 libgbm1 amd64 25.0.1-2ubuntu1 [33.4 kB] 241s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-client0 amd64 1.23.1-3 [29.7 kB] 241s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 libegl-mesa0 amd64 25.0.1-2ubuntu1 [136 kB] 241s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 libepoxy0 amd64 1.5.10-2 [218 kB] 241s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 libvulkan1 amd64 1.4.304.0-1 [147 kB] 241s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 libgl1-mesa-dri amd64 25.0.1-2ubuntu1 [35.7 kB] 241s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 libglvnd0 amd64 1.7.0-1build1 [69.6 kB] 241s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-glx0 amd64 1.17.0-2 [24.8 kB] 241s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 libxxf86vm1 amd64 1:1.1.4-1build4 [9282 B] 241s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 libglx-mesa0 amd64 25.0.1-2ubuntu1 [146 kB] 241s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 libglx0 amd64 1.7.0-1build1 [38.6 kB] 241s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 libgl1 amd64 1.7.0-1build1 [102 kB] 241s Get:134 http://ftpmaster.internal/ubuntu plucky/universe amd64 libglew2.2 amd64 2.2.0-4build1 [187 kB] 241s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 241s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 241s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 241s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 241s Get:139 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.1-1 [255 kB] 241s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [52.6 kB] 241s Get:141 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [29.1 kB] 241s Get:142 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-cursor0 amd64 1.23.1-3 [10.9 kB] 241s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-egl1 amd64 1.23.1-3 [6168 B] 241s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcomposite1 amd64 1:0.4.6-1 [6642 B] 241s Get:145 http://ftpmaster.internal/ubuntu plucky/main amd64 libxfixes3 amd64 1:6.0.0-2build1 [10.8 kB] 241s Get:146 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcursor1 amd64 1:1.2.3-1 [23.1 kB] 241s Get:147 http://ftpmaster.internal/ubuntu plucky/main amd64 libxdamage1 amd64 1:1.1.6-1build1 [6150 B] 241s Get:148 http://ftpmaster.internal/ubuntu plucky/main amd64 libxinerama1 amd64 2:1.1.4-3build1 [6396 B] 241s Get:149 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrandr2 amd64 2:1.5.4-1 [19.6 kB] 241s Get:150 http://ftpmaster.internal/ubuntu plucky/main amd64 libgtk-3-common all 3.24.48-3ubuntu1 [1424 kB] 241s Get:151 http://ftpmaster.internal/ubuntu plucky/main amd64 libgtk-3-0t64 amd64 3.24.48-3ubuntu1 [3169 kB] 241s Get:152 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [62.6 kB] 242s Get:153 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 242s Get:154 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 242s Get:155 http://ftpmaster.internal/ubuntu plucky/main amd64 libwacom-common all 2.14.0-1 [103 kB] 242s Get:156 http://ftpmaster.internal/ubuntu plucky/main amd64 libwacom9 amd64 2.14.0-1 [27.3 kB] 242s Get:157 http://ftpmaster.internal/ubuntu plucky/main amd64 libinput-bin amd64 1.27.1-1 [23.4 kB] 242s Get:158 http://ftpmaster.internal/ubuntu plucky/main amd64 libmtdev1t64 amd64 1.1.7-1 [16.3 kB] 242s Get:159 http://ftpmaster.internal/ubuntu plucky/main amd64 libinput10 amd64 1.27.1-1 [155 kB] 242s Get:160 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 242s Get:161 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 242s Get:162 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 242s Get:163 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmd4c0 amd64 0.5.2-2 [50.1 kB] 242s Get:164 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnetcdf22 amd64 1:4.9.3-1 [574 kB] 242s Get:165 http://ftpmaster.internal/ubuntu plucky/main amd64 libnotify4 amd64 0.8.4-1 [26.9 kB] 242s Get:166 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-16-0 amd64 10.45-1 [268 kB] 242s Get:167 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-32-0 amd64 10.45-1 [251 kB] 242s Get:168 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 242s Get:169 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5core5t64 amd64 5.15.15+dfsg-4ubuntu1 [2038 kB] 242s Get:170 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5dbus5t64 amd64 5.15.15+dfsg-4ubuntu1 [221 kB] 242s Get:171 http://ftpmaster.internal/ubuntu plucky/main amd64 libegl1 amd64 1.7.0-1build1 [28.7 kB] 242s Get:172 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5network5t64 amd64 5.15.15+dfsg-4ubuntu1 [725 kB] 242s Get:173 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 242s Get:174 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-icccm4 amd64 0.4.2-1 [11.1 kB] 242s Get:175 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-util1 amd64 0.4.1-1 [11.2 kB] 242s Get:176 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-image0 amd64 0.4.0-2build1 [10.8 kB] 242s Get:177 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-keysyms1 amd64 0.4.1-1 [8738 B] 242s Get:178 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render-util0 amd64 0.3.10-1 [10.8 kB] 242s Get:179 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shape0 amd64 1.17.0-2 [6092 B] 242s Get:180 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xinerama0 amd64 1.17.0-2 [5412 B] 242s Get:181 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xinput0 amd64 1.17.0-2 [33.2 kB] 242s Get:182 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xkb1 amd64 1.17.0-2 [32.3 kB] 242s Get:183 http://ftpmaster.internal/ubuntu plucky/main amd64 libxkbcommon-x11-0 amd64 1.7.0-2 [15.2 kB] 242s Get:184 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5gui5t64 amd64 5.15.15+dfsg-4ubuntu1 [3791 kB] 242s Get:185 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5widgets5t64 amd64 5.15.15+dfsg-4ubuntu1 [2560 kB] 242s Get:186 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5xml5t64 amd64 5.15.15+dfsg-4ubuntu1 [124 kB] 242s Get:187 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5designer5 amd64 5.15.15-6build1 [2827 kB] 243s Get:188 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5sql5t64 amd64 5.15.15+dfsg-4ubuntu1 [122 kB] 243s Get:189 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5help5 amd64 5.15.15-6build1 [162 kB] 243s Get:190 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5opengl5t64 amd64 5.15.15+dfsg-4ubuntu1 [150 kB] 243s Get:191 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5printsupport5t64 amd64 5.15.15+dfsg-4ubuntu1 [208 kB] 243s Get:192 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5test5t64 amd64 5.15.15+dfsg-4ubuntu1 [149 kB] 243s Get:193 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 243s Get:194 http://ftpmaster.internal/ubuntu plucky/universe amd64 libssm2 amd64 1.4.0-2build1 [87.7 kB] 243s Get:195 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 243s Get:196 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 243s Get:197 http://ftpmaster.internal/ubuntu plucky/universe amd64 libwxbase3.2-1t64 amd64 3.2.6+dfsg-2ubuntu1 [980 kB] 243s Get:198 http://ftpmaster.internal/ubuntu plucky/main amd64 libxtst6 amd64 2:1.2.5-1 [13.0 kB] 243s Get:199 http://ftpmaster.internal/ubuntu plucky/universe amd64 libwxgtk3.2-1t64 amd64 3.2.6+dfsg-2ubuntu1 [4967 kB] 243s Get:200 http://ftpmaster.internal/ubuntu plucky/universe amd64 libwxgtk-gl3.2-1t64 amd64 3.2.6+dfsg-2ubuntu1 [53.9 kB] 243s Get:201 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu2 [175 kB] 243s Get:202 http://ftpmaster.internal/ubuntu plucky/universe amd64 pymol-data all 3.0.0+dfsg-3build2 [1394 kB] 243s Get:203 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-7build1 [2934 kB] 243s Get:204 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.13.2-2 [884 B] 243s Get:205 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build4 [367 kB] 243s Get:206 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-legacy-cgi all 2.6.2-1 [16.6 kB] 243s Get:207 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pycbf amd64 0.9.7+dfsg1-5build1 [166 kB] 243s Get:208 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py-serial amd64 3.13.0-1 [1230 kB] 243s Get:209 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py all 3.13.0-1 [7978 B] 243s Get:210 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-hdf5plugin all 5.0.0-1 [23.1 kB] 243s Get:211 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 243s Get:212 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu3 [217 kB] 243s Get:213 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 11.1.0-5build1 [583 kB] 243s Get:214 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.9-1 [116 kB] 243s Get:215 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.2-1 [107 kB] 243s Get:216 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.13.1-1 [9770 B] 243s Get:217 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 11.1.0-5build1 [9828 B] 243s Get:218 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.1-1build1 [218 kB] 243s Get:219 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 243s Get:220 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-platformdirs all 4.3.6-1 [16.8 kB] 243s Get:221 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-7 [90.8 kB] 243s Get:222 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.1-1build1 [1408 kB] 243s Get:223 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.4.0+dfsg-1build1 [27.0 kB] 243s Get:224 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 243s Get:225 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.14.1-4ubuntu2 [18.7 MB] 244s Get:226 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 244s Get:227 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-5 [4229 kB] 245s Get:228 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 245s Get:229 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 245s Get:230 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.55.3-2build1 [1536 kB] 245s Get:231 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-3build1 [55.6 kB] 245s Get:232 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 245s Get:233 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-7build1 [17.4 MB] 246s Get:234 http://ftpmaster.internal/ubuntu plucky/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 246s Get:235 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mrcfile all 1.5.4-2 [116 kB] 246s Get:236 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-natsort all 8.0.2-2 [33.8 kB] 246s Get:237 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-flexcache all 0.3-2 [13.4 kB] 246s Get:238 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-flexparser all 0.4-1 [43.8 kB] 246s Get:239 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pint all 0.24.4-1 [203 kB] 246s Get:240 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-nxmx all 0.0.4-1 [16.4 kB] 246s Get:241 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ordered-set all 4.1.0-1 [9778 B] 246s Get:242 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-procrunner all 2.3.3-2 [12.0 kB] 246s Get:243 http://ftpmaster.internal/ubuntu plucky/main amd64 libopengl0 amd64 1.7.0-1build1 [32.8 kB] 246s Get:244 http://ftpmaster.internal/ubuntu plucky/main amd64 libglu1-mesa amd64 9.0.2-1.1build1 [152 kB] 246s Get:245 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-opengl all 3.1.7+dfsg-1 [612 kB] 246s Get:246 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyqt5.sip amd64 12.17.0-1build1 [76.5 kB] 246s Get:247 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyqt5 amd64 5.15.11+dfsg-2 [2725 kB] 246s Get:248 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyqt5.qtopengl amd64 5.15.11+dfsg-2 [128 kB] 246s Get:249 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pymol amd64 3.0.0+dfsg-3build2 [4131 kB] 246s Get:250 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.17.0-1 [13.2 kB] 246s Get:251 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-tqdm all 4.67.1-2 [92.5 kB] 246s Get:252 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-wxgtk4.0 amd64 4.2.2+dfsg-3build1 [7838 kB] 247s Get:253 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-cctbx amd64 2024.10+ds2+~3.22.1+ds1-4build2 [29.0 MB] 249s Get:254 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 249s Get:255 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 249s Get:256 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.4-1 [252 kB] 250s Fetched 262 MB in 29s (9078 kB/s) 250s Selecting previously unselected package fonts-lato. 250s (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 ... 115816 files and directories currently installed.) 250s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ... 250s Unpacking fonts-lato (2.015-1) ... 250s Selecting previously unselected package python3-numpy-dev:amd64. 250s Preparing to unpack .../001-python3-numpy-dev_1%3a2.2.3+ds-4_amd64.deb ... 250s Unpacking python3-numpy-dev:amd64 (1:2.2.3+ds-4) ... 250s Selecting previously unselected package libblas3:amd64. 250s Preparing to unpack .../002-libblas3_3.12.1-2_amd64.deb ... 250s Unpacking libblas3:amd64 (3.12.1-2) ... 250s Selecting previously unselected package libgfortran5:amd64. 250s Preparing to unpack .../003-libgfortran5_15-20250222-0ubuntu1_amd64.deb ... 250s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ... 250s Selecting previously unselected package liblapack3:amd64. 250s Preparing to unpack .../004-liblapack3_3.12.1-2_amd64.deb ... 250s Unpacking liblapack3:amd64 (3.12.1-2) ... 250s Selecting previously unselected package python3-numpy. 250s Preparing to unpack .../005-python3-numpy_1%3a2.2.3+ds-4_amd64.deb ... 250s Unpacking python3-numpy (1:2.2.3+ds-4) ... 251s Selecting previously unselected package libgdk-pixbuf2.0-common. 251s Preparing to unpack .../006-libgdk-pixbuf2.0-common_2.42.12+dfsg-2_all.deb ... 251s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... 251s Selecting previously unselected package libjpeg-turbo8:amd64. 251s Preparing to unpack .../007-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 251s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 251s Selecting previously unselected package libjpeg8:amd64. 251s Preparing to unpack .../008-libjpeg8_8c-2ubuntu11_amd64.deb ... 251s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 251s Selecting previously unselected package libdeflate0:amd64. 251s Preparing to unpack .../009-libdeflate0_1.23-1_amd64.deb ... 251s Unpacking libdeflate0:amd64 (1.23-1) ... 251s Selecting previously unselected package libjbig0:amd64. 251s Preparing to unpack .../010-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 251s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 251s Selecting previously unselected package liblerc4:amd64. 251s Preparing to unpack .../011-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 251s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 251s Selecting previously unselected package libsharpyuv0:amd64. 251s Preparing to unpack .../012-libsharpyuv0_1.5.0-0.1_amd64.deb ... 251s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 251s Selecting previously unselected package libwebp7:amd64. 251s Preparing to unpack .../013-libwebp7_1.5.0-0.1_amd64.deb ... 251s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 251s Selecting previously unselected package libtiff6:amd64. 251s Preparing to unpack .../014-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 251s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 251s Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. 251s Preparing to unpack .../015-libgdk-pixbuf-2.0-0_2.42.12+dfsg-2_amd64.deb ... 251s Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... 251s Selecting previously unselected package gtk-update-icon-cache. 251s Preparing to unpack .../016-gtk-update-icon-cache_4.17.5+ds-3ubuntu1_amd64.deb ... 251s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 251s 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. 251s Unpacking gtk-update-icon-cache (4.17.5+ds-3ubuntu1) ... 251s Selecting previously unselected package hicolor-icon-theme. 251s Preparing to unpack .../017-hicolor-icon-theme_0.18-2_all.deb ... 251s Unpacking hicolor-icon-theme (0.18-2) ... 251s Selecting previously unselected package adwaita-icon-theme. 251s Preparing to unpack .../018-adwaita-icon-theme_48~beta-3_all.deb ... 251s Unpacking adwaita-icon-theme (48~beta-3) ... 251s Selecting previously unselected package at-spi2-common. 251s Preparing to unpack .../019-at-spi2-common_2.55.90-1_all.deb ... 251s Unpacking at-spi2-common (2.55.90-1) ... 251s Selecting previously unselected package libtcl8.6:amd64. 251s Preparing to unpack .../020-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 251s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 252s Selecting previously unselected package fonts-dejavu-mono. 252s Preparing to unpack .../021-fonts-dejavu-mono_2.37-8_all.deb ... 252s Unpacking fonts-dejavu-mono (2.37-8) ... 252s Selecting previously unselected package fonts-dejavu-core. 252s Preparing to unpack .../022-fonts-dejavu-core_2.37-8_all.deb ... 252s Unpacking fonts-dejavu-core (2.37-8) ... 252s Selecting previously unselected package fontconfig-config. 252s Preparing to unpack .../023-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 252s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 252s Selecting previously unselected package libfontconfig1:amd64. 252s Preparing to unpack .../024-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 252s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 252s Selecting previously unselected package libxrender1:amd64. 252s Preparing to unpack .../025-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 252s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 252s Selecting previously unselected package libxft2:amd64. 252s Preparing to unpack .../026-libxft2_2.3.6-1build1_amd64.deb ... 252s Unpacking libxft2:amd64 (2.3.6-1build1) ... 252s Selecting previously unselected package x11-common. 252s Preparing to unpack .../027-x11-common_1%3a7.7+23ubuntu3_all.deb ... 252s Unpacking x11-common (1:7.7+23ubuntu3) ... 252s Selecting previously unselected package libxss1:amd64. 252s Preparing to unpack .../028-libxss1_1%3a1.2.3-1build3_amd64.deb ... 252s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 252s Selecting previously unselected package libtk8.6:amd64. 252s Preparing to unpack .../029-libtk8.6_8.6.16-1_amd64.deb ... 252s Unpacking libtk8.6:amd64 (8.6.16-1) ... 252s Selecting previously unselected package tk8.6-blt2.5. 252s Preparing to unpack .../030-tk8.6-blt2.5_2.5.3+dfsg-8_amd64.deb ... 252s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 252s Selecting previously unselected package blt. 252s Preparing to unpack .../031-blt_2.5.3+dfsg-8_amd64.deb ... 252s Unpacking blt (2.5.3+dfsg-8) ... 252s Selecting previously unselected package libisl23:amd64. 252s Preparing to unpack .../032-libisl23_0.27-1_amd64.deb ... 252s Unpacking libisl23:amd64 (0.27-1) ... 252s Selecting previously unselected package libmpc3:amd64. 252s Preparing to unpack .../033-libmpc3_1.3.1-1build2_amd64.deb ... 252s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 252s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 252s Preparing to unpack .../034-cpp-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 252s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 253s Selecting previously unselected package cpp-14. 253s Preparing to unpack .../035-cpp-14_14.2.0-17ubuntu3_amd64.deb ... 253s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 253s Selecting previously unselected package cpp-x86-64-linux-gnu. 253s Preparing to unpack .../036-cpp-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 253s Unpacking cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 253s Selecting previously unselected package cpp. 253s Preparing to unpack .../037-cpp_4%3a14.2.0-1ubuntu1_amd64.deb ... 253s Unpacking cpp (4:14.2.0-1ubuntu1) ... 253s Selecting previously unselected package libdconf1:amd64. 253s Preparing to unpack .../038-libdconf1_0.40.0-5_amd64.deb ... 253s Unpacking libdconf1:amd64 (0.40.0-5) ... 253s Selecting previously unselected package dconf-service. 253s Preparing to unpack .../039-dconf-service_0.40.0-5_amd64.deb ... 253s Unpacking dconf-service (0.40.0-5) ... 253s Selecting previously unselected package dconf-gsettings-backend:amd64. 253s Preparing to unpack .../040-dconf-gsettings-backend_0.40.0-5_amd64.deb ... 253s Unpacking dconf-gsettings-backend:amd64 (0.40.0-5) ... 253s Selecting previously unselected package fontconfig. 253s Preparing to unpack .../041-fontconfig_2.15.0-2ubuntu1_amd64.deb ... 253s Unpacking fontconfig (2.15.0-2ubuntu1) ... 253s Selecting previously unselected package fonts-font-awesome. 253s Preparing to unpack .../042-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 253s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 253s Selecting previously unselected package fonts-lyx. 253s Preparing to unpack .../043-fonts-lyx_2.4.3-1_all.deb ... 253s Unpacking fonts-lyx (2.4.3-1) ... 253s Selecting previously unselected package libcc1-0:amd64. 253s Preparing to unpack .../044-libcc1-0_15-20250222-0ubuntu1_amd64.deb ... 253s Unpacking libcc1-0:amd64 (15-20250222-0ubuntu1) ... 253s Selecting previously unselected package libgomp1:amd64. 253s Preparing to unpack .../045-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 253s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 253s Selecting previously unselected package libitm1:amd64. 253s Preparing to unpack .../046-libitm1_15-20250222-0ubuntu1_amd64.deb ... 253s Unpacking libitm1:amd64 (15-20250222-0ubuntu1) ... 253s Selecting previously unselected package libasan8:amd64. 253s Preparing to unpack .../047-libasan8_15-20250222-0ubuntu1_amd64.deb ... 253s Unpacking libasan8:amd64 (15-20250222-0ubuntu1) ... 253s Selecting previously unselected package liblsan0:amd64. 253s Preparing to unpack .../048-liblsan0_15-20250222-0ubuntu1_amd64.deb ... 253s Unpacking liblsan0:amd64 (15-20250222-0ubuntu1) ... 253s Selecting previously unselected package libtsan2:amd64. 253s Preparing to unpack .../049-libtsan2_15-20250222-0ubuntu1_amd64.deb ... 253s Unpacking libtsan2:amd64 (15-20250222-0ubuntu1) ... 253s Selecting previously unselected package libubsan1:amd64. 253s Preparing to unpack .../050-libubsan1_15-20250222-0ubuntu1_amd64.deb ... 253s Unpacking libubsan1:amd64 (15-20250222-0ubuntu1) ... 253s Selecting previously unselected package libhwasan0:amd64. 253s Preparing to unpack .../051-libhwasan0_15-20250222-0ubuntu1_amd64.deb ... 253s Unpacking libhwasan0:amd64 (15-20250222-0ubuntu1) ... 253s Selecting previously unselected package libquadmath0:amd64. 253s Preparing to unpack .../052-libquadmath0_15-20250222-0ubuntu1_amd64.deb ... 253s Unpacking libquadmath0:amd64 (15-20250222-0ubuntu1) ... 254s Selecting previously unselected package libgcc-14-dev:amd64. 254s Preparing to unpack .../053-libgcc-14-dev_14.2.0-17ubuntu3_amd64.deb ... 254s Unpacking libgcc-14-dev:amd64 (14.2.0-17ubuntu3) ... 254s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 254s Preparing to unpack .../054-gcc-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 254s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 254s Selecting previously unselected package gcc-14. 254s Preparing to unpack .../055-gcc-14_14.2.0-17ubuntu3_amd64.deb ... 254s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 254s Selecting previously unselected package gcc-x86-64-linux-gnu. 254s Preparing to unpack .../056-gcc-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 254s Unpacking gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 254s Selecting previously unselected package gcc. 254s Preparing to unpack .../057-gcc_4%3a14.2.0-1ubuntu1_amd64.deb ... 254s Unpacking gcc (4:14.2.0-1ubuntu1) ... 254s Selecting previously unselected package libstdc++-14-dev:amd64. 254s Preparing to unpack .../058-libstdc++-14-dev_14.2.0-17ubuntu3_amd64.deb ... 254s Unpacking libstdc++-14-dev:amd64 (14.2.0-17ubuntu3) ... 254s Selecting previously unselected package g++-14-x86-64-linux-gnu. 254s Preparing to unpack .../059-g++-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 254s Unpacking g++-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 255s Selecting previously unselected package g++-14. 255s Preparing to unpack .../060-g++-14_14.2.0-17ubuntu3_amd64.deb ... 255s Unpacking g++-14 (14.2.0-17ubuntu3) ... 255s Selecting previously unselected package g++-x86-64-linux-gnu. 255s Preparing to unpack .../061-g++-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 255s Unpacking g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 255s Selecting previously unselected package g++. 255s Preparing to unpack .../062-g++_4%3a14.2.0-1ubuntu1_amd64.deb ... 255s Unpacking g++ (4:14.2.0-1ubuntu1) ... 255s Selecting previously unselected package libaec0:amd64. 255s Preparing to unpack .../063-libaec0_1.1.3-1_amd64.deb ... 255s Unpacking libaec0:amd64 (1.1.3-1) ... 255s Selecting previously unselected package libann-cctbx0. 255s Preparing to unpack .../064-libann-cctbx0_1.1.2+doc-9build1_amd64.deb ... 255s Unpacking libann-cctbx0 (1.1.2+doc-9build1) ... 255s Selecting previously unselected package libann-cctbx-dev. 255s Preparing to unpack .../065-libann-cctbx-dev_1.1.2+doc-9build1_amd64.deb ... 255s Unpacking libann-cctbx-dev (1.1.2+doc-9build1) ... 255s Selecting previously unselected package libantlr3c-3.4-0:amd64. 255s Preparing to unpack .../066-libantlr3c-3.4-0_3.4+dfsg-4build2_amd64.deb ... 255s Unpacking libantlr3c-3.4-0:amd64 (3.4+dfsg-4build2) ... 255s Selecting previously unselected package libatk1.0-0t64:amd64. 255s Preparing to unpack .../067-libatk1.0-0t64_2.55.90-1_amd64.deb ... 255s Unpacking libatk1.0-0t64:amd64 (2.55.90-1) ... 255s Selecting previously unselected package libxi6:amd64. 255s Preparing to unpack .../068-libxi6_2%3a1.8.2-1_amd64.deb ... 255s Unpacking libxi6:amd64 (2:1.8.2-1) ... 255s Selecting previously unselected package libatspi2.0-0t64:amd64. 255s Preparing to unpack .../069-libatspi2.0-0t64_2.55.90-1_amd64.deb ... 255s Unpacking libatspi2.0-0t64:amd64 (2.55.90-1) ... 255s Selecting previously unselected package libatk-bridge2.0-0t64:amd64. 255s Preparing to unpack .../070-libatk-bridge2.0-0t64_2.55.90-1_amd64.deb ... 255s Unpacking libatk-bridge2.0-0t64:amd64 (2.55.90-1) ... 255s Selecting previously unselected package libavahi-common-data:amd64. 255s Preparing to unpack .../071-libavahi-common-data_0.8-16ubuntu1_amd64.deb ... 255s Unpacking libavahi-common-data:amd64 (0.8-16ubuntu1) ... 255s Selecting previously unselected package libavahi-common3:amd64. 255s Preparing to unpack .../072-libavahi-common3_0.8-16ubuntu1_amd64.deb ... 255s Unpacking libavahi-common3:amd64 (0.8-16ubuntu1) ... 255s Selecting previously unselected package libavahi-client3:amd64. 255s Preparing to unpack .../073-libavahi-client3_0.8-16ubuntu1_amd64.deb ... 255s Unpacking libavahi-client3:amd64 (0.8-16ubuntu1) ... 255s Selecting previously unselected package libboost-python1.83.0. 255s Preparing to unpack .../074-libboost-python1.83.0_1.83.0-4.1ubuntu1_amd64.deb ... 255s Unpacking libboost-python1.83.0 (1.83.0-4.1ubuntu1) ... 255s Selecting previously unselected package libboost-numpy1.83.0. 255s Preparing to unpack .../075-libboost-numpy1.83.0_1.83.0-4.1ubuntu1_amd64.deb ... 255s Unpacking libboost-numpy1.83.0 (1.83.0-4.1ubuntu1) ... 255s Selecting previously unselected package libboost1.83-dev:amd64. 255s Preparing to unpack .../076-libboost1.83-dev_1.83.0-4.1ubuntu1_amd64.deb ... 255s Unpacking libboost1.83-dev:amd64 (1.83.0-4.1ubuntu1) ... 258s Selecting previously unselected package libexpat1-dev:amd64. 258s Preparing to unpack .../077-libexpat1-dev_2.6.4-1_amd64.deb ... 258s Unpacking libexpat1-dev:amd64 (2.6.4-1) ... 258s Selecting previously unselected package 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libcctbx-dev. 259s Preparing to unpack .../104-libcctbx-dev_2024.10+ds2+~3.22.1+ds1-4build2_amd64.deb ... 259s Unpacking libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4build2) ... 259s Selecting previously unselected package liblcms2-2:amd64. 259s Preparing to unpack .../105-liblcms2-2_2.16-2_amd64.deb ... 259s Unpacking liblcms2-2:amd64 (2.16-2) ... 259s Selecting previously unselected package libcolord2:amd64. 259s Preparing to unpack .../106-libcolord2_1.4.7-3_amd64.deb ... 259s Unpacking libcolord2:amd64 (1.4.7-3) ... 259s Selecting previously unselected package libcups2t64:amd64. 260s Preparing to unpack .../107-libcups2t64_2.4.11-0ubuntu2_amd64.deb ... 260s Unpacking libcups2t64:amd64 (2.4.11-0ubuntu2) ... 260s Selecting previously unselected package libdatrie1:amd64. 260s Preparing to unpack .../108-libdatrie1_0.2.13-3build1_amd64.deb ... 260s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 260s Selecting previously unselected package libdouble-conversion3:amd64. 260s Preparing to unpack .../109-libdouble-conversion3_3.3.1-1_amd64.deb ... 260s Unpacking libdouble-conversion3:amd64 (3.3.1-1) ... 260s Selecting previously unselected package libpciaccess0:amd64. 260s Preparing to unpack .../110-libpciaccess0_0.17-3build1_amd64.deb ... 260s Unpacking libpciaccess0:amd64 (0.17-3build1) ... 260s Selecting previously unselected package libdrm-intel1:amd64. 260s Preparing to unpack .../111-libdrm-intel1_2.4.123-1_amd64.deb ... 260s Unpacking libdrm-intel1:amd64 (2.4.123-1) ... 260s Selecting previously unselected package libwayland-server0:amd64. 260s Preparing to unpack .../112-libwayland-server0_1.23.1-3_amd64.deb ... 260s Unpacking libwayland-server0:amd64 (1.23.1-3) ... 260s Selecting previously unselected package libx11-xcb1:amd64. 260s Preparing to unpack .../113-libx11-xcb1_2%3a1.8.10-2_amd64.deb ... 260s Unpacking libx11-xcb1:amd64 (2:1.8.10-2) ... 260s Selecting previously unselected package libxcb-dri3-0:amd64. 260s Preparing to unpack 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libxshmfence1:amd64 (1.3-1build5) ... 260s Selecting previously unselected package mesa-libgallium:amd64. 260s Preparing to unpack .../120-mesa-libgallium_25.0.1-2ubuntu1_amd64.deb ... 260s Unpacking mesa-libgallium:amd64 (25.0.1-2ubuntu1) ... 260s Selecting previously unselected package libgbm1:amd64. 260s Preparing to unpack .../121-libgbm1_25.0.1-2ubuntu1_amd64.deb ... 260s Unpacking libgbm1:amd64 (25.0.1-2ubuntu1) ... 260s Selecting previously unselected package libwayland-client0:amd64. 260s Preparing to unpack .../122-libwayland-client0_1.23.1-3_amd64.deb ... 260s Unpacking libwayland-client0:amd64 (1.23.1-3) ... 260s Selecting previously unselected package libegl-mesa0:amd64. 260s Preparing to unpack .../123-libegl-mesa0_25.0.1-2ubuntu1_amd64.deb ... 260s Unpacking libegl-mesa0:amd64 (25.0.1-2ubuntu1) ... 260s Selecting previously unselected package libepoxy0:amd64. 261s Preparing to unpack .../124-libepoxy0_1.5.10-2_amd64.deb ... 261s Unpacking libepoxy0:amd64 (1.5.10-2) ... 261s Selecting previously unselected package libvulkan1:amd64. 261s Preparing to unpack .../125-libvulkan1_1.4.304.0-1_amd64.deb ... 261s Unpacking libvulkan1:amd64 (1.4.304.0-1) ... 261s Selecting previously unselected package libgl1-mesa-dri:amd64. 261s Preparing to unpack .../126-libgl1-mesa-dri_25.0.1-2ubuntu1_amd64.deb ... 261s Unpacking libgl1-mesa-dri:amd64 (25.0.1-2ubuntu1) ... 261s Selecting previously unselected package libglvnd0:amd64. 261s Preparing to unpack .../127-libglvnd0_1.7.0-1build1_amd64.deb ... 261s Unpacking libglvnd0:amd64 (1.7.0-1build1) ... 261s Selecting previously unselected package libxcb-glx0:amd64. 261s Preparing to unpack .../128-libxcb-glx0_1.17.0-2_amd64.deb ... 261s Unpacking libxcb-glx0:amd64 (1.17.0-2) ... 261s Selecting previously unselected package libxxf86vm1:amd64. 261s Preparing to unpack .../129-libxxf86vm1_1%3a1.1.4-1build4_amd64.deb ... 261s Unpacking libxxf86vm1:amd64 (1:1.1.4-1build4) ... 261s Selecting previously unselected package 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(1:1.2.3-1) ... 261s Selecting previously unselected package libxdamage1:amd64. 262s Preparing to unpack .../146-libxdamage1_1%3a1.1.6-1build1_amd64.deb ... 262s Unpacking libxdamage1:amd64 (1:1.1.6-1build1) ... 262s Selecting previously unselected package libxinerama1:amd64. 262s Preparing to unpack .../147-libxinerama1_2%3a1.1.4-3build1_amd64.deb ... 262s Unpacking libxinerama1:amd64 (2:1.1.4-3build1) ... 262s Selecting previously unselected package libxrandr2:amd64. 262s Preparing to unpack .../148-libxrandr2_2%3a1.5.4-1_amd64.deb ... 262s Unpacking libxrandr2:amd64 (2:1.5.4-1) ... 262s Selecting previously unselected package libgtk-3-common. 262s Preparing to unpack .../149-libgtk-3-common_3.24.48-3ubuntu1_all.deb ... 262s Unpacking libgtk-3-common (3.24.48-3ubuntu1) ... 262s Selecting previously unselected package libgtk-3-0t64:amd64. 262s Preparing to unpack .../150-libgtk-3-0t64_3.24.48-3ubuntu1_amd64.deb ... 262s Unpacking libgtk-3-0t64:amd64 (3.24.48-3ubuntu1) ... 262s Selecting previously unselected package libhdf5-hl-310:amd64. 262s Preparing to unpack .../151-libhdf5-hl-310_1.14.5+repack-3_amd64.deb ... 262s Unpacking libhdf5-hl-310:amd64 (1.14.5+repack-3) ... 262s Selecting previously unselected package libice6:amd64. 262s Preparing to unpack .../152-libice6_2%3a1.1.1-1_amd64.deb ... 262s Unpacking libice6:amd64 (2:1.1.1-1) ... 262s Selecting previously unselected package libimagequant0:amd64. 262s Preparing to unpack .../153-libimagequant0_2.18.0-1build1_amd64.deb ... 262s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 262s Selecting previously unselected package libwacom-common. 262s Preparing to unpack .../154-libwacom-common_2.14.0-1_all.deb ... 262s Unpacking libwacom-common (2.14.0-1) ... 262s Selecting previously unselected package libwacom9:amd64. 262s Preparing to unpack .../155-libwacom9_2.14.0-1_amd64.deb ... 262s Unpacking libwacom9:amd64 (2.14.0-1) ... 262s Selecting previously unselected package libinput-bin. 262s Preparing to unpack .../156-libinput-bin_1.27.1-1_amd64.deb ... 262s Unpacking libinput-bin (1.27.1-1) ... 262s Selecting previously unselected package libmtdev1t64:amd64. 262s Preparing to unpack .../157-libmtdev1t64_1.1.7-1_amd64.deb ... 262s Unpacking libmtdev1t64:amd64 (1.1.7-1) ... 262s Selecting previously unselected package libinput10:amd64. 262s Preparing to unpack .../158-libinput10_1.27.1-1_amd64.deb ... 262s Unpacking libinput10:amd64 (1.27.1-1) ... 262s Selecting previously unselected package libjs-jquery-ui. 262s Preparing to unpack .../159-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 262s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 262s Selecting previously unselected package liblbfgsb0:amd64. 262s Preparing to unpack .../160-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 262s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 262s Selecting previously unselected package liblzf1:amd64. 262s Preparing to unpack .../161-liblzf1_3.6-4_amd64.deb ... 262s Unpacking liblzf1:amd64 (3.6-4) ... 262s Selecting previously unselected package libmd4c0:amd64. 262s Preparing to unpack .../162-libmd4c0_0.5.2-2_amd64.deb ... 262s Unpacking libmd4c0:amd64 (0.5.2-2) ... 262s Selecting previously unselected package libnetcdf22:amd64. 262s Preparing to unpack .../163-libnetcdf22_1%3a4.9.3-1_amd64.deb ... 262s Unpacking libnetcdf22:amd64 (1:4.9.3-1) ... 263s Selecting previously unselected package libnotify4:amd64. 263s Preparing to unpack .../164-libnotify4_0.8.4-1_amd64.deb ... 263s Unpacking libnotify4:amd64 (0.8.4-1) ... 263s Selecting previously unselected package libpcre2-16-0:amd64. 263s Preparing to unpack .../165-libpcre2-16-0_10.45-1_amd64.deb ... 263s Unpacking libpcre2-16-0:amd64 (10.45-1) ... 263s Selecting previously unselected package libpcre2-32-0:amd64. 263s Preparing to unpack .../166-libpcre2-32-0_10.45-1_amd64.deb ... 263s Unpacking libpcre2-32-0:amd64 (10.45-1) ... 263s Selecting previously unselected package libqhull-r8.0:amd64. 263s Preparing to unpack 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263s Preparing to unpack .../172-libsm6_2%3a1.2.4-1_amd64.deb ... 263s Unpacking libsm6:amd64 (2:1.2.4-1) ... 263s Selecting previously unselected package libxcb-icccm4:amd64. 263s Preparing to unpack .../173-libxcb-icccm4_0.4.2-1_amd64.deb ... 263s Unpacking libxcb-icccm4:amd64 (0.4.2-1) ... 263s Selecting previously unselected package libxcb-util1:amd64. 263s Preparing to unpack .../174-libxcb-util1_0.4.1-1_amd64.deb ... 263s Unpacking libxcb-util1:amd64 (0.4.1-1) ... 263s Selecting previously unselected package libxcb-image0:amd64. 263s Preparing to unpack .../175-libxcb-image0_0.4.0-2build1_amd64.deb ... 263s Unpacking libxcb-image0:amd64 (0.4.0-2build1) ... 263s Selecting previously unselected package libxcb-keysyms1:amd64. 263s Preparing to unpack .../176-libxcb-keysyms1_0.4.1-1_amd64.deb ... 263s Unpacking libxcb-keysyms1:amd64 (0.4.1-1) ... 263s Selecting previously unselected package libxcb-render-util0:amd64. 263s Preparing to unpack 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... 263s Unpacking libxkbcommon-x11-0:amd64 (1.7.0-2) ... 263s Selecting previously unselected package libqt5gui5t64:amd64. 263s Preparing to unpack .../183-libqt5gui5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 263s Unpacking libqt5gui5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 264s Selecting previously unselected package libqt5widgets5t64:amd64. 264s Preparing to unpack .../184-libqt5widgets5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 264s Unpacking libqt5widgets5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 264s Selecting previously unselected package libqt5xml5t64:amd64. 264s Preparing to unpack .../185-libqt5xml5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 264s Unpacking libqt5xml5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 264s Selecting previously unselected package libqt5designer5:amd64. 264s Preparing to unpack .../186-libqt5designer5_5.15.15-6build1_amd64.deb ... 264s Unpacking libqt5designer5:amd64 (5.15.15-6build1) ... 264s Selecting previously unselected package libqt5sql5t64:amd64. 264s Preparing to unpack .../187-libqt5sql5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 264s Unpacking libqt5sql5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 264s Selecting previously unselected package libqt5help5:amd64. 264s Preparing to unpack .../188-libqt5help5_5.15.15-6build1_amd64.deb ... 264s Unpacking libqt5help5:amd64 (5.15.15-6build1) ... 264s Selecting previously unselected package libqt5opengl5t64:amd64. 264s Preparing to unpack .../189-libqt5opengl5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 264s Unpacking libqt5opengl5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 264s Selecting previously unselected package libqt5printsupport5t64:amd64. 264s Preparing to unpack .../190-libqt5printsupport5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 264s Unpacking libqt5printsupport5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 264s Selecting previously unselected package libqt5test5t64:amd64. 264s Preparing to unpack .../191-libqt5test5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 264s Unpacking libqt5test5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 264s Selecting previously unselected package libraqm0:amd64. 264s Preparing to unpack .../192-libraqm0_0.10.2-1_amd64.deb ... 264s Unpacking libraqm0:amd64 (0.10.2-1) ... 264s Selecting previously unselected package libssm2:amd64. 264s Preparing to unpack .../193-libssm2_1.4.0-2build1_amd64.deb ... 264s Unpacking libssm2:amd64 (1.4.0-2build1) ... 264s Selecting previously unselected package libwebpdemux2:amd64. 264s Preparing to unpack .../194-libwebpdemux2_1.5.0-0.1_amd64.deb ... 264s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 264s Selecting previously unselected package libwebpmux3:amd64. 264s Preparing to unpack .../195-libwebpmux3_1.5.0-0.1_amd64.deb ... 264s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 264s Selecting previously unselected package libwxbase3.2-1t64:amd64. 264s Preparing to unpack .../196-libwxbase3.2-1t64_3.2.6+dfsg-2ubuntu1_amd64.deb ... 264s Unpacking libwxbase3.2-1t64:amd64 (3.2.6+dfsg-2ubuntu1) ... 264s Selecting previously unselected package libxtst6:amd64. 264s Preparing to unpack .../197-libxtst6_2%3a1.2.5-1_amd64.deb ... 264s Unpacking libxtst6:amd64 (2:1.2.5-1) ... 264s Selecting previously unselected package libwxgtk3.2-1t64:amd64. 264s Preparing to unpack .../198-libwxgtk3.2-1t64_3.2.6+dfsg-2ubuntu1_amd64.deb ... 264s Unpacking libwxgtk3.2-1t64:amd64 (3.2.6+dfsg-2ubuntu1) ... 264s Selecting previously unselected package libwxgtk-gl3.2-1t64:amd64. 264s Preparing to unpack .../199-libwxgtk-gl3.2-1t64_3.2.6+dfsg-2ubuntu1_amd64.deb ... 264s Unpacking libwxgtk-gl3.2-1t64:amd64 (3.2.6+dfsg-2ubuntu1) ... 264s Selecting previously unselected package libxslt1.1:amd64. 265s Preparing to unpack .../200-libxslt1.1_1.1.39-0exp1ubuntu2_amd64.deb ... 265s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu2) ... 265s Selecting previously unselected package pymol-data. 265s Preparing to unpack .../201-pymol-data_3.0.0+dfsg-3build2_all.deb ... 265s Unpacking pymol-data (3.0.0+dfsg-3build2) ... 265s Selecting previously unselected package python-matplotlib-data. 265s Preparing to unpack .../202-python-matplotlib-data_3.8.3-7build1_all.deb ... 265s Unpacking python-matplotlib-data (3.8.3-7build1) ... 265s Selecting previously unselected package python3-all. 265s Preparing to unpack .../203-python3-all_3.13.2-2_amd64.deb ... 265s Unpacking python3-all (3.13.2-2) ... 265s Selecting previously unselected package python3-brotli. 265s Preparing to unpack .../204-python3-brotli_1.1.0-2build4_amd64.deb ... 265s Unpacking python3-brotli (1.1.0-2build4) ... 265s Selecting previously unselected package python3-legacy-cgi. 265s Preparing to unpack .../205-python3-legacy-cgi_2.6.2-1_all.deb ... 265s Unpacking python3-legacy-cgi (2.6.2-1) ... 265s Selecting previously unselected package python3-pycbf. 265s Preparing to unpack .../206-python3-pycbf_0.9.7+dfsg1-5build1_amd64.deb ... 265s Unpacking python3-pycbf (0.9.7+dfsg1-5build1) ... 265s Selecting previously unselected package python3-h5py-serial. 265s Preparing to unpack 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(11.1.0-5build1) ... 265s Selecting previously unselected package python3.12-tk. 265s Preparing to unpack .../213-python3.12-tk_3.12.9-1_amd64.deb ... 265s Unpacking python3.12-tk (3.12.9-1) ... 265s Selecting previously unselected package python3.13-tk. 265s Preparing to unpack .../214-python3.13-tk_3.13.2-1_amd64.deb ... 265s Unpacking python3.13-tk (3.13.2-1) ... 265s Selecting previously unselected package python3-tk:amd64. 265s Preparing to unpack .../215-python3-tk_3.13.1-1_amd64.deb ... 265s Unpacking python3-tk:amd64 (3.13.1-1) ... 265s Selecting previously unselected package python3-pil.imagetk:amd64. 265s Preparing to unpack .../216-python3-pil.imagetk_11.1.0-5build1_amd64.deb ... 265s Unpacking python3-pil.imagetk:amd64 (11.1.0-5build1) ... 265s Selecting previously unselected package python3-contourpy. 265s Preparing to unpack .../217-python3-contourpy_1.3.1-1build1_amd64.deb ... 265s Unpacking python3-contourpy (1.3.1-1build1) ... 265s Selecting previously unselected package python3-cycler. 265s Preparing to unpack .../218-python3-cycler_0.12.1-1_all.deb ... 265s Unpacking python3-cycler (0.12.1-1) ... 266s Selecting previously unselected package python3-platformdirs. 266s Preparing to unpack .../219-python3-platformdirs_4.3.6-1_all.deb ... 266s Unpacking python3-platformdirs (4.3.6-1) ... 266s Selecting previously unselected package python3-fs. 266s Preparing to unpack .../220-python3-fs_2.4.16-7_all.deb ... 266s Unpacking python3-fs (2.4.16-7) ... 266s Selecting previously unselected package python3-lxml:amd64. 266s Preparing to unpack .../221-python3-lxml_5.3.1-1build1_amd64.deb ... 266s Unpacking python3-lxml:amd64 (5.3.1-1build1) ... 266s Selecting previously unselected package python3-lz4. 266s Preparing to unpack .../222-python3-lz4_4.4.0+dfsg-1build1_amd64.deb ... 266s Unpacking python3-lz4 (4.4.0+dfsg-1build1) ... 266s Selecting previously unselected package python3-decorator. 266s Preparing to unpack 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previously unselected package python3-fonttools. 267s Preparing to unpack .../229-python3-fonttools_4.55.3-2build1_amd64.deb ... 267s Unpacking python3-fonttools (4.55.3-2build1) ... 267s Selecting previously unselected package python3-kiwisolver. 267s Preparing to unpack .../230-python3-kiwisolver_1.4.7-3build1_amd64.deb ... 267s Unpacking python3-kiwisolver (1.4.7-3build1) ... 267s Selecting previously unselected package python3-packaging. 267s Preparing to unpack .../231-python3-packaging_24.2-1_all.deb ... 267s Unpacking python3-packaging (24.2-1) ... 267s Selecting previously unselected package python3-matplotlib. 267s Preparing to unpack .../232-python3-matplotlib_3.8.3-7build1_amd64.deb ... 267s Unpacking python3-matplotlib (3.8.3-7build1) ... 268s Selecting previously unselected package sphinx-rtd-theme-common. 268s Preparing to unpack .../233-sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb ... 268s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 268s Selecting previously 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up libccp4-dev:amd64 (8.0.0-4) ... 289s Setting up python3.13-dev (3.13.2-1) ... 289s Setting up libtk8.6:amd64 (8.6.16-1) ... 289s Setting up libpango-1.0-0:amd64 (1.56.1-1) ... 289s Setting up python3.12-tk (3.12.9-1) ... 289s Setting up libnetcdf22:amd64 (1:4.9.3-1) ... 289s Setting up python3-h5py-serial (3.13.0-1) ... 289s Setting up libcairo2:amd64 (1.18.2-2) ... 289s Setting up python3.13-tk (3.13.2-1) ... 290s Setting up python3-pil:amd64 (11.1.0-5build1) ... 290s Setting up libgl1:amd64 (1.7.0-1build1) ... 290s Setting up adwaita-icon-theme (48~beta-3) ... 290s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 290s Setting up libnotify4:amd64 (0.8.4-1) ... 290s Setting up python3-dev (3.13.2-2) ... 290s Setting up libboost-python1.83-dev (1.83.0-4.1ubuntu1) ... 290s Setting up python3-pycbf (0.9.7+dfsg1-5build1) ... 290s Setting up python3-h5py (3.13.0-1) ... 290s Setting up libglew2.2:amd64 (2.2.0-4build1) ... 290s Setting up python3-hdf5plugin (5.0.0-1) ... 290s Setting up cpp (4:14.2.0-1ubuntu1) ... 290s Setting up libcairo-gobject2:amd64 (1.18.2-2) ... 290s Setting up gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 290s Setting up libpangoft2-1.0-0:amd64 (1.56.1-1) ... 290s Setting up python3-nxmx (0.0.4-1) ... 290s Setting up libcups2t64:amd64 (2.4.11-0ubuntu2) ... 290s Setting up libgtk-3-common (3.24.48-3ubuntu1) ... 290s Setting up libpangocairo-1.0-0:amd64 (1.56.1-1) ... 290s Setting up libcctbx0 (2024.10+ds2+~3.22.1+ds1-4build2) ... 290s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 290s Setting up gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 290s Setting up blt (2.5.3+dfsg-8) ... 290s Setting up python3-tk:amd64 (3.13.1-1) ... 290s Setting up python3-opengl (3.1.7+dfsg-1) ... 291s /usr/lib/python3/dist-packages/OpenGL/GL/AMD/vertex_shader_tessellator.py:1: SyntaxWarning: invalid escape sequence '\ ' 291s '''OpenGL extension AMD.vertex_shader_tessellator 292s Setting up gcc-14 (14.2.0-17ubuntu3) ... 292s Setting up libboost-python-dev (1.83.0.2ubuntu1) ... 292s Setting up libqt5gui5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 292s Setting up python3-pil.imagetk:amd64 (11.1.0-5build1) ... 292s Setting up g++-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 292s Setting up g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 292s Setting up g++-14 (14.2.0-17ubuntu3) ... 292s Setting up libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4build2) ... 292s Setting up libqt5widgets5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 292s Setting up libqt5help5:amd64 (5.15.15-6build1) ... 292s Setting up gcc (4:14.2.0-1ubuntu1) ... 292s Setting up g++ (4:14.2.0-1ubuntu1) ... 292s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 292s Setting up libqt5opengl5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 292s Setting up libqt5printsupport5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 292s Setting up libqt5designer5:amd64 (5.15.15-6build1) ... 292s Setting up python3-pyqt5 (5.15.11+dfsg-2) ... 292s Setting up python3-pyqt5.qtopengl (5.15.11+dfsg-2) ... 292s Setting up python3-pymol (3.0.0+dfsg-3build2) ... 293s Setting up python3-fonttools (4.55.3-2build1) ... 294s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 294s Setting up python3-matplotlib (3.8.3-7build1) ... 295s Processing triggers for libc-bin (2.41-1ubuntu1) ... 295s Processing triggers for man-db (2.13.0-1) ... 297s Processing triggers for libglib2.0-0t64:amd64 (2.84.0-1) ... 297s Setting up libgtk-3-0t64:amd64 (3.24.48-3ubuntu1) ... 297s Processing triggers for udev (257.3-1ubuntu3) ... 297s Setting up libwxgtk3.2-1t64:amd64 (3.2.6+dfsg-2ubuntu1) ... 297s Setting up libwxgtk-gl3.2-1t64:amd64 (3.2.6+dfsg-2ubuntu1) ... 297s Setting up python3-wxgtk4.0 (4.2.2+dfsg-3build1) ... 299s Setting up python3-cctbx (2024.10+ds2+~3.22.1+ds1-4build2) ... 301s /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:8: SyntaxWarning: invalid escape sequence '\{' 301s """ Iterator to generate strings of length n_chars, using upper-case, 301s /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:46: SyntaxWarning: invalid escape sequence '\/' 301s special_characters = """[]_,.;:"&<>()\/\{}'`~!@#$%*|+-""" 311s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:724: SyntaxWarning: invalid escape sequence '\o' 311s width=pairwise_differences_db, label='$\omega_{hkl}$' 311s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:739: SyntaxWarning: invalid escape sequence '\o' 311s axes[0].set_ylabel('Distribution of $\omega_{hbk}$') 311s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:740: SyntaxWarning: invalid escape sequence '\o' 311s axes[0].set_xlabel('Normalized PD ($\omega_{hbk}$)') 311s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:759: SyntaxWarning: invalid escape sequence '\o' 311s axes[1].set_xlabel('Sorted Normalized PD ($\omega_{hbk}$)') 311s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:778: SyntaxWarning: invalid escape sequence '\s' 311s axes[2].set_ylabel('Standard Deviation of $I_{hbk}/\sigma_{hbk}$') 311s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:807: SyntaxWarning: invalid escape sequence '\m' 311s axes_sadd.set_ylabel('$s_{\mathrm{fac}}^2 \\times s_{\mathrm{add}}^2$') 312s Processing triggers for libc-bin (2.41-1ubuntu1) ... 313s autopkgtest [10:53:40]: test cctbx: [----------------------- 314s Testing cctbx with python3.13: 314s Running 546 tests on 2 processors: 314s libtbx.python "/usr/lib/python3/dist-packages/annlib_adaptbx/annlib_adaptbx/sample.py" 314s libtbx.python "/usr/lib/python3/dist-packages/annlib_adaptbx/annlib_adaptbx/self_match.py" 314s "/usr/lib/cctbx/python3.13/boost_adaptbx/tests/tst_optional_copy" 314s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_libc_backtrace.py" 314s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_rational.py" 314s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_optional.py" 314s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_std_pair.py" 314s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_tuple.py" 314s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_stdout.py" 314s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_stderr_stdout.py" 314s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_deprecation_tools.py" 314s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_python_streambuf.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sf_low_res_accuracy.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_double_step_filtration.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_is_periodic.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_reindexing.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_map_to_asu_isym.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_data_manipulation.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_bfgs.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_dev.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry/tests/tst_geometry.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/covariance/tests/tst_covariance.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_goodness_of_symmetry.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_from_map.py" P312 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_aniso_restraints.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/math/boost_python/tst_math.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_targets_fd.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_xray.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray.py" I41/acd 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_r1.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_shelxl_wght_ls.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_f_model.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/array_family/boost_python/tst_flex.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_uctbx.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_crystal_orientation.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_sgtbx.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_N_fold_rot.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_ext.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_distance_based_connectivity.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_super_cell.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adptbx/boost_python/tst_adptbx.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/boost_python/tst_miller.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_chemical_elements.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_xray_scattering.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_henke.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_icsd_radii.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_covalent_radii.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_neutron.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_sasaki.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_tiny_pse.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_wavelengths.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_formula.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_attenuation_coefficient.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/boost_python/tst_maptbx.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_bcr.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_loft.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/dmtbx/boost_python/tst_dmtbx.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/translation_search/boost_python/tst_translation_search.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_ext.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_proxy_registry.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_nonbonded_overlaps.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_process_nonbonded_proxies.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_angle_derivs.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_motif.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adp_restraints/tst_ext.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_math_module.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_krivy_gruber.py" --Quick 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_itvb_2001_table_a1427_hall_symbols.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_space_group_type_tidy_cb_op_t.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_denominators.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_subgroups.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_lattice_symmetry.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints.py" P3 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints_cartesian.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_site_constraints.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reflection_statistics.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_harker.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_special_op_simplifier.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_twin_target.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/symbol_confidence.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/bravais_types.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_lookup_utils.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal.py" I41/acd 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_direct_space_asu.py" I41/acd 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pair_asu_table.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_asu_clusters.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_coordination_sequences.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_close_packing.py" R-3mr 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fourier_transform_real_part_at_x.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem_2.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reciprocal_space_asu.py" P312 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_triplet_generator.py" P41 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_emma.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_expand_to_p1.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_change_basis.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wilson_plot.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_derivatives.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_fast_gradients.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F_sq P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_structure_factors.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_weights_for_symmetry_summation.py" Pmmm 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_real_space_refinement_simple.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation_2.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_loc_res.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_target_and_gradients.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_merge_equivalents.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grouped_data.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_fft_map.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sampled_model_density.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fast_nv1995.py" F222 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_lbfgs.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_2.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grm_pickling.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_french_wilson.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/make_cns_input.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/tst_cns_epsilon.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/tst_cns_hl.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/run_shelx76.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pointgroup_tools.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/sub_lattice_tools.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/rational_matrices_point_groups.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/cosets.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_pg_tools.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_twin_laws.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_find_best_cell.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_amplitude_normalisation.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_statistics_graphs.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_web_change_basis.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/direct_space_asu/proto/tst_asu.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_tidy_pickling.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/masks/tests/tst_flood_fill.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_r_free_utils.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/observations/tst_observations.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_ccp.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_mask.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_map_peak_3d_as_2d.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_asymmetric_map.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_peak_volume_estimate.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_resolution_from_map_and_model.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_curves.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_radius_as_central_peak_width.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_get_percentile_cutoffs.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_box.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_create_models_or_maps.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sphericity.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_statistics.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/merging/brehm_diederichs.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/multipolar/regression/tst_multipolar.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity_allsym.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grm_modifications.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_prepare_map_for_docking.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wavelength_units.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fcalc_fft_stability.py" 314s libtbx.python "/usr/lib/python3/dist-packages/cma_es/tst_cma_es.py" 314s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_ext.py" 314s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_equivalence.py" 314s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_read.py" 314s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_cout.py" 314s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_show_calls.py" 314s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_command_line.py" 314s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_separate_files.py" 314s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_cout_compile.py" stop 314s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_io.py" 314s libtbx.python "/usr/lib/python3/dist-packages/gltbx/tst_ellipsoids.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mrc_io.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_wildcard.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/gui_tools/tst.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_parser.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phil.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_cif_inputs.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_manager.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager_wrapping.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_2.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_3.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_4.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_model_sharpening_5.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_model_sharpening_5_cif.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_call_consistency.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_external_sharpening_7.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_half_map_sharpening_6.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_tls_from_map_8.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_cif.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry_cif.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_local_resolution_10.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_tools.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_patterson.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_restraints_merge.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_atom_selections_10k.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/ranges.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_crystal_symmetry_from_any.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_poscar.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/kriber/tst_strudat.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_geometry.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_lex_parse_build.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_restraints.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_parser.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_citations.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model_builder.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_lex_parse_build.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_hklf.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_writer.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_fvar_encoding.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_pdb.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy_2.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_tls.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/hybrid_36.py" exercise 314s "/usr/lib/cctbx/python3.13/iotbx/pdb/hybrid_36_fem" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy_atom_sort.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy_flip_symmetric.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_selected_hierarchy_flip.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_ext.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_rna_dna_atom_names.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_name_interpretation.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_extract_rfactors_resolutions_sigma.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/modified_aa_names.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/modified_rna_dna_names.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_sheet.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation_long.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/secondary_structure.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection_string.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_secondary_structure.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_utils.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_secondary_structure_2.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/remediation/tst_remediator.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_to_map_simple.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_truncate_to_ala/tst.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_tardy_conf_sampling_simple.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_examples.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/space_group_symbols.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/tst_cns.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_merge.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/no_merge_original_index.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/ccp4_map/tst.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_ext.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_extract_from_symmetry_lib.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_dano.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_miller_dict.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_unmerged.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/tst_mtz_free_flipper.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_utils.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_adsc.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_detectors.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xplor/tst_xplormap.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phases.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdbx_mmcif_tutorial.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_statistics.py" Fdd2 P31m 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_plots.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_csv_utils.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_file_reader.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_bioinformatics.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_segids.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_input.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_forward_compatible_pdb.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_multimodel.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_add_conformations.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_symmetry.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reindex.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_editor.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_as_fasta.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_link_records.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_merging_statistics.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_map_coefficients.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_xparm.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_xds_inp.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_integrate_hkl.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_spots_xds.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_as_cif.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_no_merge_original_index.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_export_scalepack_unmerged.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/dsn6/tst.py" P31 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_mtrix_biomt_cmdl.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_mmcif_biomt_reduction_output.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_ligs.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_broken_chain.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_shortcut_1.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_groups_preprocessing.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_input.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_user_selections.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_without_validation.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_read_mtrix_records_from_cif.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_show_systematic_absences.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_miller_sort_asu.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_reader.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_xray_scale.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_alignment_as_hsearch.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_ebi_wu_blast_xml.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_ncbi_blast_xml.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/pdb_info.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_as_pdb_1atom.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_1.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_all_chain_ids.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_extract_xtal_data.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cli_parser.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mtz_as_cif.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_group_rounding.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_occupancies_rounding.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_merge_atoms_at_end_to_residues.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_chain_ids_1.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_1.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_2.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_3.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_4.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_copy_select.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_id_str.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_altlocs.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_fetch.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_debug_write.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_reordered_chains.py" 314s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_to_from_hierarchy.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/metric_prefixes.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_utils.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/test_utils/__init__.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/queuing_system_utils/pbs_utils.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/queuing_system_utils/sge_utils.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/introspection.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_thread_utils.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp_state.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_pickle.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_fully_buffered_timeout.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_scheduling.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/easy_run.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_containers.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_path.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_math_utils.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/assert_utils.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_str_utils.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/table_utils.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_dlite.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_tokenizer.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_experimental.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_interface.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_object_oriented_patterns.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/find_reference_cycles.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_binary_search.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_topological_sort.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/clusterTests.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_citations.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_python_code_parsing.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_representation.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_find_unused_imports.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_program_template.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_version.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp_multicore.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_runtime_utils.py" 314s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_xmlrpc_utils.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_smoothing.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_genetic_algorithm_with_mp.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_basic.py" 314s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_1" 314s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_2" 314s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_3" 314s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_4" 314s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_5" 314s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_vec3" 314s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_unsigned_float_arithmetic" 314s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_mat3" 314s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_sym_mat3" 314s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_ref_matrix_facet" 314s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_accessors" 314s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_optional_copy" 314s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_rectangular_full_packed" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex_argument_passing.py" 314s "/usr/lib/cctbx/python3.13/scitbx/serialization/tst_base_256" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_minimum_covering_ellipsoid.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian_fit_1d_analytical.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_cubic_equation.py" 314s "/usr/lib/cctbx/python3.13/scitbx/math/tests/tst" 314s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_givens" 314s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_householder" 314s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_svd" 314s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_cholesky" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/tests/tst_row_echelon.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/tests/tst_householder.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_matrix.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_cholesky.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_svd.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_eigensystem.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_svd.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_dsyev.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/error/tst_error.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_map.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_set.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_vector.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/regression_test.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_numpy_bridge.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_smart_selection.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_shared.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_integer_offsets_vs_pointers.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_cost_of_m_handle_in_af_shared.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_cubicle_neighbors.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_r3_utils.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_regular_grid_on_unit_sphere.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/__init__.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_random_transform.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_graph.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_robust.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/superpose.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/spe.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/incremental_SO3_sampling.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_curve_fitting.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_weighted_correlation.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_similarity_indices.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_exp_functions.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_fit_quadratic_function.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gcd.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_math.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_r3_rotation.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_resample.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_line_search.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_quadrature.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_bessel.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_halton.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_euler_angles.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_superpose.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_uniform_rotation_matrix.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike_mom.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/sieve_of_eratosthenes.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/besselk.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/scale_curves.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_fit_peak.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_clustering.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_orthonormal_basis.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_g_function.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_angle_derivative.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_periodogram.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_error_propagation_matrix_inverse.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_tetrahedron.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_undirected_graph.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_so3_lie_algebra.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/minpack/tst.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_ext.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_curvatures.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_func_free_line_search.py" 314s "/usr/lib/cctbx/python3.13/scitbx/lbfgs/tst_lbfgs" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgsb/boost_python/tst_lbfgsb.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/fftpack/boost_python/tst_fftpack.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_grid.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_array_loops.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/principal_axes_of_inertia.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_recipe.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_linear_least_squares_fit.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/chebyshev_lsq_example.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/immoptibox_ports.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/rigid_body_refinement_core.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/integrating_a_weighted_sinc_function.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/minimizer_comparisons.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_utils.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/rigidity.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_rigidity.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/rigidity_matrix_symbolic.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree_find_paths.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/test_cases_tardy_pdb.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_basic.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_tardy.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_energy_plots.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/tst.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/free_motion_reference_impl.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_featherstone.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion_hard.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_joint_lib.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_singular.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_spherical_refinement.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_molecules.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_sparse.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_lu_factorization.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/iso_surface/tst_iso_surface.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/simplex.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/differential_evolution.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/golden_section_search.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/direct_search_simulated_annealing.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/random/tests/tst_random.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/tst_normal_equations.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/test_problems.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/glmtbx/tests/tst.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_basic.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_booth.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_twisted.py" 314s libtbx.python "/usr/lib/python3/dist-packages/scitbx/suffixtree/test/tst_single.py" 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/absolute_structure/tests/tst_absolute_structure.py" --fix_random_seeds 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/ab_initio/tests/tst_ab_initio_ext.py" 314s 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" 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/masks/tests/tst_masks.py" 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/structure_factors/direct/tests/tst_standard_xray.py" 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_weighting_schemes.py" --fix_random_seeds 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_lbfgs.py" 314s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_reparametrisation" 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_occupancies.py" 314s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens" 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_same_group.py" 314s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_special_position" 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_reparametrisation.py" 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=naive 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_disorder.py" 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=levenberg-marquardt 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_rigid.py" 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_direction.py" 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_adp_restraints.py" 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_manager.py" 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_restraints.py" --verbose --scatterers=5 --resolution=0.2 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_refine.py" 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py" 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/tests/tst_utils.py" 314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_least_squares.py" 314s libtbx.python "/usr/lib/python3/dist-packages/rstbx/dps_core/tst_iotbx_converter.py" 314s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_predict.py" 314s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_ewald_sphere.py" 314s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_partial_derivatives.py" 314s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/fastbragg/tst_bragg_minimal.py" 314s libtbx.python "/usr/lib/python3/dist-packages/rstbx/sublattice_support/tst_sublattice.py" 314s libtbx.python -c "from rstbx.run_tests import run; run()" 314s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/core_toolbox/boost_python/tst_small_image.py" 314s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/diffraction/geometry.py" 314s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/math_support/sphere_formulae.py" 314s 314s libtbx.python "/usr/lib/python3/dist-packages/annlib_adaptbx/annlib_adaptbx/self_match.py" [OK] 0.2s 314s Time: 0.25 314s Return code: 0 314s OKs: 1 314s Standard out: 314s OK 314s "/usr/lib/cctbx/python3.13/boost_adaptbx/tests/tst_optional_copy" [OK] 0.0s 314s Time: 0.01 314s Return code: 0 314s OKs: 1 314s Standard out: 314s OK 314s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_libc_backtrace.py" [OK] 0.1s 314s Time: 0.08 314s Return code: 0 314s OKs: 1 314s Standard out: 314s OK 314s Standard error: 314s show_stack(1): /usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_libc_backtrace.py(9) run 314s show_stack(2): /usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_libc_backtrace.py(15) 314s libc backtrace (20 frames, most recent call last): 314s /usr/bin/python3.13(_start+0x25) [0x648435] 314s /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b) [0x78053802a3fb] 314s /lib/x86_64-linux-gnu/libc.so.6(+0x2a338) [0x78053802a338] 314s /usr/bin/python3.13(Py_BytesMain+0x2d) [0x64908d] 314s /usr/bin/python3.13(Py_RunMain+0x3ea) [0x68e57a] 314s /usr/bin/python3.13() [0x68f805] 314s /usr/bin/python3.13() [0x68f9c5] 314s /usr/bin/python3.13() [0x690424] 314s /usr/bin/python3.13() [0x6764ae] 314s /usr/bin/python3.13() [0x67ade2] 314s /usr/bin/python3.13(PyEval_EvalCode+0xcd) [0x659a7d] 314s /usr/bin/python3.13(_PyEval_EvalFrameDefault+0x3251) [0x564831] 314s /usr/bin/python3.13(_PyObject_MakeTpCall+0x283) [0x547d73] 314s /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0(+0x23a0e) [0x780537859a0e] 314s /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0(boost::python::handle_exception_impl(boost::function0)+0x7b) [0x78053785990b] 314s /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0(+0x276c4) [0x78053785d6c4] 314s /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0(boost::python::objects::function::call(_object*, _object*) const+0x94) [0x78053785d244] 314s /usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-313-x86_64-linux-gnu.so(+0x19972) [0x78053788d972] 314s /usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-313-x86_64-linux-gnu.so(+0x219ec) [0x7805378959ec] 314s /usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-313-x86_64-linux-gnu.so(+0x2157a) [0x78053789557a] 315s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_rational.py" [OK] 0.1s 315s Time: 0.12 315s Return code: 0 315s OKs: 1 315s Standard out: 315s OK 315s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_optional.py" [OK] 0.1s 315s Time: 0.09 315s Return code: 0 315s OKs: 1 315s Standard out: 315s exercise_wstring: 315s OK 315s libtbx.python "/usr/lib/python3/dist-packages/annlib_adaptbx/annlib_adaptbx/sample.py" [OK] 0.6s 315s Time: 0.56 315s Return code: 0 315s OKs: 1 315s Standard out: 315s OK 315s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_tuple.py" [OK] 0.1s 315s Time: 0.06 315s Return code: 0 315s OKs: 1 315s Standard out: 315s OK 315s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_std_pair.py" [OK] 0.1s 315s Time: 0.12 315s Return code: 0 315s OKs: 1 315s Standard out: 315s OK 315s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_stderr_stdout.py" [OK] 0.1s 315s Time: 0.06 315s Return code: 0 315s OKs: 1 315s Standard out: 315s OK 315s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_stdout.py" [OK] 0.1s 315s Time: 0.13 315s Return code: 0 315s OKs: 1 315s Standard out: 315s OK 315s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_deprecation_tools.py" [OK] 0.1s 315s Time: 0.06 315s Return code: 0 315s OKs: 1 315s Standard out: 315s OK 318s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 318s 1 318s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 318s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_python_streambuf.py" [EXPECTED FAIL] 2.8s 318s Time: 2.80 318s Return code: 1 318s OKs: 0 318s Standard error: 318s Traceback (most recent call last): 318s File "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_python_streambuf.py", line 7, in 318s import StringIO 318s ModuleNotFoundError: No module named 'StringIO' 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/regression/tst_sf_low_res_accuracy.py" [FAIL] 3.8s 319s Time: 3.85 319s Return code: 139 319s OKs: 0 319s Standard error: 319s Segmentation fault (core dumped) 322s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 322s 139 322s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 322s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_double_step_filtration.py" [FAIL] 4.3s 322s Time: 4.26 322s Return code: 139 322s OKs: 0 322s Standard error: 322s Segmentation fault (core dumped) 325s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 325s 139 325s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 325s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_is_periodic.py" [FAIL] 6.2s 325s Time: 6.16 325s Return code: 139 325s OKs: 0 325s Standard error: 325s Segmentation fault (core dumped) 325s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_map_to_asu_isym.py" [OK] 0.3s 325s Time: 0.35 325s Return code: 0 325s OKs: 1 325s Standard out: 325s OK 328s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 328s 139 328s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 328s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_reindexing.py" [FAIL] 6.0s 328s Time: 6.00 328s Return code: 139 328s OKs: 0 328s Standard error: 328s Segmentation fault (core dumped) 331s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 331s 139 331s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 331s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_data_manipulation.py" [FAIL] 5.8s 331s Time: 5.78 331s Return code: 139 331s OKs: 0 331s Standard error: 331s 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/omz/tst_bfgs.py" [FAIL] 6.0s 334s Time: 5.98 334s Return code: 139 334s OKs: 0 334s Standard error: 334s Segmentation fault (core dumped) 337s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 337s 139 337s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 337s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_dev.py" P31 [FAIL] 6.0s 337s Time: 5.98 337s Return code: 139 337s OKs: 0 337s Standard error: 337s Segmentation fault (core dumped) 340s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 340s 139 340s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 340s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry/tests/tst_geometry.py" [FAIL] 6.2s 340s Time: 6.23 340s Return code: 139 340s OKs: 0 340s Standard error: 340s Segmentation fault (core dumped) 343s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 343s 139 343s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/covariance/tests/tst_covariance.py" [FAIL] 6.3s 343s Time: 6.31 343s Return code: 139 343s OKs: 0 343s Standard error: 343s Segmentation fault (core dumped) 346s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 346s 139 346s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 346s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_goodness_of_symmetry.py" [FAIL] 6.2s 346s Time: 6.21 346s Return code: 139 346s OKs: 0 346s Standard error: 346s Segmentation fault (core dumped) 347s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_aniso_restraints.py" [OK] 0.2s 347s Time: 0.24 347s Return code: 0 347s OKs: 1 347s Standard out: 347s Skipping exercise(): chem_data directory not available 347s OK 347s libtbx.python "/usr/lib/python3/dist-packages/cctbx/math/boost_python/tst_math.py" [OK] 0.1s 347s Time: 0.11 347s Return code: 0 347s OKs: 1 347s Standard out: 347s OK 347s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_targets_fd.py" [OK] 0.4s 347s Time: 0.36 347s Return code: 0 347s OKs: 1 347s Standard out: 347s OK 349s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 349s 139 349s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 349s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_from_map.py" P312 [FAIL] 6.1s 349s Time: 6.09 349s Return code: 139 349s OKs: 0 349s Standard error: 349s Segmentation fault (core dumped) 353s Standard error: 353s Segmentation fault (core dumped) 353s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 353s 139 353s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 353s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_xray.py" [FAIL] 5.6s 353s Time: 5.61 353s Return code: 139 353s OKs: 0 356s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 356s 139 356s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 356s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray.py" I41/acd [FAIL] 6.5s 356s Time: 6.45 356s Return code: 139 356s OKs: 0 356s Standard error: 356s Segmentation fault (core dumped) 359s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 359s 139 359s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 359s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_r1.py" [FAIL] 6.2s 359s Time: 6.25 359s Return code: 139 359s OKs: 0 359s Standard error: 359s Segmentation fault (core dumped) 362s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 362s 139 362s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 362s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_shelxl_wght_ls.py" [FAIL] 6.1s 362s Time: 6.08 362s Return code: 139 362s OKs: 0 362s Standard error: 362s Segmentation fault (core dumped) 365s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 365s 139 365s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 365s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_f_model.py" [FAIL] 6.1s 365s Time: 6.14 365s Return code: 139 365s OKs: 0 365s Standard error: 365s 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/array_family/boost_python/tst_flex.py" [FAIL] 6.2s 368s Time: 6.19 368s Return code: 139 368s OKs: 0 368s Standard error: 368s Segmentation fault (core dumped) 371s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 371s 139 371s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 371s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_uctbx.py" [FAIL] 6.1s 371s Time: 6.12 371s Return code: 139 371s OKs: 0 371s Standard error: 371s Segmentation fault (core dumped) 374s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 374s 139 374s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 374s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_crystal_orientation.py" [FAIL] 6.1s 374s Time: 6.06 374s Return code: 139 374s OKs: 0 374s Standard error: 374s Segmentation fault (core dumped) 374s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_N_fold_rot.py" [OK] 0.2s 374s Time: 0.23 374s Return code: 0 374s OKs: 1 374s Standard out: 374s OK 377s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 377s 139 377s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 377s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_sgtbx.py" [FAIL] 6.3s 377s Time: 6.30 377s Return code: 139 377s OKs: 0 377s Standard error: 377s Segmentation fault (core dumped) 381s Standard error: 381s Segmentation fault (core dumped) 381s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 381s 139 381s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 381s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_ext.py" [FAIL] 6.2s 381s Time: 6.21 381s Return code: 139 381s OKs: 0 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/crystal/tst_distance_based_connectivity.py" [FAIL] 6.1s 384s Time: 6.13 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/crystal/tst_super_cell.py" [FAIL] 6.9s 388s Time: 6.92 388s Return code: 139 388s OKs: 0 388s Standard error: 388s Segmentation fault (core dumped) 391s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 391s 139 391s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 391s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adptbx/boost_python/tst_adptbx.py" [FAIL] 7.2s 391s Time: 7.17 391s Return code: 139 391s OKs: 0 391s Standard error: 391s Segmentation fault (core dumped) 391s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_chemical_elements.py" [OK] 0.1s 391s Time: 0.10 391s Return code: 0 391s OKs: 1 391s Standard out: 391s OK 394s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 394s 139 394s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 394s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/boost_python/tst_miller.py" [FAIL] 6.6s 394s Time: 6.63 394s Return code: 139 394s OKs: 0 394s Standard error: 394s Segmentation fault (core dumped) 394s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_henke.py" [OK] 0.1s 394s Time: 0.11 394s Return code: 0 394s OKs: 1 394s Standard out: 394s OK 394s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_icsd_radii.py" [OK] 0.1s 394s Time: 0.10 394s Return code: 0 394s OKs: 1 394s Standard out: 394s OK 394s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_covalent_radii.py" [OK] 0.1s 394s Time: 0.11 394s Return code: 0 394s OKs: 1 394s Standard out: 394s OK 395s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_neutron.py" [OK] 0.1s 395s Time: 0.11 395s Return code: 0 395s OKs: 1 395s Standard out: 395s OK 395s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_sasaki.py" [OK] 0.1s 395s Time: 0.11 395s Return code: 0 395s OKs: 1 395s Standard out: 395s OK 395s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_tiny_pse.py" [OK] 0.1s 395s Time: 0.11 395s Return code: 0 395s OKs: 1 395s Standard out: 395s OK 395s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_wavelengths.py" [OK] 0.1s 395s Time: 0.10 395s Return code: 0 395s OKs: 1 395s Standard out: 395s OK 398s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 398s 139 398s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 398s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_xray_scattering.py" [FAIL] 6.7s 398s Time: 6.65 398s Return code: 139 398s OKs: 0 398s Standard error: 398s Segmentation fault (core dumped) 401s Standard error: 401s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 401s 139 401s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 401s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_formula.py" [FAIL] 5.8s 401s Time: 5.81 401s Return code: 139 401s OKs: 0 401s Segmentation fault (core dumped) 404s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 404s 139 404s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 404s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_attenuation_coefficient.py" [FAIL] 6.2s 404s Time: 6.18 404s Return code: 139 404s OKs: 0 404s Standard error: 404s Segmentation fault (core dumped) 407s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 407s 139 407s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 407s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/boost_python/tst_maptbx.py" [FAIL] 6.1s 407s Time: 6.14 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/maptbx/tst_bcr.py" [FAIL] 6.9s 411s Time: 6.93 411s Return code: 139 411s OKs: 0 411s Standard error: 411s Segmentation fault (core dumped) 414s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 414s 139 414s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 414s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_loft.py" [FAIL] 6.8s 414s Time: 6.80 414s Return code: 139 414s OKs: 0 414s Standard error: 414s Segmentation fault (core dumped) 417s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 417s 139 417s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 417s libtbx.python "/usr/lib/python3/dist-packages/cctbx/dmtbx/boost_python/tst_dmtbx.py" [FAIL] 6.0s 417s Time: 6.02 417s Return code: 139 417s OKs: 0 417s Standard error: 417s Segmentation fault (core dumped) 420s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 420s 139 420s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 420s libtbx.python "/usr/lib/python3/dist-packages/cctbx/translation_search/boost_python/tst_translation_search.py" [FAIL] 5.9s 420s Time: 5.95 420s Return code: 139 420s OKs: 0 420s Standard error: 420s Segmentation fault (core dumped) 420s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_proxy_registry.py" [OK] 0.2s 420s Time: 0.22 420s Return code: 0 420s OKs: 1 420s Standard out: 420s OK 421s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_nonbonded_overlaps.py" [OK] 0.7s 421s Time: 0.69 421s Return code: 0 421s OKs: 0 421s Standard out: 421s chem_data not present, skipping 421s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_process_nonbonded_proxies.py" [OK] 0.7s 421s Time: 0.69 421s Return code: 0 421s OKs: 0 421s Standard out: 421s Test skipped, need monomer library 423s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 423s 139 423s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 423s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_ext.py" [FAIL] 6.3s 423s Time: 6.30 423s Return code: 139 423s OKs: 0 423s Standard error: 423s Segmentation fault (core dumped) 423s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_motif.py" [OK] 0.3s 423s Time: 0.31 423s Return code: 0 423s OKs: 0 423s Standard out: 423s u+s,u,s: 0.26 0.22 0.04 426s Standard error: 426s Segmentation fault (core dumped) 426s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 426s 139 426s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 426s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_angle_derivs.py" [FAIL] 4.7s 426s Time: 4.68 426s Return code: 139 426s OKs: 0 426s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_math_module.py" [OK] 0.1s 426s Time: 0.10 426s Return code: 0 426s OKs: 1 426s Standard out: 426s OK 429s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 429s 139 429s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 429s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adp_restraints/tst_ext.py" [FAIL] 5.9s 429s Time: 5.91 429s Return code: 139 429s OKs: 0 429s Standard error: 429s Segmentation fault (core dumped) 432s Standard error: 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_krivy_gruber.py" --Quick [FAIL] 6.1s 432s Time: 6.10 432s Return code: 139 432s OKs: 0 432s Segmentation fault (core dumped) 432s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_itvb_2001_table_a1427_hall_symbols.py" [OK] 0.2s 432s Time: 0.21 432s Return code: 0 432s OKs: 1 432s Standard out: 432s Skipping exercise(): input file not available 432s OK 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.py" [FAIL] 6.1s 435s Time: 6.06 435s Return code: 139 435s OKs: 0 435s Standard error: 435s Segmentation fault (core dumped) 438s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 438s 139 438s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 438s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_space_group_type_tidy_cb_op_t.py" [FAIL] 6.1s 438s Time: 6.13 438s Return code: 139 438s OKs: 0 438s Standard error: 438s 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_sgtbx_denominators.py" P31 [FAIL] 6.4s 442s Time: 6.36 442s Return code: 139 442s OKs: 0 442s Standard error: 442s Segmentation fault (core dumped) 445s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 445s 139 445s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 445s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_subgroups.py" [FAIL] 6.4s 445s Time: 6.38 445s Return code: 139 445s OKs: 0 445s Standard error: 445s Segmentation fault (core dumped) 448s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 448s 139 448s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 448s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_lattice_symmetry.py" [FAIL] 6.5s 448s Time: 6.54 448s Return code: 139 448s OKs: 0 448s Standard error: 448s Segmentation fault (core dumped) 451s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 451s 139 451s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 451s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints.py" P3 [FAIL] 6.6s 451s Time: 6.56 451s Return code: 139 451s OKs: 0 451s Standard error: 451s Segmentation fault (core dumped) 452s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_site_constraints.py" [OK] 0.4s 452s Time: 0.41 452s Return code: 0 452s OKs: 0 452s Standard out: 452s Skipping process_zeolite_atlas(): input file not available 452s u+s,u,s: 0.33 0.27 0.06 455s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 455s 139 455s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 455s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints_cartesian.py" [FAIL] 6.5s 455s Time: 6.51 455s Return code: 139 455s OKs: 0 455s Standard error: 455s Segmentation fault (core dumped) 458s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 458s 139 458s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 458s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reflection_statistics.py" [FAIL] 6.0s 458s Time: 6.03 458s Return code: 139 458s OKs: 0 458s Standard error: 458s Segmentation fault (core dumped) 461s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 461s 139 461s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 461s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_harker.py" [FAIL] 6.5s 461s Time: 6.54 461s Return code: 139 461s OKs: 0 461s Standard error: 461s Segmentation fault (core dumped) 465s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 465s 139 465s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 465s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_special_op_simplifier.py" [FAIL] 6.8s 465s Time: 6.80 465s Return code: 139 465s OKs: 0 465s Standard error: 465s Segmentation fault (core dumped) 468s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 468s 139 468s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 468s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_twin_target.py" [FAIL] 6.9s 468s Time: 6.94 468s Return code: 139 468s OKs: 0 468s Standard error: 468s Segmentation fault (core dumped) 471s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 471s 139 471s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 471s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/symbol_confidence.py" [FAIL] 6.8s 471s Time: 6.80 471s Return code: 139 471s OKs: 0 471s Standard error: 471s Segmentation fault (core dumped) 475s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 475s 139 475s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 475s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/bravais_types.py" [FAIL] 6.7s 475s Time: 6.68 475s Return code: 139 475s OKs: 0 475s Standard error: 475s 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_lookup_utils.py" [FAIL] 6.9s 478s Time: 6.86 478s Return code: 139 478s OKs: 0 478s Standard error: 478s Segmentation fault (core dumped) 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_crystal.py" I41/acd [FAIL] 7.1s 482s Time: 7.07 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_direct_space_asu.py" I41/acd [FAIL] 7.1s 485s Time: 7.09 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_pair_asu_table.py" [FAIL] 7.1s 489s Time: 7.12 489s Return code: 139 489s OKs: 0 489s Standard error: 489s Segmentation fault (core dumped) 489s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_coordination_sequences.py" [OK] 0.4s 489s Time: 0.42 489s Return code: 0 489s OKs: 1 489s Standard out: 489s Skipping exercise(): input file not available 489s OK 492s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 492s 139 492s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 492s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_asu_clusters.py" [FAIL] 6.8s 492s Time: 6.78 492s Return code: 139 492s OKs: 0 492s Standard error: 492s Segmentation fault (core dumped) 496s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 496s 139 496s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 496s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_close_packing.py" R-3mr [FAIL] 6.4s 496s Time: 6.41 496s Return code: 139 496s OKs: 0 496s Standard error: 496s Segmentation fault (core dumped) 499s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 499s 139 499s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 499s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fourier_transform_real_part_at_x.py" P31 [FAIL] 6.8s 499s Standard error: 499s Segmentation fault (core dumped) 499s Time: 6.78 499s Return code: 139 499s OKs: 0 503s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 503s 139 503s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 503s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller.py" P31 [FAIL] 7.0s 503s Time: 6.97 503s Return code: 139 503s OKs: 0 503s Standard error: 503s Segmentation fault (core dumped) 503s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem_2.py" [OK] 0.4s 503s Time: 0.37 503s Return code: 0 503s OKs: 0 503s Standard out: 503s Skipping test: phenix not available 506s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 506s 139 506s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 506s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem.py" [FAIL] 7.3s 506s Time: 7.26 506s Return code: 139 506s OKs: 0 506s Standard error: 506s Segmentation fault (core dumped) 510s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 510s 139 510s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 510s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reciprocal_space_asu.py" P312 [FAIL] 6.4s 510s Time: 6.44 510s Return code: 139 510s OKs: 0 510s Standard error: 510s Segmentation fault (core dumped) 513s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 513s 139 513s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 513s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_triplet_generator.py" P41 [FAIL] 6.6s 513s Time: 6.62 513s Return code: 139 513s OKs: 0 513s Standard error: 513s Segmentation fault (core dumped) 517s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 517s 139 517s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 517s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_emma.py" P31 [FAIL] 7.0s 517s Time: 6.97 517s Return code: 139 517s OKs: 0 517s Standard error: 517s Segmentation fault (core dumped) 520s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 520s 139 520s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 520s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_expand_to_p1.py" P31 [FAIL] 6.9s 520s Time: 6.88 520s Return code: 139 520s OKs: 0 520s Standard error: 520s Segmentation fault (core dumped) 523s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 523s 139 523s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 523s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_change_basis.py" P31 [FAIL] 6.5s 523s Time: 6.47 523s Return code: 139 523s OKs: 0 523s Standard error: 523s Segmentation fault (core dumped) 526s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 526s 139 526s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 526s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wilson_plot.py" P31 [FAIL] 6.6s 526s Time: 6.62 526s Return code: 139 526s OKs: 0 526s Standard error: 526s Segmentation fault (core dumped) 530s Standard error: 530s Segmentation fault (core dumped) 530s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 530s 139 530s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 530s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_derivatives.py" P31 [FAIL] 6.7s 530s Time: 6.71 530s Return code: 139 530s OKs: 0 533s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 533s 139 533s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 533s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_fast_gradients.py" P31 [FAIL] 6.7s 533s Time: 6.69 533s Return code: 139 533s OKs: 0 533s Standard error: 533s Segmentation fault (core dumped) 536s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 536s 139 536s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 536s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F P31 [FAIL] 6.3s 536s Time: 6.30 536s Return code: 139 536s OKs: 0 536s Standard error: 536s Segmentation fault (core dumped) 536s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 536s 139 536s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 536s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F_sq P31 [FAIL] 3.0s 536s Time: 3.01 536s Return code: 139 536s OKs: 0 536s Standard error: 536s Segmentation fault (core dumped) 539s Standard error: 539s Segmentation fault (core dumped) 539s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 539s 139 539s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 539s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_weights_for_symmetry_summation.py" Pmmm [FAIL] 3.4s 539s Time: 3.39 539s Return code: 139 539s OKs: 0 543s Standard error: 543s Segmentation fault (core dumped) 543s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 543s 139 543s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 543s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_structure_factors.py" P31 [FAIL] 6.6s 543s Time: 6.58 543s Return code: 139 543s OKs: 0 546s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 546s 139 546s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 546s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_real_space_refinement_simple.py" [FAIL] 6.4s 546s Time: 6.41 546s Return code: 139 546s OKs: 0 546s Standard error: 546s Segmentation fault (core dumped) 549s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 549s 139 549s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 549s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation.py" [FAIL] 6.2s 549s Time: 6.23 549s Return code: 139 549s OKs: 0 549s Standard error: 549s Segmentation fault (core dumped) 552s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 552s 139 552s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 552s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation_2.py" [FAIL] 6.2s 552s Time: 6.17 552s Return code: 139 552s OKs: 0 552s Standard error: 552s Segmentation fault (core dumped) 556s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 556s 139 556s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 556s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_loc_res.py" [FAIL] 7.3s 556s Time: 7.33 556s Return code: 139 556s OKs: 0 556s Standard error: 556s 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/maptbx/tst_target_and_gradients.py" [FAIL] 7.4s 559s Time: 7.43 559s Return code: 139 559s OKs: 0 559s Standard error: 559s Segmentation fault (core dumped) 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_miller_merge_equivalents.py" P31 [FAIL] 6.6s 563s Time: 6.58 563s Return code: 139 563s OKs: 0 563s Standard error: 563s Segmentation fault (core dumped) 566s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 566s 139 566s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 566s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grouped_data.py" P31 [FAIL] 6.7s 566s Time: 6.67 566s Return code: 139 566s OKs: 0 566s Standard error: 566s Segmentation fault (core dumped) 570s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 570s 139 570s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 570s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_fft_map.py" P31 [FAIL] 6.8s 570s Time: 6.75 570s Return code: 139 570s OKs: 0 570s Standard error: 570s Segmentation fault (core dumped) 573s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 573s 139 573s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 573s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sampled_model_density.py" P31 [FAIL] 6.6s 573s Time: 6.59 573s Return code: 139 573s OKs: 0 573s Standard error: 573s Segmentation fault (core dumped) 573s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints.py" [OK] 0.7s 573s Time: 0.69 573s Return code: 0 573s OKs: 1 573s Standard out: 573s OK 576s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 576s 139 576s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 576s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fast_nv1995.py" F222 [FAIL] 6.4s 576s Time: 6.37 576s Return code: 139 576s OKs: 0 576s Standard error: 576s Segmentation fault (core dumped) 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/regression/tst_geometry_restraints_lbfgs.py" [FAIL] 5.9s 579s Time: 5.90 579s Return code: 139 579s OKs: 0 579s Standard error: 579s Segmentation fault (core dumped) 580s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grm_pickling.py" [OK] 0.4s 580s Time: 0.43 580s Return code: 0 580s OKs: 0 580s Standard out: 580s Can not initialize monomer_library, skipping test. 583s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 583s 139 583s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 583s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_2.py" [FAIL] 7.0s 583s Time: 7.05 583s Return code: 139 583s OKs: 0 583s Standard error: 583s 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/regression/tst_french_wilson.py" [FAIL] 6.2s 586s Time: 6.19 586s Return code: 139 586s OKs: 0 586s Standard error: 586s Segmentation fault (core dumped) 586s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/tst_cns_epsilon.py" P31 [OK] 0.2s 586s Time: 0.24 586s Return code: 0 586s OKs: 0 586s Standard out: 586s Skipping tests: cns not available. 586s u+s,u,s: 0.20 0.15 0.05 586s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/tst_cns_hl.py" P31 [OK] 0.2s 586s Time: 0.24 586s Return code: 0 586s OKs: 0 586s Standard out: 586s Skipping tests: cns not available. 586s u+s,u,s: 0.19 0.15 0.04 587s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/run_shelx76.py" P31 [OK] 0.3s 587s Time: 0.27 587s Return code: 0 587s OKs: 0 587s Standard out: 587s shelx76 not available. 589s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 589s 139 589s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 589s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/make_cns_input.py" P31 [FAIL] 6.1s 589s Time: 6.13 589s Return code: 139 589s OKs: 0 589s Standard error: 589s Segmentation fault (core dumped) 592s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 592s 139 592s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 592s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pointgroup_tools.py" [FAIL] 5.4s 592s Time: 5.41 592s Return code: 139 592s OKs: 0 592s Standard error: 592s Segmentation fault (core dumped) 595s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 595s 139 595s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 595s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/sub_lattice_tools.py" [FAIL] 6.2s 595s Standard error: 595s Segmentation fault (core dumped) 595s Time: 6.16 595s Return code: 139 595s 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/rational_matrices_point_groups.py" [FAIL] 6.1s 598s Time: 6.11 598s Return code: 139 598s OKs: 0 598s Standard error: 598s Segmentation fault (core dumped) 601s Standard error: 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/cosets.py" [FAIL] 5.9s 601s Time: 5.86 601s Return code: 139 601s OKs: 0 601s Segmentation fault (core dumped) 604s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 604s 139 604s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 604s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_pg_tools.py" [FAIL] 6.0s 604s Time: 6.01 604s Return code: 139 604s OKs: 0 604s Standard error: 604s Segmentation fault (core dumped) 608s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 608s 139 608s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 608s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_twin_laws.py" [FAIL] 6.6s 608s Time: 6.57 608s Return code: 139 608s OKs: 0 608s Standard error: 608s Segmentation fault (core dumped) 611s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 611s 139 611s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 611s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_find_best_cell.py" [FAIL] 6.5s 611s Time: 6.47 611s Return code: 139 611s OKs: 0 611s Standard error: 611s Segmentation fault (core dumped) 614s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 614s 139 614s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 614s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_amplitude_normalisation.py" [FAIL] 6.2s 614s Time: 6.23 614s Return code: 139 614s OKs: 0 614s Standard error: 614s 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_statistics_graphs.py" [FAIL] 6.4s 617s Time: 6.41 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/regression/tst_web_change_basis.py" [FAIL] 6.5s 620s Time: 6.52 620s Return code: 139 620s OKs: 0 620s Standard error: 620s Segmentation fault (core dumped) 623s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 623s 139 623s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 623s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/direct_space_asu/proto/tst_asu.py" [FAIL] 6.3s 623s Time: 6.31 623s Return code: 139 623s OKs: 0 623s Standard error: 623s Segmentation fault (core dumped) 627s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 627s 139 627s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 627s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_tidy_pickling.py" [FAIL] 6.3s 627s Time: 6.26 627s Return code: 139 627s OKs: 0 627s Standard error: 627s Segmentation fault (core dumped) 630s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 630s 139 630s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 630s libtbx.python "/usr/lib/python3/dist-packages/cctbx/masks/tests/tst_flood_fill.py" [FAIL] 6.2s 630s Time: 6.24 630s Return code: 139 630s OKs: 0 630s Standard error: 630s Segmentation fault (core dumped) 630s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/observations/tst_observations.py" [OK] 0.3s 630s Time: 0.27 630s Return code: 0 630s OKs: 1 630s Standard out: 630s OK 633s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 633s 139 633s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 633s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_r_free_utils.py" [FAIL] 6.1s 633s Time: 6.14 633s Return code: 139 633s OKs: 0 633s Standard error: 633s Segmentation fault (core dumped) 636s Standard error: 636s 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] 6.3s 636s Time: 6.27 636s Return code: 139 636s OKs: 0 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] 6.9s 640s Time: 6.93 640s Return code: 139 640s OKs: 0 640s Standard error: 640s Segmentation fault (core dumped) 643s Standard error: 643s Segmentation fault (core dumped) 643s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 643s 139 643s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 643s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_map_peak_3d_as_2d.py" [FAIL] 6.8s 643s Time: 6.85 643s Return code: 139 643s OKs: 0 646s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 646s 139 646s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 646s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_asymmetric_map.py" [FAIL] 6.7s 646s Time: 6.74 646s Return code: 139 646s OKs: 0 646s Standard error: 646s Segmentation fault (core dumped) 650s Standard error: 650s Segmentation fault (core dumped) 650s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 650s 139 650s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 650s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_peak_volume_estimate.py" [FAIL] 6.8s 650s Time: 6.78 650s Return code: 139 650s OKs: 0 653s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 653s 139 653s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 653s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_resolution_from_map_and_model.py" [FAIL] 6.8s 653s Time: 6.82 653s Return code: 139 653s OKs: 0 653s Standard error: 653s Segmentation fault (core dumped) 657s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 657s 139 657s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 657s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_curves.py" [FAIL] 6.9s 657s Time: 6.87 657s Return code: 139 657s OKs: 0 657s Standard error: 657s Segmentation fault (core dumped) 660s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 660s 139 660s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 660s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_radius_as_central_peak_width.py" [FAIL] 6.7s 660s Time: 6.72 660s Return code: 139 660s OKs: 0 660s Standard error: 660s Segmentation fault (core dumped) 661s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_box.py" [OK] 0.7s 661s Time: 0.74 661s Return code: 0 661s OKs: 0 661s Standard out: 661s phenix is not available, skipping test 662s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_create_models_or_maps.py" [OK] 0.8s 662s Time: 0.76 662s Return code: 0 662s OKs: 1 662s Standard out: 662s Skipping exercise(): chem_data directory not available 662s OK 664s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 664s 139 664s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 664s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_get_percentile_cutoffs.py" [FAIL] 6.8s 664s Time: 6.82 664s Return code: 139 664s OKs: 0 664s Standard error: 664s Segmentation fault (core dumped) 667s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 667s 139 667s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 667s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sphericity.py" [FAIL] 5.6s 667s Time: 5.57 667s Return code: 139 667s OKs: 0 667s Standard error: 667s Segmentation fault (core dumped) 667s libtbx.python "/usr/lib/python3/dist-packages/cctbx/merging/brehm_diederichs.py" [OK] 0.3s 667s Time: 0.29 667s Return code: 0 667s OKs: 1 667s Standard out: 667s OK 668s libtbx.python "/usr/lib/python3/dist-packages/cctbx/multipolar/regression/tst_multipolar.py" [OK] 0.2s 668s Time: 0.21 668s Return code: 0 668s OKs: 3 668s Standard out: 668s OK 668s 0 668s 1 668s 2 668s OK 668s Skipping exercise(): chem_data directory not available 668s OK 671s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 671s 139 671s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 671s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_statistics.py" [FAIL] 7.0s 671s Time: 6.98 671s Return code: 139 671s OKs: 0 671s Standard error: 671s Segmentation fault (core dumped) 674s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 674s 139 674s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 674s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity.py" [FAIL] 6.3s 674s Time: 6.34 674s Return code: 139 674s OKs: 0 674s Standard error: 674s Segmentation fault (core dumped) 677s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 677s 139 677s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 677s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity_allsym.py" [FAIL] 6.7s 677s Time: 6.65 677s Return code: 139 677s OKs: 0 677s Standard error: 677s Segmentation fault (core dumped) 678s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grm_modifications.py" [OK] 0.8s 678s Time: 0.77 678s Return code: 0 678s OKs: 1 678s Standard out: 678s Can not initialize monomer_library, skipping test. 678s OK 683s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 683s 1 683s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 683s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py" [FAIL] 9.2s 683s Time: 9.22 683s Return code: 1 683s OKs: 0 683s Standard error: 683s Segmentation fault (core dumped) 683s Traceback (most recent call last): 683s File "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py", line 140, in 683s exercise() 683s ~~~~~~~~^^ 683s File "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py", line 126, in exercise 683s assert not easy_run.call(cmd) 683s ^^^^^^^^^^^^^^^^^^^^^^ 683s AssertionError 685s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 685s 139 685s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 685s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_prepare_map_for_docking.py" [FAIL] 7.0s 685s Time: 6.96 685s Return code: 139 685s OKs: 0 685s Standard error: 685s Segmentation fault (core dumped) 686s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wavelength_units.py" [OK] 2.6s 686s Time: 2.55 686s Return code: 0 686s OKs: 1 686s Standard out: 686s OK 689s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 689s 139 689s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 689s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fcalc_fft_stability.py" [EXPECTED UNSTABLE] 3.7s 689s Time: 3.72 689s Return code: 139 689s OKs: 0 689s Standard error: 689s Segmentation fault (core dumped) 689s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_ext.py" [OK] 0.1s 689s Time: 0.11 689s Return code: 0 689s OKs: 1 689s Standard out: 689s OK 689s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_equivalence.py" [OK] 0.1s 689s Time: 0.11 689s Return code: 0 689s OKs: 1 689s Standard out: 689s OK 690s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_read.py" [OK] 0.7s 690s Time: 0.69 690s Return code: 0 690s OKs: 1 690s Standard out: 690s OK 690s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_cout.py" [OK] 0.5s 690s Time: 0.46 690s Return code: 0 690s OKs: 1 690s Standard out: 690s OK 690s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_show_calls.py" [OK] 0.4s 690s Time: 0.39 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/cma_es/tst_cma_es.py" [FAIL] 5.9s 692s Time: 5.85 692s Return code: 139 692s OKs: 0 692s Standard error: 692s Segmentation fault (core dumped) 698s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_command_line.py" [OK] 7.5s 698s Time: 7.46 698s Return code: 0 698s OKs: 1 698s Standard out: 698s fable.split "/usr/lib/python3/dist-packages/fable/test/valid/subroutine_1.f" 698s fable.read --each "/usr/lib/python3/dist-packages/fable/test/valid/write_star.f" 698s fable.read --warnings "/usr/lib/python3/dist-packages/fable/test/valid/equivalence_mixed.f" 698s fable.show_calls --write-graphviz-dot=tmp.dot --top-procedure=sub "/usr/lib/python3/dist-packages/fable/test/valid/external_arg_layers.f" 698s fable.show_calls "/usr/lib/python3/dist-packages/fable/test/valid/dependency_cycle.f" 698s fable.fem_include_search_paths --with-quotes 698s fable.cout --each "/usr/lib/python3/dist-packages/fable/test/valid/write_star.f" 698s fable.cout "/usr/lib/python3/dist-packages/fable/test/valid/common_variants.f" 698s fable.cout "/usr/lib/python3/dist-packages/fable/test/valid/subroutine_3.f" --top-procedure=sub3 --fortran-file-comments 698s fable.cout --compile "/usr/lib/python3/dist-packages/fable/test/valid/write_star.f" 698s fable.cout --namespace=test --run "/usr/lib/python3/dist-packages/fable/test/valid/write_star.f" 698s fable.cout --example 698s fable.cout /usr/lib/python3/dist-packages/fable/test/valid/sf.f --namespace example --run 698s fable.cout "/usr/lib/python3/dist-packages/fable/test/valid/dynamic_parameters_1.f" --dynamic-parameter="int root_size=1" 698s OK 702s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_cout_compile.py" stop [OK] 4.2s 702s Time: 4.23 702s Return code: 0 702s OKs: 1 702s Standard out: 702s 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" 702s 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" 702s 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" 702s OK 702s usr+sys time: 0.15 seconds 702s wall clock time: 4.18 seconds 705s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_separate_files.py" [OK] 13.3s 705s Time: 13.26 705s Return code: 0 705s OKs: 1 705s Standard out: 705s 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" 705s 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" 705s 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" 705s 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" 705s 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" 705s 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" 705s 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" 705s 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" 705s 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" 705s 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" 705s 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" 705s 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" 705s 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" 705s 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" 705s 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" 705s 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" 705s 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" 705s OK 705s usr+sys time: 0.26 seconds 705s wall clock time: 13.22 seconds 705s libtbx.python "/usr/lib/python3/dist-packages/gltbx/tst_ellipsoids.py" [OK] 0.3s 705s Time: 0.33 705s Return code: 0 705s OKs: 1 705s Standard out: 705s OK 709s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 709s 139 709s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 709s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mrc_io.py" [FAIL] 3.6s 709s Time: 3.56 709s Return code: 139 709s OKs: 0 709s Standard error: 709s Segmentation fault (core dumped) 709s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_wildcard.py" [OK] 0.1s 709s Time: 0.10 709s Return code: 0 709s OKs: 1 709s Standard out: 709s OK 711s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_io.py" [OK] 9.0s 711s Time: 8.98 711s Return code: 0 711s OKs: 1 711s Standard out: 711s OK 711s usr+sys time: 0.21 seconds 711s wall clock time: 8.93 seconds 711s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_parser.py" [OK] 0.1s 711s Time: 0.07 711s Return code: 0 711s OKs: 1 711s Standard out: 711s OK 713s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 713s 139 713s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 713s libtbx.python "/usr/lib/python3/dist-packages/iotbx/gui_tools/tst.py" [FAIL] 3.8s 713s Time: 3.84 713s Return code: 139 713s OKs: 0 713s Standard error: 713s Segmentation fault (core dumped) 713s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_cif_inputs.py" [OK] 0.3s 713s Time: 0.30 713s Return code: 0 713s OKs: 1 713s Standard out: 713s OK 716s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 716s 139 716s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 716s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phil.py" [FAIL] 4.7s 716s Time: 4.74 716s Return code: 139 716s OKs: 0 716s Standard error: 716s Segmentation fault (core dumped) 720s Standard error: 720s Segmentation fault (core dumped) 720s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 720s 139 720s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 720s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_manager.py" [FAIL] 7.1s 720s Time: 7.07 720s Return code: 139 720s OKs: 0 723s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 723s 139 723s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 723s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager_wrapping.py" [FAIL] 7.3s 723s Time: 7.34 723s Return code: 139 723s OKs: 0 723s Standard error: 723s Segmentation fault (core dumped) 724s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager.py" [OK] 0.8s 724s Time: 0.77 724s Return code: 0 724s OKs: 1 724s Standard out: 724s Skip test_01, chem_data not available 724s OK 725s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_2.py" [OK] 0.8s 725s Time: 0.79 725s Return code: 0 725s OKs: 0 725s Standard out: 725s chem_data is not available, skipping 726s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_3.py" [OK] 0.7s 726s Time: 0.73 726s Return code: 0 726s OKs: 1 726s Standard out: 726s Skipped: Requires phenix module 726s OK 726s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_4.py" [OK] 0.2s 726s Time: 0.18 726s Return code: 0 726s OKs: 1 726s Standard out: 726s Skipping tst_map_model_manager_4 tests becuase Phenix is not available. 726s OK 726s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_model_sharpening_5.py" [OK] 0.7s 726s Time: 0.71 726s Return code: 0 726s OKs: 1 726s Standard out: 726s Skip test_01, chem_data not available 726s OK 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_map_manager.py" [FAIL] 6.6s 727s Time: 6.60 727s Return code: 139 727s OKs: 0 727s Standard error: 727s Segmentation fault (core dumped) 727s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_model_sharpening_5_cif.py" [OK] 0.7s 727s Time: 0.72 727s Return code: 0 727s OKs: 1 727s Standard out: 727s Skip test_01, chem_data not available 727s OK 727s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_call_consistency.py" [OK] 0.7s 727s Time: 0.70 727s Return code: 0 727s OKs: 1 727s Standard out: 727s 727s Expected and actual args in calls for with_bounds 727s 727s box.with_bounds.__init__ : 727s 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'] 727s 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'] 727s 727s box_all_maps_with_bounds_and_shift_origin : 727s 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'] 727s 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'] 727s 727s extract_all_maps_with_bounds : 727s Expected :['lower_bounds', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'upper_bounds', 'use_cubic_boxing'] 727s 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'] 727s 727s Expected and actual args in calls for around_model 727s 727s box.around_model.__init__ : 727s 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'] 727s 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'] 727s 727s box_all_maps_around_model_and_shift_origin : 727s 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'] 727s 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'] 727s 727s extract_all_maps_around_model : 727s 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'] 727s 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'] 727s 727s Expected and actual args in calls for around_density 727s 727s box.around_density.__init__ : 727s 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'] 727s 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'] 727s 727s box_all_maps_around_density_and_shift_origin : 727s 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'] 727s 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'] 727s 727s extract_all_maps_around_density : 727s 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'] 727s 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'] 727s 727s Expected and actual args in calls for around_mask 727s 727s box.around_mask.__init__ : 727s 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'] 727s 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'] 727s 727s box_all_maps_around_mask_and_shift_origin : 727s 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'] 727s 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'] 727s 727s extract_all_maps_around_mask : 727s Expected :['box_cushion', 'mask_id', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'use_cubic_boxing'] 727s 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'] 727s 727s Expected and actual args in calls for around_unique 727s 727s box.around_unique.__init__ : 727s 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'] 727s 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'] 727s 727s box_all_maps_around_unique_and_shift_origin : 727s 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'] 727s 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'] 727s 727s extract_all_maps_around_unique : 727s 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'] 727s 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'] 727s 727s Expected and actual args in calls for around_atoms 727s 727s cctbx.maptbx.mask.create_mask_around_atoms.__init__ : 727s Expected :['invert_mask', 'map_manager', 'mask_atoms_atom_radius', 'model', 'n_real', 'self', 'wrapping', 'xray_structure'] 727s Found : ['invert_mask', 'map_manager', 'mask_atoms_atom_radius', 'model', 'n_real', 'self', 'wrapping', 'xray_structure'] 727s 727s map_model_manager.create_mask_around_atoms : 727s Expected :['invert_mask', 'mask_atoms_atom_radius', 'mask_id', 'model', 'self', 'soft_mask', 'soft_mask_radius'] 727s Found : ['invert_mask', 'mask_atoms_atom_radius', 'mask_id', 'model', 'self', 'soft_mask', 'soft_mask_radius'] 727s 727s Expected and actual args in calls for around_edges 727s 727s cctbx.maptbx.mask.create_mask_around_edges.__init__ : 727s Expected :['boundary_radius', 'map_manager', 'self'] 727s Found : ['boundary_radius', 'map_manager', 'self'] 727s 727s map_model_manager.create_mask_around_edges : 727s Expected :['boundary_radius', 'mask_id', 'self'] 727s Found : ['boundary_radius', 'boundary_to_smoothing_ratio', 'mask_id', 'self', 'soft_mask_radius'] 727s 727s Expected and actual args in calls for around_density 727s 727s cctbx.maptbx.mask.create_mask_around_density.__init__ : 727s Expected :['map_manager', 'molecular_mass', 'resolution', 'self', 'sequence', 'solvent_content'] 727s Found : ['map_manager', 'molecular_mass', 'resolution', 'self', 'sequence', 'solvent_content'] 727s 727s map_model_manager.create_mask_around_density : 727s Expected :['map_id', 'mask_id', 'resolution', 'self', 'soft_mask', 'soft_mask_radius', 'solvent_content'] 727s Found : ['map_id', 'mask_id', 'resolution', 'self', 'soft_mask', 'soft_mask_radius', 'solvent_content'] 727s OK 728s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_external_sharpening_7.py" [OK] 0.7s 728s Time: 0.72 728s Return code: 0 728s OKs: 1 728s Standard out: 728s Skip test_01, chem_data not available 728s OK 728s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_half_map_sharpening_6.py" [OK] 0.7s 728s Time: 0.71 728s Return code: 0 728s OKs: 1 728s Standard out: 728s Skip test_01, chem_data not available 728s OK 729s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_tls_from_map_8.py" [OK] 0.7s 729s Time: 0.74 729s Return code: 0 729s OKs: 1 729s Standard out: 729s Skip test_01, chem_data not available 729s OK 729s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_cif.py" [OK] 0.7s 729s Time: 0.73 729s Return code: 0 729s OKs: 1 729s Standard out: 729s Skip test_01, chem_data not available 729s OK 733s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 733s 139 733s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 733s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry.py" [FAIL] 4.8s 733s Time: 4.83 733s Return code: 139 733s OKs: 0 733s Standard error: 733s Segmentation fault (core dumped) 734s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_local_resolution_10.py" [OK] 0.7s 734s Time: 0.65 734s Return code: 0 734s OKs: 1 734s Standard out: 734s Skip test_01, chem_data not available 734s OK 737s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 737s 139 737s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 737s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry_cif.py" [FAIL] 8.6s 737s Time: 8.62 737s Return code: 139 737s OKs: 0 737s Standard error: 737s Segmentation fault (core dumped) 737s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_patterson.py" [OK] 0.1s 737s Time: 0.08 737s Return code: 0 737s OKs: 1 737s Standard out: 737s phenix_regression not available, skipping 737s OK 738s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_restraints_merge.py" [OK] 0.3s 738s Time: 0.30 738s Return code: 0 738s OKs: 0 741s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 741s 139 741s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 741s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_tools.py" [FAIL] 6.5s 741s Time: 6.45 741s Return code: 139 741s OKs: 0 741s Standard error: 741s Segmentation fault (core dumped) 741s libtbx.python "/usr/lib/python3/dist-packages/iotbx/ranges.py" [OK] 0.0s 741s Time: 0.03 741s Return code: 0 741s OKs: 1 741s Standard out: 741s OK 744s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 744s 139 744s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_atom_selections_10k.py" [FAIL] 6.1s 744s Time: 6.10 744s Return code: 139 744s OKs: 0 744s Standard error: 744s Segmentation fault (core dumped) 744s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_poscar.py" [OK] 0.1s 744s Time: 0.08 744s Return code: 0 744s OKs: 1 744s Standard out: 744s Skipping POSCAR tests: input files not available 744s OK 747s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 747s 139 747s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 747s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_crystal_symmetry_from_any.py" [FAIL] 6.6s 747s Time: 6.56 747s Return code: 139 747s OKs: 0 747s Standard error: 747s Segmentation fault (core dumped) 750s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 750s 139 750s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 750s libtbx.python "/usr/lib/python3/dist-packages/iotbx/kriber/tst_strudat.py" [FAIL] 6.3s 750s Time: 6.30 750s Return code: 139 750s OKs: 0 750s Standard error: 750s Segmentation fault (core dumped) 753s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 753s 139 753s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 753s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_geometry.py" [FAIL] 6.2s 753s Time: 6.24 753s Return code: 139 753s OKs: 0 753s Standard error: 753s Segmentation fault (core dumped) 757s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 757s 139 757s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 757s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_lex_parse_build.py" [FAIL] 6.6s 757s Time: 6.57 757s Return code: 139 757s OKs: 0 757s Standard error: 757s Segmentation fault (core dumped) 760s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 760s 139 760s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 760s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model.py" [FAIL] 6.6s 760s Time: 6.58 760s Return code: 139 760s OKs: 0 760s Standard error: 760s Segmentation fault (core dumped) 762s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 762s 1 762s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 762s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py" [FAIL] 2.5s 762s Time: 2.48 762s Return code: 1 762s OKs: 0 762s Standard out: 762s Skipping tst_validation.exercise_smart_load() because of URLError. 762s Standard error: 762s Traceback (most recent call last): 762s File "/usr/lib/python3.13/urllib/request.py", line 1541, in ftp_open 762s fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout) 762s File "/usr/lib/python3.13/urllib/request.py", line 1561, in connect_ftp 762s return ftpwrapper(user, passwd, host, port, dirs, timeout, 762s persistent=False) 762s File "/usr/lib/python3.13/urllib/request.py", line 2409, in __init__ 762s self.init() 762s ~~~~~~~~~^^ 762s File "/usr/lib/python3.13/urllib/request.py", line 2418, in init 762s self.ftp.connect(self.host, self.port, self.timeout) 762s ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 762s File "/usr/lib/python3.13/ftplib.py", line 158, in connect 762s self.sock = socket.create_connection((self.host, self.port), self.timeout, 762s ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 762s source_address=self.source_address) 762s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 762s File "/usr/lib/python3.13/socket.py", line 864, in create_connection 762s raise exceptions[0] 762s File "/usr/lib/python3.13/socket.py", line 849, in create_connection 762s sock.connect(sa) 762s ~~~~~~~~~~~~^^^^ 762s ConnectionRefusedError: [Errno 111] Connection refused 762s 762s The above exception was the direct cause of the following exception: 762s 762s Traceback (most recent call last): 762s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 327, in 762s exercise(sys.argv[1:]) 762s ~~~~~~~~^^^^^^^^^^^^^^ 762s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 26, in exercise 762s exercise_validation() 762s ~~~~~~~~~~~~~~~~~~~^^ 762s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 29, in exercise_validation 762s cd = validation.smart_load_dictionary(name="cif_core.dic") 762s File "/usr/lib/python3/dist-packages/iotbx/cif/validation.py", line 111, in smart_load_dictionary 762s url = locate_dictionary(name, registry_location=registry_location) 762s File "/usr/lib/python3/dist-packages/iotbx/cif/validation.py", line 129, in locate_dictionary 762s cm = cif.reader(file_object=urlopen(registry_location)).model() 762s ~~~~~~~^^^^^^^^^^^^^^^^^^^ 762s File "/usr/lib/python3.13/urllib/request.py", line 189, in urlopen 762s return opener.open(url, data, timeout) 762s ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 762s File "/usr/lib/python3.13/urllib/request.py", line 489, in open 762s response = self._open(req, data) 762s File "/usr/lib/python3.13/urllib/request.py", line 506, in _open 762s result = self._call_chain(self.handle_open, protocol, protocol + 762s '_open', req) 762s File "/usr/lib/python3.13/urllib/request.py", line 466, in _call_chain 762s result = func(*args) 762s File "/usr/lib/python3.13/urllib/request.py", line 1558, in ftp_open 762s raise URLError(exp) from exp 762s urllib.error.URLError: 763s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_parser.py" [OK] 0.3s 763s Time: 0.27 763s Return code: 0 763s OKs: 0 763s Standard out: 763s 1 0 0 763s 1 0 0 763s 1 0 0 763s 1 0 0 763s 1 0 0 763s 1 0 0 763s 1 0 0 763s 1 0 0 763s 1 0 0 763s 0 0 0 763s 0 0 0 763s 1 0 0 763s 0 0 0 763s 0 0 0 763s 1 0 0 763s 1 0 0 763s 1 0 0 763s 1 0 0 763s 1 0 0 763s 1 0 0 763s 1 0 0 763s 1 0 0 763s 1 0 0 763s 1 0 0 763s 1 0 0 763s 1 0 0 763s 0 0 0 763s 1 0 0 763s 1 0 0 763s 1 0 0 763s 1 0 0 763s 1 0 0 763s 0 0 0 763s 0 1 0 763s 0 1 0 763s 0 0 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 0 1 0 763s 1 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s 2 0 0 763s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_citations.py" [OK] 0.4s 763s Time: 0.38 763s Return code: 0 763s OKs: 1 763s Standard out: 763s OK 763s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model_builder.py" [OK] 0.3s 763s Time: 0.26 763s Return code: 0 763s OKs: 0 763s Standard error: 763s 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/cif/tests/tst_restraints.py" [FAIL] 6.5s 763s Time: 6.52 763s Return code: 139 763s OKs: 0 767s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 767s 139 767s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 767s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_hklf.py" [FAIL] 3.6s 767s Time: 3.56 767s Return code: 139 767s OKs: 0 767s Standard error: 767s 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/shelx/tst_lex_parse_build.py" [FAIL] 6.9s 770s Time: 6.90 770s Return code: 139 770s OKs: 0 770s Standard error: 770s Segmentation fault (core dumped) 773s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 773s 139 773s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 773s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_writer.py" [FAIL] 6.5s 773s Time: 6.51 773s Return code: 139 773s OKs: 0 773s Standard error: 773s Segmentation fault (core dumped) 776s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 776s 139 776s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 776s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_fvar_encoding.py" [FAIL] 6.2s 776s Standard error: 776s Segmentation fault (core dumped) 776s Time: 6.25 776s Return code: 139 776s OKs: 0 777s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif.py" [OK] 0.3s 777s Time: 0.31 777s Return code: 0 777s OKs: 1 777s Standard out: 777s OK 780s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 780s 134 780s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 780s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_pdb.py" [FAIL] 6.4s 780s Time: 6.38 780s Return code: 134 780s OKs: 0 780s Standard error: 780s *** buffer overflow detected ***: terminated 780s Aborted (core dumped) 782s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy_2.py" [OK] 2.5s 782s Time: 2.50 782s Return code: 0 782s OKs: 1 782s Standard out: 782s OK 783s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_tls.py" [OK] 0.7s 783s Time: 0.67 783s Return code: 0 783s OKs: 1 783s Standard out: 783s Skipping exercise_mmcif_tls(): missing phenix_regression directory. 783s OK 783s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/hybrid_36.py" exercise [OK] 0.1s 783s Time: 0.11 783s Return code: 0 783s OKs: 1 783s Standard out: 783s OK 784s Standard error: 784s *** buffer overflow detected ***: terminated 784s Aborted (core dumped) 784s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 784s 134 784s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 784s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy.py" [FAIL] 7.0s 784s Time: 7.05 784s Return code: 134 784s OKs: 0 784s "/usr/lib/cctbx/python3.13/iotbx/pdb/hybrid_36_fem" [OK] 0.9s 784s Time: 0.95 784s Return code: 0 784s OKs: 0 784s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy_atom_sort.py" [OK] 0.3s 784s Time: 0.31 784s Return code: 0 784s OKs: 1 784s Standard out: 784s OK 785s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy_flip_symmetric.py" [OK] 0.3s 785s Time: 0.27 785s Return code: 0 785s OKs: 0 785s Standard out: 785s chem_data is missing, skipping test 785s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_selected_hierarchy_flip.py" [OK] 0.3s 785s Time: 0.33 785s Return code: 0 785s OKs: 0 788s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 788s 139 788s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 788s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy.py" [FAIL] 4.0s 788s Time: 3.96 788s Return code: 139 788s OKs: 0 788s Standard error: 788s Segmentation fault (core dumped) 791s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 791s 139 791s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 791s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_ext.py" [FAIL] 6.2s 791s Time: 6.16 791s Return code: 139 791s OKs: 0 791s Standard error: 791s Segmentation fault (core dumped) 791s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_rna_dna_atom_names.py" [OK] 0.3s 791s Time: 0.26 791s Return code: 0 791s OKs: 1 791s Standard out: 791s OK 792s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_name_interpretation.py" [OK] 0.3s 792s Time: 0.25 792s Return code: 0 792s OKs: 1 792s Standard out: 792s OK 792s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_extract_rfactors_resolutions_sigma.py" [OK] 0.2s 792s Time: 0.25 792s Return code: 0 792s OKs: 1 792s Standard out: 792s OK 792s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/modified_aa_names.py" [OK] 0.0s 792s Time: 0.04 792s Return code: 0 792s OKs: 0 792s Standard out: 792s 2141 792s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/modified_rna_dna_names.py" [OK] 0.0s 792s Time: 0.03 792s Return code: 0 792s OKs: 0 792s Standard out: 792s 792 792s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_sheet.py" [OK] 0.3s 792s Time: 0.27 792s Return code: 0 792s OKs: 1 792s Standard out: 792s OK 792s u+s,u,s: 0.21 0.18 0.03 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/pdb/tst_atom_selection.py" [FAIL] 6.5s 794s Time: 6.47 794s Return code: 139 794s OKs: 0 794s Standard error: 794s Segmentation fault (core dumped) 795s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation_long.py" [OK] 0.3s 795s Time: 0.28 795s Return code: 0 795s OKs: 1 795s Standard out: 795s OK time = 0.013 795s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/secondary_structure.py" [OK] 0.3s 795s Time: 0.29 795s Return code: 0 795s OKs: 0 798s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 798s 139 798s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 798s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation.py" [FAIL] 5.5s 798s Time: 5.53 798s Return code: 139 798s OKs: 0 798s Standard error: 798s Segmentation fault (core dumped) 799s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_secondary_structure.py" [OK] 0.8s 799s Time: 0.77 799s Return code: 0 799s OKs: 5 799s Standard out: 799s OK 799s OK 799s OK 799s OK 799s OK 801s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 801s 139 801s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 801s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection_string.py" [FAIL] 6.1s 801s Time: 6.09 801s Return code: 139 801s OKs: 0 801s Standard error: 801s Segmentation fault (core dumped) 803s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_secondary_structure_2.py" [OK] 1.6s 803s Time: 1.61 803s Return code: 0 803s OKs: 2 803s Standard out: 803s OK 803s OK 803s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/remediation/tst_remediator.py" [OK] 0.7s 803s Time: 0.68 803s Return code: 0 803s OKs: 0 803s Standard out: 803s chem_data is not available for remediator tests, skipping 803s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_to_map_simple.py" [OK] 0.3s 803s Time: 0.26 803s Return code: 0 803s OKs: 0 803s Standard out: 803s Usage: iotbx.python pdb_to_map_simple.py [options] pdb_file... 803s 803s Options: 803s -h, --help show this help message and exit 803s --d_min=FLOAT high-resolution limit for structure-factor calculation 804s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 804s 139 804s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 804s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_utils.py" [FAIL] 5.5s 804s Time: 5.53 804s Return code: 139 804s OKs: 0 804s Standard error: 804s Segmentation fault (core dumped) 804s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_tardy_conf_sampling_simple.py" [OK] 0.3s 804s Time: 0.28 804s Return code: 0 804s OKs: 0 804s Standard out: 804s Time importing extensions: 0.21 804s skipping test: phenix_regression not available. 807s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 807s 134 807s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 807s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_truncate_to_ala/tst.py" [FAIL] 3.7s 807s Time: 3.69 807s Return code: 134 807s OKs: 0 807s Standard error: 807s *** buffer overflow detected ***: terminated 807s Aborted (core dumped) 811s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 811s 139 811s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 811s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_examples.py" [FAIL] 6.7s 811s Time: 6.70 811s Return code: 139 811s OKs: 0 811s Standard error: 811s Segmentation fault (core dumped) 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/cns/space_group_symbols.py" [FAIL] 6.7s 814s Time: 6.65 814s Return code: 139 814s OKs: 0 814s Standard error: 814s Segmentation fault (core dumped) 817s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 817s 139 817s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 817s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/tst_cns.py" [FAIL] 5.8s 817s Time: 5.82 817s Return code: 139 817s OKs: 0 817s Standard error: 817s Segmentation fault (core dumped) 820s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 820s 139 820s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 820s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_merge.py" P31 [FAIL] 5.9s 820s Time: 5.90 820s Return code: 139 820s OKs: 0 820s Standard error: 820s Segmentation fault (core dumped) 823s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 823s 139 823s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 823s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/no_merge_original_index.py" [FAIL] 5.8s 823s Time: 5.80 823s Return code: 139 823s OKs: 0 823s Standard error: 823s Segmentation fault (core dumped) 826s Standard error: 826s Segmentation fault (core dumped) 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/ccp4_map/tst.py" [FAIL] 5.9s 826s Time: 5.85 826s Return code: 139 826s OKs: 0 829s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 829s 139 829s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 829s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_ext.py" [FAIL] 6.4s 829s Time: 6.44 829s Return code: 139 829s OKs: 0 829s Standard error: 829s Segmentation fault (core dumped) 832s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 832s 139 832s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 832s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_extract_from_symmetry_lib.py" [FAIL] 6.6s 832s Time: 6.63 832s Return code: 139 832s OKs: 0 832s Standard error: 832s /usr/lib/python3/dist-packages/ccp4io_adaptbx/__init__.py:25: UserWarning: ccp4io_adaptbx: cannot locate syminfo.lib 832s warnings.warn("ccp4io_adaptbx: cannot locate syminfo.lib") 832s Segmentation fault (core dumped) 832s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_miller_dict.py" [OK] 0.2s 832s Time: 0.24 832s Return code: 0 832s OKs: 0 833s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_unmerged.py" [OK] 0.2s 833s Time: 0.24 833s Return code: 0 833s OKs: 0 833s Standard out: 833s Title: . 833s Space group symbol from file: I23 833s Space group number from file: 197 833s Space group from matrices: I 2 3 (No. 197) 833s Point group symbol from file: PG23 833s Number of batches: 45 833s Number of crystals: 2 833s Number of Miller indices: 13 833s Resolution range: 39.0022 31.8451 833s History: 833s From MTZUTILS 21/11/2017 16:26:11 after history: 833s From MOSFLM run on 1/ 7/08 833s From MOSFLM run on 1/ 7/08 833s Crystal 1: 833s Name: HKL_base 833s Project: HKL_base 833s Id: 1 833s Unit cell: (78.0043, 78.0043, 78.0043, 90, 90, 90) 833s Number of datasets: 1 833s Dataset 1: 833s Name: HKL_base 833s Id: 0 833s Wavelength: 0 833s Number of columns: 18 833s label #valid %valid min max type 833s H 13 100.00% 0.00 1.00 H: index h,k,l 833s K 13 100.00% 2.00 2.00 H: index h,k,l 833s L 13 100.00% 0.00 1.00 H: index h,k,l 833s M_ISYM 13 100.00% 6.00 272.00 Y: M/ISYM, packed partial/reject flag and symmetry number 833s BATCH 13 100.00% 16.00 43.00 B: BATCH number 833s I 13 100.00% -19.71 7.39 J: intensity 833s SIGI 13 100.00% 0.41 3.05 Q: standard deviation 833s IPR 13 100.00% -10.84 4.99 J: intensity 833s SIGIPR 13 100.00% 0.41 3.05 Q: standard deviation 833s FRACTIONCALC 13 100.00% 0.07 1.15 R: real 833s XDET 13 100.00% 1099.43 1215.80 R: real 833s YDET 13 100.00% 1110.92 1201.06 R: real 833s ROT 13 100.00% 15.33 41.55 R: real 833s WIDTH 13 100.00% 0.37 2.19 R: real 833s LP 13 100.00% 0.00 0.03 R: real 833s MPART 13 100.00% 0.00 303.00 I: integer 833s FLAG 13 100.00% 0.00 40.00 I: integer 833s BGPKRATIOS 13 100.00% 8.04 10610.05 R: real 833s Crystal 2: 833s Name: DEFAULT 833s Project: AUTOMATIC 833s Id: 2 833s Unit cell: (78.0043, 78.0043, 78.0043, 90, 90, 90) 833s Number of datasets: 1 833s Dataset 1: 833s Name: NATIVE_SWEEP1 833s Id: 1 833s Wavelength: 0.979 833s Number of columns: 0 833s asu: (1, 2, 1) orig: (-1, 1, -2) M/ISYM: 15 833s asu: (1, 2, 1) orig: (1, -1, 2) M/ISYM: 272 833s asu: (1, 2, 1) orig: (1, -1, 2) M/ISYM: 272 833s asu: (1, 2, 1) orig: (-1, 2, 1) M/ISYM: 6 833s asu: (1, 2, 1) orig: (1, -2, -1) M/ISYM: 261 833s asu: (1, 2, 1) orig: (-1, 2, -1) M/ISYM: 263 833s asu: (1, 2, 1) orig: (1, -2, -1) M/ISYM: 261 833s asu: (1, 2, 1) orig: (-1, 2, -1) M/ISYM: 263 833s asu: (1, 2, 1) orig: (1, -2, 1) M/ISYM: 264 833s asu: (1, 2, 1) orig: (1, -2, 1) M/ISYM: 264 833s asu: (0, 2, 0) orig: (0, 0, -2) M/ISYM: 266 833s asu: (0, 2, 0) orig: (0, 0, -2) M/ISYM: 266 833s asu: (0, 2, 0) orig: (0, 0, -2) M/ISYM: 266 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/mtz/tst_dano.py" [FAIL] 6.1s 835s Time: 6.08 835s Return code: 139 835s OKs: 0 835s Standard error: 835s Segmentation fault (core dumped) 835s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/tst_mtz_free_flipper.py" [OK] 0.3s 835s Time: 0.30 835s Return code: 0 835s OKs: 0 835s Standard out: 835s Skipping exercise(): input file not available 835s u+s,u,s: 0.25 0.18 0.07 838s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 838s 139 838s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 838s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst.py" P31 [FAIL] 5.5s 838s Time: 5.55 838s Return code: 139 838s OKs: 0 838s Standard error: 838s Segmentation fault (core dumped) 839s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_adsc.py" [OK] 0.3s 839s Time: 0.26 839s Return code: 0 839s OKs: 1 839s Standard out: 839s Skipping exercise_adscread(): input file not available 839s OK 839s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_detectors.py" [OK] 0.1s 839s Time: 0.08 839s Return code: 0 839s OKs: 0 839s Standard out: 839s bpcx_regression not configured, skipping test 842s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 842s 139 842s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 842s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_utils.py" [FAIL] 6.3s 842s Time: 6.26 842s Return code: 139 842s OKs: 0 842s Standard error: 842s Segmentation fault (core dumped) 845s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 845s 139 845s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 845s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xplor/tst_xplormap.py" [FAIL] 6.2s 845s Time: 6.20 845s Return code: 139 845s OKs: 0 845s Standard error: 845s Segmentation fault (core dumped) 845s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdbx_mmcif_tutorial.py" [OK] 0.1s 845s Time: 0.08 845s Return code: 0 845s OKs: 1 845s Standard out: 845s phenix_regression not configured, skipping tst_pdbx_mmcif_tutorial.py 845s OK 848s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 848s 139 848s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 848s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phases.py" P31 [FAIL] 6.1s 848s Time: 6.12 848s Return code: 139 848s OKs: 0 848s Standard error: 848s Segmentation fault (core dumped) 853s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 853s 1 853s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 853s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py" [FAIL] 8.5s 853s Time: 8.50 853s Return code: 1 853s OKs: 0 853s Standard error: 853s Traceback (most recent call last): 853s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 477, in 853s exercise(sys.argv[1:]) 853s ~~~~~~~~^^^^^^^^^^^^^^ 853s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 22, in exercise 853s run_and_compare( 853s ~~~~~~~~~~~~~~~^ 853s ['iotbx.lattice_symmetry' 853s ^^^^^^^^^^^^^^^^^^^^^^^^^ 853s ...<31 lines>... 853s 853s 853s """) 853s ^^^^ 853s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 17, in run_and_compare 853s command=command).raise_if_errors().stdout_lines 853s ~~~~~~~~~~~~~~~^^ 853s File "/usr/lib/python3/dist-packages/libtbx/easy_run.py", line 46, in raise_if_errors 853s raise Error(msg) 853s RuntimeError: child process stderr output: 853s command: 'iotbx.lattice_symmetry --unit_cell="12.7923,12.8923,29.4356,102.846,103.846,22.7475"' 853s Segmentation fault (core dumped) 853s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_plots.py" [OK] 0.1s 853s Time: 0.09 853s Return code: 0 853s OKs: 1 853s Standard out: 853s OK 854s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_csv_utils.py" [OK] 0.2s 854s Time: 0.18 854s Return code: 0 854s OKs: 1 854s Standard out: 854s OK 855s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 855s 139 855s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 855s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_statistics.py" Fdd2 P31m [FAIL] 6.7s 855s Time: 6.74 855s Return code: 139 855s OKs: 0 855s Standard error: 855s Segmentation fault (core dumped) 855s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_bioinformatics.py" [OK] 0.1s 855s Time: 0.12 855s Return code: 0 855s OKs: 3 855s Standard out: 855s Testing guess_chain_types ... OK 855s Testing merge_sequences ... OK 855s testEquality (__main__.test_sequence.testEquality) ... ok 855s testNonEquality (__main__.test_sequence.testNonEquality) ... ok 855s testFormat (__main__.test_fasta_sequence.testFormat) ... ok 855s testStr (__main__.test_fasta_sequence.testStr) ... ok 855s testFormat (__main__.test_pir_sequence.testFormat) ... ok 855s testStr (__main__.test_pir_sequence.testStr) ... ok 855s testConservationCode (__main__.test_midline.testConservationCode) ... ok 855s testMidline (__main__.test_midline.testMidline) ... ok 855s test__str__ (__main__.test_alignment.test__str__) ... ok 855s test_copy (__main__.test_alignment.test_copy) ... ok 855s test_error (__main__.test_alignment.test_error) ... ok 855s test_extend (__main__.test_alignment.test_extend) ... ok 855s test_identity_count (__main__.test_alignment.test_identity_count) ... ok 855s test_identity_fraction (__main__.test_alignment.test_identity_fraction) ... ok 855s test_length (__main__.test_alignment.test_length) ... ok 855s test_multiplicity (__main__.test_alignment.test_multiplicity) ... ok 855s test__str__ (__main__.test_fasta_alignment.test__str__) ... ok 855s test_copy (__main__.test_fasta_alignment.test_copy) ... ok 855s test_error (__main__.test_fasta_alignment.test_error) ... ok 855s test_format (__main__.test_fasta_alignment.test_format) ... ok 855s test__str__ (__main__.test_pir_alignment.test__str__) ... ok 855s test_copy (__main__.test_pir_alignment.test_copy) ... ok 855s test_error (__main__.test_pir_alignment.test_error) ... ok 855s test_format (__main__.test_pir_alignment.test_format) ... ok 855s test__str__ (__main__.test_clustal_alignment.test__str__) ... ok 855s test_copy (__main__.test_clustal_alignment.test_copy) ... ok 855s test_format (__main__.test_clustal_alignment.test_format) ... ok 855s testFasta (__main__.test_sequence_parse.testFasta) ... ok 855s testPir (__main__.test_sequence_parse.testPir) ... ok 855s testSequence (__main__.test_sequence_parse.testSequence) ... ok 855s testTolerantPir (__main__.test_sequence_parse.testTolerantPir) ... ok 855s test_dbfetch_parse (__main__.test_sequence_parse.test_dbfetch_parse) ... ok 855s test_filename_selection (__main__.test_sequence_parse.test_filename_selection) ... ok 855s test_known_formats (__main__.test_sequence_parse.test_known_formats) ... ok 855s test_ls_parse (__main__.test_sequence_parse.test_ls_parse) ... ok 855s test_tf_parse (__main__.test_sequence_parse.test_tf_parse) ... ok 855s testAli (__main__.test_alignment_parse.testAli) ... ok 855s testClustal (__main__.test_alignment_parse.testClustal) ... ok 855s testFasta (__main__.test_alignment_parse.testFasta) ... ok 855s testPir (__main__.test_alignment_parse.testPir) ... ok 855s test_filename_selection (__main__.test_alignment_parse.test_filename_selection) ... ok 855s test_known_formats (__main__.test_alignment_parse.test_known_formats) ... ok 855s test_process_header (__main__.test_hhsearch_parser.test_process_header) ... ok 855s test_process_hits (__main__.test_hhsearch_parser.test_process_hits) ... ok 855s test_process_header (__main__.test_hhalign_parser.test_process_header) ... ok 855s test_process_hits (__main__.test_hhalign_parser.test_process_hits) ... ok 855s 855s ---------------------------------------------------------------------- 855s Ran 46 tests in 0.010s 855s 855s OK 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/regression/tst_file_reader.py" [FAIL] 4.3s 858s Time: 4.30 858s Return code: 139 858s OKs: 0 858s Standard error: 858s Segmentation fault (core dumped) 864s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 864s 1 864s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 864s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py" [FAIL] 9.4s 864s Time: 9.41 864s Return code: 1 864s OKs: 0 864s Standard out: 864s Starting iotbx.pdb.box_around_molecule 864s on Thu Mar 13 11:02:42 2025 by ubuntu 864s =============================================================================== 864s 864s Standard error: 864s *** buffer overflow detected ***: terminated 864s Aborted (core dumped) 864s Traceback (most recent call last): 864s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py", line 138, in 864s exercise() 864s ~~~~~~~~^^ 864s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py", line 48, in exercise 864s assert not easy_run.call("iotbx.pdb.box_around_molecule %s.pdb" % ( 864s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 864s prefix)) 864s ^^^^^^^^ 864s AssertionError 864s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_input.py" [OK] 0.2s 864s Time: 0.25 864s Return code: 0 864s OKs: 0 865s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 865s 134 865s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 865s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_segids.py" [FAIL] 7.1s 865s Time: 7.07 865s Return code: 134 865s OKs: 0 865s Standard error: 865s *** buffer overflow detected ***: terminated 865s Aborted (core dumped) 866s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_multimodel.py" [OK] 0.7s 866s Time: 0.66 866s Return code: 0 866s OKs: 0 866s Standard out: 866s ['_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'] 866s ['_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'] 866s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_add_conformations.py" [OK] 0.3s 866s Time: 0.26 866s Return code: 0 866s OKs: 0 866s Standard out: 866s phenix_regression not available, skipping test. 868s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 868s 134 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/regression/tst_hierarchy_forward_compatible_pdb.py" [FAIL] 3.7s 868s Time: 3.68 868s Return code: 134 868s OKs: 0 868s Standard error: 868s *** buffer overflow detected ***: terminated 868s Aborted (core dumped) 868s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reindex.py" [OK] 0.1s 868s Time: 0.08 868s Return code: 0 868s OKs: 1 868s Standard out: 868s Skipping 868s OK 871s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 871s 139 871s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 871s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_symmetry.py" [FAIL] 4.9s 871s Standard error: 871s Segmentation fault (core dumped) 871s Time: 4.91 871s Return code: 139 871s OKs: 0 874s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 874s 139 874s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 874s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_editor.py" [FAIL] 5.7s 874s Time: 5.74 874s Return code: 139 874s OKs: 0 874s Standard error: 874s Segmentation fault (core dumped) 874s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_as_fasta.py" [OK] 0.3s 874s Time: 0.27 874s Return code: 0 874s OKs: 1 874s Standard out: 874s OK 874s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_link_records.py" [OK] 0.3s 874s Time: 0.31 874s Return code: 0 874s OKs: 0 874s Standard out: 874s Can not initialize monomer_library, skipping test. 875s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_merging_statistics.py" [OK] 0.2s 875s Time: 0.21 875s Return code: 0 875s OKs: 1 875s Standard out: 875s phenix_regression not configured, skipping. 875s OK 879s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 879s 1 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_split_models.py" [FAIL] 8.2s 879s Time: 8.24 879s Return code: 1 879s OKs: 0 879s Standard error: 879s Traceback (most recent call last): 879s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py", line 60, in 879s exercise() 879s ~~~~~~~~^^ 879s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py", line 48, in exercise 879s assert (len(out.stdout_lines) == 2) and (len(out.stderr_lines) == 0) 879s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 879s AssertionError 880s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 880s 139 880s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 880s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_map_coefficients.py" [FAIL] 5.3s 880s Time: 5.25 880s Return code: 139 880s OKs: 0 880s Standard error: 880s Segmentation fault (core dumped) 880s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_xparm.py" [OK] 0.1s 880s Time: 0.09 880s Return code: 0 880s OKs: 3 880s Standard out: 880s OK 880s OK 880s OK 880s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_xds_inp.py" [OK] 0.1s 880s Time: 0.08 880s Return code: 0 880s OKs: 1 880s Standard out: 880s OK 886s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 886s 1 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_sort_atoms.py" [FAIL] 6.8s 886s Time: 6.80 886s Return code: 1 886s OKs: 0 886s Standard out: 886s iotbx.pdb.sort_atoms tst_sort_atoms_1.pdb 886s Standard error: 886s Segmentation fault (core dumped) 886s Traceback (most recent call last): 886s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py", line 815, in 886s exercise_1() 886s ~~~~~~~~~~^^ 886s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py", line 806, in exercise_1 886s assert not easy_run.call(cmd) 886s ^^^^^^^^^^^^^^^^^^^^^^ 886s AssertionError 886s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_spots_xds.py" [OK] 0.1s 886s Time: 0.08 886s Return code: 0 886s OKs: 1 886s Standard out: 886s OK 886s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_as_cif.py" [OK] 0.4s 886s Time: 0.42 886s Return code: 0 886s OKs: 1 886s Standard out: 886s Can not initialize monomer_library, skipping tst_pdb_as_cif. 886s OK 887s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 887s 139 887s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 887s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_integrate_hkl.py" [FAIL] 7.0s 887s Time: 7.01 887s Return code: 139 887s OKs: 0 887s Standard error: 887s Segmentation fault (core dumped) 890s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 890s 139 890s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 890s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_no_merge_original_index.py" [FAIL] 3.7s 890s Time: 3.70 890s Return code: 139 890s OKs: 0 890s Standard error: 890s Segmentation fault (core dumped) 893s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 893s 139 893s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 893s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_export_scalepack_unmerged.py" [FAIL] 6.2s 893s Time: 6.20 893s Return code: 139 893s OKs: 0 893s Standard error: 893s Segmentation fault (core dumped) 894s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_mtrix_biomt_cmdl.py" [OK] 0.3s 894s Time: 0.25 894s Return code: 0 894s OKs: 0 894s Standard out: 894s Skipping tests: phenix not found 894s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_mmcif_biomt_reduction_output.py" [OK] 0.7s 894s Time: 0.66 894s Return code: 0 894s OKs: 0 894s Standard out: 894s chem_data is not available, skipping 896s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 896s 139 896s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 896s libtbx.python "/usr/lib/python3/dist-packages/iotbx/dsn6/tst.py" P31 [FAIL] 6.2s 896s Time: 6.24 896s Return code: 139 896s OKs: 0 896s Standard error: 896s Segmentation fault (core dumped) 900s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 900s 139 900s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 900s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_ligs.py" [FAIL] 5.4s 900s Time: 5.40 900s Return code: 139 900s OKs: 0 900s Standard error: 900s Segmentation fault (core dumped) 903s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 903s 139 903s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 903s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_broken_chain.py" [FAIL] 6.6s 903s Time: 6.56 903s Return code: 139 903s OKs: 0 903s Standard error: 903s Segmentation fault (core dumped) 906s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 906s 139 906s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 906s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_shortcut_1.py" [FAIL] 6.6s 906s Time: 6.59 906s Return code: 139 906s OKs: 0 906s Standard error: 906s Segmentation fault (core dumped) 910s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 910s 139 910s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 910s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_groups_preprocessing.py" [FAIL] 7.3s 910s Time: 7.33 910s Return code: 139 910s OKs: 0 910s Standard error: 910s Segmentation fault (core dumped) 914s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 914s 139 914s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 914s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_input.py" [FAIL] 7.4s 914s Time: 7.39 914s Return code: 139 914s OKs: 0 914s Standard error: 914s Segmentation fault (core dumped) 917s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 917s 139 917s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 917s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_user_selections.py" [FAIL] 6.7s 917s Time: 6.70 917s Return code: 139 917s OKs: 0 917s Standard error: 917s Segmentation fault (core dumped) 921s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 921s 139 921s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 921s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs.py" [FAIL] 7.4s 921s Time: 7.38 921s Return code: 139 921s OKs: 0 921s Standard error: 921s Segmentation fault (core dumped) 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/regression/ncs/tst_ncs_without_validation.py" [FAIL] 7.2s 924s Time: 7.19 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/pdb/tst_read_mtrix_records_from_cif.py" [FAIL] 6.9s 928s Time: 6.93 928s Return code: 139 928s OKs: 0 928s Standard error: 928s Segmentation fault (core dumped) 931s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 931s 139 931s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 931s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_show_systematic_absences.py" [FAIL] 7.0s 931s Time: 7.04 931s Return code: 139 931s OKs: 0 931s Standard error: 931s Segmentation fault (core dumped) 931s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_reader.py" [OK] 0.3s 931s Time: 0.32 931s Return code: 0 931s OKs: 1 931s Standard out: 931s OK 934s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 934s 139 934s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 934s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_miller_sort_asu.py" [FAIL] 6.2s 934s Time: 6.22 934s Return code: 139 934s OKs: 0 934s Standard error: 934s Segmentation fault (core dumped) 934s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_alignment_as_hsearch.py" [OK] 0.1s 934s Time: 0.11 934s Return code: 0 934s OKs: 0 934s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_ebi_wu_blast_xml.py" [OK] 0.1s 934s Time: 0.11 934s Return code: 0 934s OKs: 0 934s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_ncbi_blast_xml.py" [OK] 0.1s 934s Time: 0.11 934s Return code: 0 934s OKs: 0 935s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/pdb_info.py" [OK] 0.8s 935s Time: 0.85 935s Return code: 0 935s OKs: 0 938s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 938s 134 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/tst_xray_scale.py" [FAIL] 6.5s 938s Time: 6.46 938s Return code: 134 938s OKs: 0 938s Standard error: 938s *** buffer overflow detected ***: terminated 938s Aborted (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/tst_cif_as_pdb_1atom.py" [FAIL] 6.6s 942s Time: 6.63 942s Return code: 139 942s OKs: 0 942s Standard error: 942s Segmentation fault (core dumped) 946s Standard error: 946s 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/tst_cif_1.py" [FAIL] 7.8s 946s Time: 7.81 946s Return code: 139 946s OKs: 0 952s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 952s 1 952s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 952s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py" [FAIL] 10.1s 952s Standard error: 952s Traceback (most recent call last): 952s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py", line 395, in 952s tst_1() 952s ~~~~~^^ 952s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py", line 370, in tst_1 952s assert os.path.isfile('%s.cif_%s_000.mtz' % (prefix, bn)) 952s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 952s AssertionError 952s Time: 10.07 952s Return code: 1 952s OKs: 0 954s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 954s 134 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/tst_all_chain_ids.py" [FAIL] 8.1s 954s Time: 8.10 954s Return code: 134 954s OKs: 0 954s Standard error: 954s *** buffer overflow detected ***: terminated 954s Aborted (core dumped) 957s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 957s 139 957s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 957s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_extract_xtal_data.py" [FAIL] 5.2s 957s Time: 5.20 957s Return code: 139 957s OKs: 0 957s Standard error: 957s Segmentation fault (core dumped) 958s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mtz_as_cif.py" [OK] 0.4s 958s Time: 0.39 958s Return code: 0 958s OKs: 1 958s Standard out: 958s Skipping 1akg.mtz test: input file not available 958s Skipping 1zff.mtz test: input file not available 958s Skipping l.mtz test: input file not available 958s Skipping outside_4_exptl_fobs_phases_freeR_flags.mtz test: input file not available 958s Skipping r1wqzsf.mtz test: input file not available 958s Skipping ur0013.sf.mtz test: input file not available 958s Skipping 1aba_test.mtz test: input file not available 958s OK 958s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_group_rounding.py" [OK] 0.3s 958s Time: 0.27 958s Return code: 0 958s OKs: 0 961s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 961s 139 961s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 961s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cli_parser.py" [FAIL] 7.5s 961s Time: 7.47 961s Return code: 139 961s OKs: 0 961s Standard error: 961s Segmentation fault (core dumped) 962s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_merge_atoms_at_end_to_residues.py" [OK] 0.2s 962s Time: 0.24 962s Return code: 0 962s OKs: 1 962s Standard out: 962s [('1', 22), ('3', 17), ('1', 1), ('3', 1)] 962s [('1', 22), ('3', 18), ('1', 1)] 962s OK 963s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_chain_ids_1.py" [OK] 1.1s 963s Time: 1.15 963s Return code: 0 963s OKs: 1 963s Standard out: 963s 963s total number of: 963s models: 1 963s chains: 3 963s alt. conf.: 0 963s residues: 12 963s atoms: 174 963s anisou: 0 963s number of atom element+charge types: 4 963s histogram of atom element+charge frequency: 963s " H " 78 963s " C " 60 963s " O " 21 963s " N " 15 963s residue name classes: 963s "common_amino_acid" 12 963s number of chain ids: 3 963s histogram of chain id frequency: 963s "A" 1 963s "A-2" 1 963s "A-5" 1 963s number of alt. conf. ids: 0 963s number of residue names: 4 963s histogram of residue name frequency: 963s "ASN" 3 963s "PHE" 3 963s "SER" 3 963s "THR" 3 963s Can not initialize monomer_library, skipping test. 963s OK. Time: 0.493 963s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_1.py" [OK] 0.7s 963s Time: 0.72 963s Return code: 0 963s OKs: 1 963s Standard out: 963s OK. Time: 0.459 964s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_2.py" [OK] 0.7s 964s Time: 0.68 964s Return code: 0 964s OKs: 1 964s Standard out: 964s Can not initialize monomer_library, skipping test. 964s OK. Time: 0.013 964s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 964s 134 964s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 964s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_occupancies_rounding.py" [FAIL] 6.5s 964s Time: 6.53 964s Return code: 134 964s OKs: 0 964s Standard error: 964s *** buffer overflow detected ***: terminated 964s Aborted (core dumped) 965s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_3.py" [OK] 0.7s 965s Time: 0.68 965s Return code: 0 965s OKs: 1 965s Standard out: 965s Can not initialize monomer_library, skipping test. 965s OK. Time: 0.015 965s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_4.py" [OK] 0.6s 965s Time: 0.65 965s Return code: 0 965s OKs: 1 965s Standard out: 965s Can not initialize monomer_library, skipping test. 965s OK. Time: 0.013 965s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_copy_select.py" [OK] 0.3s 965s Time: 0.30 965s Return code: 0 965s OKs: 1 965s Standard out: 965s There is no info: pdb=" N " 965s And no parent: None 965s Info is gone: pdb=" N " 965s Info is still here: pdb=" N GLY A 1 " 965s OK. Time: 0.028 965s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_id_str.py" [OK] 0.2s 965s Time: 0.25 965s Return code: 0 965s OKs: 0 965s Standard out: 965s u+s,u,s: 0.20 0.16 0.04 965s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_altlocs.py" [OK] 0.3s 965s Time: 0.27 965s Return code: 0 965s OKs: 1 965s Standard out: 965s OK 968s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 968s 139 968s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 968s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_debug_write.py" [FAIL] 3.1s 968s Time: 3.13 968s Return code: 139 968s OKs: 0 968s Standard error: 968s Segmentation fault (core dumped) 972s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 972s 139 972s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 972s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_reordered_chains.py" [EXPECTED FAIL] 3.7s 972s Time: 3.69 972s Return code: 139 972s OKs: 0 972s Standard error: 972s Segmentation fault (core dumped) 977s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 977s 134 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_mmcif_to_from_hierarchy.py" [EXPECTED FAIL] 4.5s 977s Time: 4.50 977s Return code: 134 977s OKs: 0 977s Standard error: 977s *** buffer overflow detected ***: terminated 977s Aborted (core dumped) 977s libtbx.python "/usr/lib/python3/dist-packages/libtbx/metric_prefixes.py" [OK] 0.0s 977s Time: 0.02 977s Return code: 0 977s OKs: 1 977s Standard out: 977s OK 981s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_utils.py" [OK] 4.3s 981s Time: 4.30 981s Return code: 0 981s OKs: 0 981s Standard out: 981s Skipping exercise_retrieve_unless_exists 981s ### USER = ubuntu 981s ### PID = 10138 981s multiprocessing problem: None 981s base36_timestamp(): 00m878s70k now 981s base36_timestamp(): zzydazd000 year 115855 CE 981s get_svn_revision(): None 981s get_build_tag(): None 981s u+s,u,s: 0.10 0.08 0.02 982s libtbx.python "/usr/lib/python3/dist-packages/libtbx/test_utils/__init__.py" [OK] 0.8s 982s Time: 0.81 982s Return code: 0 982s OKs: 1 982s Standard out: 982s OK 982s libtbx.python "/usr/lib/python3/dist-packages/libtbx/queuing_system_utils/pbs_utils.py" [OK] 0.0s 982s Time: 0.03 982s Return code: 0 982s OKs: 1 982s Standard out: 982s *** MY_PBS_ARRAY_SIZE = None 982s *** MY_PBS_ARRAYID_OFFSET = None 982s *** PBS_ARRAYID = None 982s *** OMPI_MCA_ns_nds_num_procs = None 982s *** OMPI_MCA_ns_nds_vpid = None 982s n,i: 1 0 982s OK 982s libtbx.python "/usr/lib/python3/dist-packages/libtbx/queuing_system_utils/sge_utils.py" [OK] 0.0s 982s Time: 0.04 982s Return code: 0 982s OKs: 1 982s Standard out: 982s *** JOB_ID = None 982s *** SGE_ARCH = None 982s *** SGE_TASK_FIRST = None 982s *** SGE_TASK_LAST = None 982s *** SGE_TASK_ID = None 982s OK 982s libtbx.python "/usr/lib/python3/dist-packages/libtbx/introspection.py" [OK] 0.1s 982s Time: 0.08 982s Return code: 0 982s OKs: 1 982s Standard out: 982s number of processors: 2 982s Virtual memory size: 21,852,160 982s Resident set size: 13,012,992 982s Stack size: 139,264 982s Virtual memory size: 21,979,136 exact max: 29,982,720 982s Resident set size: 13,688,832 approx. max: 21,590,016 982s Stack size: 139,264 approx. max: 139,264 982s Memory total: 4,106,825,728 982s Memory free: 163,569,664 982s OK 1006s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_thread_utils.py" [OK] 23.5s 1006s Time: 23.51 1006s Return code: 0 1006s OKs: 1 1006s Standard out: 1006s OK 1009s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp.py" [OK] 3.1s 1009s Time: 3.12 1009s Return code: 0 1009s OKs: 1 1009s Standard out: 1009s multiprocessing pool size: 2 1009s wall clock time: 0.01 seconds 1009s OK 1009s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp_state.py" [OK] 0.8s 1009s Time: 0.79 1009s Return code: 0 1009s OKs: 3 1009s Standard out: 1009s Running threading test with 1 processes, 1 threads, 3 tasks 1009s (0x74e4da75eba0-11358) object in state -init- 1009s (0x74e4da75eba0-11358) changing state from -init- to JFLNTL 1009s (0x74e4da75eba0-11358) changing state from JFLNTL to 6LXXV2 1009s (0x74e4da75eba0-11358) changing state from 6LXXV2 to J2DJ8T 1009s (0x74e4da75eba0-11358) object in state J2DJ8T 1009s OK 1009s Running threading test with 2 processes, 1 threads, 3 tasks 1009s (0x74e4da641d10-11358) object in state -init- 1009s (0x74e4da641d10-11358) changing state from -init- to MCC32L 1009s (0x74e4da641d10-11358) changing state from MCC32L to ZIMG6E 1009s (0x74e4da641d10-11358) changing state from ZIMG6E to 26VGCA 1009s (0x74e4da641d10-11358) object in state 26VGCA 1009s OK 1009s Running multiprocessing test with 1 processes, 1 threads, 3 tasks 1009s (0x74e4da641d10-11358) object in state -init- 1009s (0x74e4da641d10-11358) changing state from -init- to 6HYYFW 1009s (0x74e4da641d10-11358) changing state from 6HYYFW to O4MP6V 1009s (0x74e4da641d10-11358) changing state from O4MP6V to LC0JJW 1009s (0x74e4da641d10-11358) object in state LC0JJW 1009s OK 1009s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_pickle.py" [OK] 0.1s 1009s Time: 0.07 1009s Return code: 0 1009s OKs: 1 1009s Standard out: 1009s test.dat 1009s dump: 0.00 s 1009s load buffered: 0.00 s 1009s load direct: 0.00 s 1009s test.dat.gz 1009s dump: 0.00 s 1009s load buffered: 0.00 s 1009s load direct: 0.00 s 1009s dumps/loads 1009s dump: 0.00 s 1009s load buffered: 0.00 s 1009s OK 1010s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_fully_buffered_timeout.py" [OK] 0.1s 1010s Time: 0.08 1010s Return code: 0 1010s OKs: 0 1010s Standard out: 1010s Skipping test: probe not configured 1010s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_fetch.py" [OK] 44.4s 1010s Time: 44.43 1010s Return code: 0 1010s OKs: 1 1010s Standard out: 1010s data_r1yjpsf 1010s # 1010s loop_ 1010s _audit.revision_id 1010s _audit.creation_date 1010s _audit.update_record 1010s 1_0 2005-06-14 'Initial release' 1010s 1_1 2013-05-08 'Status correction and format standardization' 1010s # 1010s _cell.entry_id 1yjp 1010s _cell.length_a 21.937 1010s _cell.length_b 4.866 1010s _cell.length_c 23.477 1010s _cell.angle_alpha 90.000 1010s _cell.angle_beta 107.080 1010s _cell.angle_gamma 90.000 1010s # 1010s _diffrn_radiation_wavelength.id 1 1010s _diffrn_radiation_wavelength.wavelength 0.97500 1010s # 1010s _entry.id 1yjp 1010s # 1010s _exptl_crystal.id 1 1010s # 1010s _reflns_scale.group_code 1 1010s # 1010s _symmetry.entry_id 1yjp 1010s _symmetry.space_group_name_H-M 'P 1 21 1' 1010s # 1010s # 1010s loop_ 1010s _refln.crystal_id 1010s _refln.wavelength_id 1010s _refln.scale_group_code 1010s _refln.index_h 1010s _refln.index_k 1010s _refln.index_l 1010s _refln.status 1010s _refln.F_meas_au 1010s _refln.F_meas_sigma_au 1010s 1 1 1 -12 0 2 o 3.49 2.34 1010s 1 1 1 -12 0 3 o 3.31 2.43 1010s 1 1 1 -12 0 4 o 7.32 4.25 1010s 1 1 1 -12 0 5 o 8.88 5.39 1010s 1 1 1 -11 0 1 o 9.46 4.13 1010s 1 1 1 -11 0 2 o 4.91 3.21 1010s 1 1 1 -11 0 3 o 6.37 3.70 1010s 1 1 1 -11 0 4 o 8.50 4.91 1010s 1 1 1 -11 0 5 o 17.44 8.06 1010s 1 1 1 -11 0 6 o 5.89 3.64 1010s 1 1 1 -11 0 8 o 6.39 3.90 1010s 1 1 1 -11 1 2 o 5.69 2.18 1010s 1 1 1 -11 1 3 o 6.53 2.53 1010s 1 1 1 -11 1 5 o 7.26 3.20 1010s 1 1 1 -11 1 6 o 11.05 3.47 1010s 1 1 1 -10 0 2 o 6.32 3.74 1010s 1 1 1 -10 0 3 o 9.36 4.67 1010s 1 1 1 -10 0 5 o 7.20 4.12 1010s 1 1 1 -10 0 6 o 4.88 3.25 1010s 1 1 1 -10 0 7 o 11.84 5.41 1010s 1 1 1 -10 0 8 o 14.49 6.53 1010s 1 1 1 -10 0 9 o 6.21 3.91 1010s 1 1 1 -10 0 10 o 5.55 3.37 1010s 1 1 1 -10 1 1 o 4.58 1.49 1010s 1 1 1 -10 1 3 o 12.40 3.65 1010s 1 1 1 -10 1 4 o 9.07 2.47 1010s 1 1 1 -10 1 5 o 17.23 6.02 1010s 1 1 1 -10 1 6 o 4.60 2.10 1010s 1 1 1 -10 1 7 o 6.34 2.43 1010s 1 1 1 -10 1 8 o 9.04 2.92 1010s 1 1 1 -9 0 2 o 8.10 3.98 1010s 1 1 1 -9 0 3 o 14.22 5.11 1010s 1 1 1 -9 0 5 o 6.01 3.78 1010s 1 1 1 -9 0 6 o 10.48 4.68 1010s 1 1 1 -9 0 7 o 8.79 4.52 1010s 1 1 1 -9 0 8 o 6.15 3.63 1010s 1 1 1 -9 0 9 o 10.27 4.16 1010s 1 1 1 -9 0 10 o 4.38 3.04 1010s 1 1 1 -9 0 11 o 7.27 4.16 1010s 1 1 1 -9 1 3 o 10.75 2.38 1010s 1 1 1 -9 1 4 o 11.86 1.95 1010s 1 1 1 -9 1 5 o 10.95 3.27 1010s 1 1 1 -9 1 6 o 13.31 2.59 1010s 1 1 1 -9 1 7 o 8.06 2.92 1010s 1 1 1 -9 1 8 o 14.75 2.87 1010s 1 1 1 -9 1 9 o 9.04 2.82 1010s 1 1 1 -8 0 2 f 15.88 3.97 1010s 1 1 1 -8 0 3 o 26.78 5.79 1010s 1 1 1 -8 0 5 o 32.83 7.52 1010s 1 1 1 -8 0 7 o 12.74 3.54 1010s 1 1 1 -8 0 8 o 29.46 9.29 1010s 1 1 1 -8 0 9 f 22.09 3.59 1010s 1 1 1 -8 0 10 o 18.81 5.24 1010s 1 1 1 -8 0 11 o 12.76 7.11 1010s 1 1 1 -8 1 1 o 6.26 2.08 1010s 1 1 1 -8 1 2 o 6.97 2.14 1010s 1 1 1 -8 1 4 o 19.24 4.18 1010s 1 1 1 -8 1 5 o 15.46 2.43 1010s 1 1 1 -8 1 6 o 16.87 2.78 1010s 1 1 1 -8 1 7 o 15.66 2.34 1010s 1 1 1 -8 1 8 o 7.07 2.43 1010s 1 1 1 -8 1 9 o 8.81 2.80 1010s 1 1 1 -8 1 10 o 8.61 3.09 1010s 1 1 1 -8 2 1 o 4.39 1.52 1010s 1 1 1 -8 2 2 o 4.20 1.87 1010s 1 1 1 -8 2 3 o 6.14 1.87 1010s 1 1 1 -8 2 4 o 9.38 2.80 1010s 1 1 1 -7 0 3 o 23.46 3.83 1010s 1 1 1 -7 0 4 o 37.35 7.40 1010s 1 1 1 -7 0 6 o 7.44 3.60 1010s 1 1 1 -7 0 7 o 43.94 5.36 1010s 1 1 1 -7 0 8 o 18.96 2.98 1010s 1 1 1 -7 0 9 o 4.95 3.22 1010s 1 1 1 -7 0 10 o 31.73 4.61 1010s 1 1 1 -7 0 11 o 6.31 3.82 1010s 1 1 1 -7 0 12 o 5.05 3.33 1010s 1 1 1 -7 1 1 o 8.89 1.60 1010s 1 1 1 -7 1 2 o 13.70 1.71 1010s 1 1 1 -7 1 3 o 21.03 2.45 1010s 1 1 1 -7 1 4 f 7.57 2.36 1010s 1 1 1 -7 1 5 o 11.31 3.34 1010s 1 1 1 -7 1 6 o 19.93 3.06 1010s 1 1 1 -7 1 7 o 22.86 3.28 1010s 1 1 1 -7 1 8 o 10.32 2.58 1010s 1 1 1 -7 1 9 f 5.13 2.34 1010s 1 1 1 -7 1 10 o 9.91 3.03 1010s 1 1 1 -7 1 11 o 5.61 2.33 1010s 1 1 1 -7 2 1 o 12.28 3.86 1010s 1 1 1 -7 2 2 o 11.29 3.50 1010s 1 1 1 -7 2 3 f 7.22 2.40 1010s 1 1 1 -7 2 4 o 11.13 2.74 1010s 1 1 1 -7 2 5 o 7.86 2.92 1010s 1 1 1 -7 2 6 o 5.23 2.15 1010s 1 1 1 -6 0 2 o 35.03 5.13 1010s 1 1 1 -6 0 3 o 15.64 3.61 1010s 1 1 1 -6 0 4 o 12.60 4.22 1010s 1 1 1 -6 0 5 o 21.36 2.47 1010s 1 1 1 -6 0 6 o 31.19 3.17 1010s 1 1 1 -6 0 7 o 33.66 3.99 1010s 1 1 1 -6 0 8 o 13.70 4.22 1010s 1 1 1 -6 0 9 o 10.99 4.16 1010s 1 1 1 -6 0 10 o 24.56 3.98 1010s 1 1 1 -6 0 11 o 4.41 3.08 1010s 1 1 1 -6 0 12 o 4.07 2.83 1010s 1 1 1 -6 1 1 o 10.24 1.40 1010s 1 1 1 -6 1 2 o 20.59 2.28 1010s 1 1 1 -6 1 3 o 32.14 3.57 1010s 1 1 1 -6 1 4 f 11.60 2.18 1010s 1 1 1 -6 1 5 o 22.15 2.66 1010s 1 1 1 -6 1 6 o 7.68 2.64 1010s 1 1 1 -6 1 7 o 6.39 2.58 1010s 1 1 1 -6 1 8 o 6.60 2.60 1010s 1 1 1 -6 1 9 o 8.21 2.82 1010s 1 1 1 -6 1 10 o 13.25 3.07 1010s 1 1 1 -6 1 11 o 10.62 3.80 1010s 1 1 1 -6 2 1 o 13.78 2.98 1010s 1 1 1 -6 2 2 o 5.95 2.11 1010s 1 1 1 -6 2 3 o 8.96 3.00 1010s 1 1 1 -6 2 4 o 4.88 2.17 1010s 1 1 1 -6 2 5 o 7.35 2.58 1010s 1 1 1 -6 2 6 o 6.93 2.91 1010s 1 1 1 -6 2 7 o 8.14 2.74 1010s 1 1 1 -5 0 2 o 44.04 6.46 1010s 1 1 1 -5 0 3 o 15.30 3.69 1010s 1 1 1 -5 0 4 o 16.95 2.51 1010s 1 1 1 -5 0 5 o 14.82 4.54 1010s 1 1 1 -5 0 6 o 29.73 3.15 1010s 1 1 1 -5 0 7 f 55.71 13.43 1010s 1 1 1 -5 0 8 o 15.06 3.67 1010s 1 1 1 -5 0 9 o 8.76 4.15 1010s 1 1 1 -5 0 10 o 4.69 3.13 1010s 1 1 1 -5 0 11 o 16.56 5.19 1010s 1 1 1 -5 0 12 o 5.59 3.77 1010s 1 1 1 -5 1 1 o 26.70 2.49 1010s 1 1 1 -5 1 2 o 38.67 3.63 1010s 1 1 1 -5 1 3 o 20.45 2.09 1010s 1 1 1 -5 1 4 o 6.46 2.54 1010s 1 1 1 -5 1 5 o 20.55 2.58 1010s 1 1 1 -5 1 6 o 28.68 2.67 1010s 1 1 1 -5 1 7 o 5.68 2.48 1010s 1 1 1 -5 1 8 o 6.99 2.70 1010s 1 1 1 -5 1 9 o 20.74 2.59 1010s 1 1 1 -5 1 10 o 14.70 3.00 1010s 1 1 1 -5 1 11 o 8.62 2.89 1010s 1 1 1 -5 2 1 o 6.26 2.16 1010s 1 1 1 -5 2 2 o 7.93 2.10 1010s 1 1 1 -5 2 3 o 19.90 4.18 1010s 1 1 1 -5 2 4 o 4.98 2.02 1010s 1 1 1 -5 2 5 o 16.85 3.60 1010s 1 1 1 -5 2 7 o 8.15 2.74 1010s 1 1 1 -5 2 8 o 8.89 2.75 1010s 1 1 1 -4 0 2 o 4.55 2.74 1010s 1 1 1 -4 0 3 o 23.50 2.52 1010s 1 1 1 -4 0 4 o 19.15 3.81 1010s 1 1 1 -4 0 7 o 20.06 2.98 1010s 1 1 1 -4 0 8 o 28.85 3.55 1010s 1 1 1 -4 0 9 o 5.36 3.45 1010s 1 1 1 -4 0 10 o 25.68 3.87 1010s 1 1 1 -4 0 11 o 23.28 3.81 1010s 1 1 1 -4 0 12 o 11.39 4.82 1010s 1 1 1 -4 0 13 o 7.07 3.96 1010s 1 1 1 -4 1 1 o 31.99 4.35 1010s 1 1 1 -4 1 2 o 18.48 1.94 1010s 1 1 1 -4 1 3 f 18.93 2.01 1010s 1 1 1 -4 1 4 o 38.05 3.65 1010s 1 1 1 -4 1 5 o 36.34 3.49 1010s 1 1 1 -4 1 6 o 18.08 3.24 1010s 1 1 1 -4 1 7 o 20.11 2.29 1010s 1 1 1 -4 1 8 o 11.25 2.61 1010s 1 1 1 -4 1 9 o 27.09 3.02 1010s 1 1 1 -4 1 10 o 17.78 3.55 1010s 1 1 1 -4 1 11 o 10.45 3.55 1010s 1 1 1 -4 1 12 o 7.42 2.61 1010s 1 1 1 -4 2 1 o 7.72 2.01 1010s 1 1 1 -4 2 2 o 30.88 3.36 1010s 1 1 1 -4 2 3 o 19.14 2.65 1010s 1 1 1 -4 2 4 o 4.44 2.00 1010s 1 1 1 -4 2 5 f 26.44 8.10 1010s 1 1 1 -4 2 6 o 10.83 3.21 1010s 1 1 1 -4 2 7 o 6.03 2.73 1010s 1 1 1 -4 2 8 o 12.78 2.87 1010s 1 1 1 -3 0 2 o 3.40 2.13 1010s 1 1 1 -3 0 3 o 5.40 2.78 1010s 1 1 1 -3 0 4 o 11.52 2.39 1010s 1 1 1 -3 0 5 o 55.13 5.36 1010s 1 1 1 -3 0 6 f 31.55 3.22 1010s 1 1 1 -3 0 7 o 6.95 4.11 1010s 1 1 1 -3 0 8 o 6.00 3.79 1010s 1 1 1 -3 0 9 o 23.03 3.41 1010s 1 1 1 -3 0 10 o 4.79 3.36 1010s 1 1 1 -3 0 11 o 10.46 5.21 1010s 1 1 1 -3 0 12 o 11.53 6.07 1010s 1 1 1 -3 0 13 o 3.22 2.15 1010s 1 1 1 -3 1 1 o 53.95 5.22 1010s 1 1 1 -3 1 2 o 21.50 3.03 1010s 1 1 1 -3 1 3 o 42.88 4.08 1010s 1 1 1 -3 1 4 o 42.70 6.13 1010s 1 1 1 -3 1 5 o 41.12 3.18 1010s 1 1 1 -3 1 6 o 17.31 2.67 1010s 1 1 1 -3 1 7 o 35.59 4.21 1010s 1 1 1 -3 1 8 o 18.53 2.36 1010s 1 1 1 -3 1 9 o 11.55 2.71 1010s 1 1 1 -3 1 10 o 11.41 2.79 1010s 1 1 1 -3 1 11 o 6.92 2.69 1010s 1 1 1 -3 1 12 o 7.03 2.45 1010s 1 1 1 -3 2 1 o 18.65 2.01 1010s 1 1 1 -3 2 2 o 16.33 1.93 1010s 1 1 1 -3 2 3 o 32.88 5.01 1010s 1 1 1 -3 2 4 o 9.99 2.93 1010s 1 1 1 -3 2 5 o 20.62 2.93 1010s 1 1 1 -3 2 6 o 9.18 3.06 1010s 1 1 1 -3 2 7 o 6.90 2.83 1010s 1 1 1 -3 2 8 o 5.26 2.23 1010s 1 1 1 -2 0 1 o 37.92 5.29 1010s 1 1 1 -2 0 2 o 25.98 3.53 1010s 1 1 1 -2 0 3 o 20.20 2.27 1010s 1 1 1 -2 0 4 o 43.74 4.27 1010s 1 1 1 -2 0 5 o 32.34 3.28 1010s 1 1 1 -2 0 6 o 61.28 6.06 1010s 1 1 1 -2 0 7 o 39.92 3.91 1010s 1 1 1 -2 0 8 o 5.73 3.51 1010s 1 1 1 -2 0 9 o 34.44 8.22 1010s 1 1 1 -2 0 10 o 5.00 3.24 1010s 1 1 1 -2 0 11 o 5.95 3.63 1010s 1 1 1 -2 0 12 o 7.57 4.58 1010s 1 1 1 -2 1 1 o 5.64 1.74 1010s 1 1 1 -2 1 2 o 27.80 2.66 1010s 1 1 1 -2 1 3 f 58.08 5.70 1010s 1 1 1 -2 1 4 o 17.13 2.16 1010s 1 1 1 -2 1 5 o 17.82 1.84 1010s 1 1 1 -2 1 6 o 38.29 4.36 1010s 1 1 1 -2 1 7 o 21.32 2.41 1010s 1 1 1 -2 1 8 o 14.24 2.30 1010s 1 1 1 -2 1 9 o 23.48 2.71 1010s 1 1 1 -2 1 10 f 12.02 2.17 1010s 1 1 1 -2 1 11 o 15.91 5.89 1010s 1 1 1 -2 1 12 o 7.00 2.53 1010s 1 1 1 -2 2 1 o 15.73 2.27 1010s 1 1 1 -2 2 2 o 24.74 2.59 1010s 1 1 1 -2 2 3 o 16.53 2.59 1010s 1 1 1 -2 2 4 o 6.46 2.78 1010s 1 1 1 -2 2 5 o 13.27 4.40 1010s 1 1 1 -2 2 6 o 5.58 2.29 1010s 1 1 1 -2 2 7 o 6.76 2.38 1010s 1 1 1 -2 2 8 o 5.29 2.14 1010s 1 1 1 -1 0 1 o 28.12 3.79 1010s 1 1 1 -1 0 2 o 21.59 2.21 1010s 1 1 1 -1 0 3 o 33.14 3.24 1010s 1 1 1 -1 0 4 o 43.39 4.18 1010s 1 1 1 -1 0 5 f 46.52 4.56 1010s 1 1 1 -1 0 6 o 76.28 14.50 1010s 1 1 1 -1 0 7 o 5.12 3.18 1010s 1 1 1 -1 0 9 o 37.08 8.90 1010s 1 1 1 -1 0 10 o 6.65 3.72 1010s 1 1 1 -1 0 11 o 6.86 4.45 1010s 1 1 1 -1 0 12 o 4.18 2.86 1010s 1 1 1 -1 1 1 o 36.99 3.46 1010s 1 1 1 -1 1 2 o 40.11 3.76 1010s 1 1 1 -1 1 3 o 15.12 3.05 1010s 1 1 1 -1 1 4 o 11.44 2.42 1010s 1 1 1 -1 1 5 f 7.66 2.37 1010s 1 1 1 -1 1 6 o 37.21 3.40 1010s 1 1 1 -1 1 7 o 13.99 2.19 1010s 1 1 1 -1 1 8 o 23.42 2.40 1010s 1 1 1 -1 1 9 o 12.59 2.48 1010s 1 1 1 -1 1 10 o 14.84 2.83 1010s 1 1 1 -1 1 11 o 13.90 3.02 1010s 1 1 1 -1 2 1 o 7.71 2.59 1010s 1 1 1 -1 2 2 o 5.95 2.09 1010s 1 1 1 -1 2 3 o 25.96 3.59 1010s 1 1 1 -1 2 4 o 16.53 2.52 1010s 1 1 1 -1 2 5 o 12.51 2.97 1010s 1 1 1 -1 2 6 o 12.40 3.34 1010s 1 1 1 -1 2 7 o 5.97 2.01 1010s 1 1 1 -1 2 8 o 8.24 2.40 1010s 1 1 1 0 0 1 o 40.04 3.82 1010s 1 1 1 0 0 2 o 58.22 5.69 1010s 1 1 1 0 0 3 o 47.47 4.60 1010s 1 1 1 0 0 4 o 7.98 2.75 1010s 1 1 1 0 0 5 o 50.74 7.60 1010s 1 1 1 0 0 6 o 14.87 1.94 1010s 1 1 1 0 0 7 o 3.62 2.41 1010s 1 1 1 0 0 8 o 36.19 7.98 1010s 1 1 1 0 0 9 o 10.11 5.01 1010s 1 1 1 0 0 10 o 18.08 3.24 1010s 1 1 1 0 0 11 o 12.35 4.26 1010s 1 1 1 0 0 12 o 9.41 4.38 1010s 1 1 1 0 1 1 o 92.10 11.26 1010s 1 1 1 0 1 2 o 47.48 4.50 1010s 1 1 1 0 1 3 o 22.08 2.22 1010s 1 1 1 0 1 4 o 8.62 2.51 1010s 1 1 1 0 1 5 o 24.16 1.98 1010s 1 1 1 0 1 6 o 16.72 1.95 1010s 1 1 1 0 1 7 o 5.50 2.46 1010s 1 1 1 0 1 8 o 21.06 2.19 1010s 1 1 1 0 1 9 o 5.99 2.45 1010s 1 1 1 0 1 10 o 8.62 3.03 1010s 1 1 1 0 1 11 o 9.15 3.06 1010s 1 1 1 0 2 0 o 27.82 5.58 1010s 1 1 1 0 2 1 o 29.68 4.10 1010s 1 1 1 0 2 2 o 37.82 4.30 1010s 1 1 1 0 2 3 o 14.42 1.91 1010s 1 1 1 0 2 4 o 13.55 2.70 1010s 1 1 1 0 2 5 o 8.67 3.07 1010s 1 1 1 0 2 6 o 22.77 5.53 1010s 1 1 1 0 2 7 o 5.74 2.12 1010s 1 1 1 0 2 8 o 9.78 2.64 1010s 1 1 1 1 0 1 o 10.19 1.09 1010s 1 1 1 1 0 2 o 20.07 1.88 1010s 1 1 1 1 0 3 o 28.76 2.81 1010s 1 1 1 1 0 4 o 3.16 2.18 1010s 1 1 1 1 0 5 o 35.75 3.54 1010s 1 1 1 1 0 6 f 52.32 5.12 1010s 1 1 1 1 0 7 o 37.09 5.54 1010s 1 1 1 1 0 8 o 6.52 3.32 1010s 1 1 1 1 0 9 o 3.67 2.45 1010s 1 1 1 1 0 10 o 6.03 3.17 1010s 1 1 1 1 0 11 o 3.13 2.20 1010s 1 1 1 1 0 12 o 4.06 2.74 1010s 1 1 1 1 1 0 o 34.97 2.64 1010s 1 1 1 1 1 1 o 15.45 1.46 1010s 1 1 1 1 1 2 o 27.96 2.66 1010s 1 1 1 1 1 3 o 55.14 5.35 1010s 1 1 1 1 1 4 o 14.46 1.65 1010s 1 1 1 1 1 5 o 7.23 2.19 1010s 1 1 1 1 1 6 o 10.31 2.54 1010s 1 1 1 1 1 7 o 11.70 2.22 1010s 1 1 1 1 1 8 o 11.24 2.14 1010s 1 1 1 1 1 9 o 7.60 2.88 1010s 1 1 1 1 1 10 o 8.83 2.34 1010s 1 1 1 1 1 11 o 12.55 3.17 1010s 1 1 1 1 2 0 o 24.36 5.60 1010s 1 1 1 1 2 1 o 13.12 2.09 1010s 1 1 1 1 2 2 o 10.37 2.52 1010s 1 1 1 1 2 3 o 14.39 1.98 1010s 1 1 1 1 2 4 o 26.67 8.23 1010s 1 1 1 1 2 5 o 22.53 5.20 1010s 1 1 1 1 2 6 o 13.94 2.61 1010s 1 1 1 1 2 7 o 7.45 2.38 1010s 1 1 1 1 2 8 o 4.51 2.05 1010s 1 1 1 2 0 1 o 13.06 1.30 1010s 1 1 1 2 0 2 o 10.37 1.36 1010s 1 1 1 2 0 3 o 20.89 2.04 1010s 1 1 1 2 0 4 o 45.12 4.31 1010s 1 1 1 2 0 5 o 15.37 1.91 1010s 1 1 1 2 0 6 o 28.38 2.79 1010s 1 1 1 2 0 7 o 16.02 2.31 1010s 1 1 1 2 0 8 o 3.40 2.35 1010s 1 1 1 2 0 9 o 4.23 2.72 1010s 1 1 1 2 0 10 o 3.89 2.43 1010s 1 1 1 2 0 11 o 10.26 3.01 1010s 1 1 1 2 1 0 o 34.61 2.64 1010s 1 1 1 2 1 1 o 53.93 5.22 1010s 1 1 1 2 1 2 o 20.62 2.08 1010s 1 1 1 2 1 3 o 44.45 3.37 1010s 1 1 1 2 1 4 o 24.41 2.00 1010s 1 1 1 2 1 5 o 40.33 4.58 1010s 1 1 1 2 1 6 o 41.76 5.03 1010s 1 1 1 2 1 7 o 28.20 3.43 1010s 1 1 1 2 1 8 o 33.56 3.76 1010s 1 1 1 2 1 9 o 4.41 1.97 1010s 1 1 1 2 1 10 o 15.24 3.10 1010s 1 1 1 2 2 0 o 25.09 3.38 1010s 1 1 1 2 2 1 o 9.96 2.30 1010s 1 1 1 2 2 2 o 15.79 2.28 1010s 1 1 1 2 2 3 f 23.73 2.57 1010s 1 1 1 2 2 4 o 31.55 3.47 1010s 1 1 1 2 2 5 o 22.42 5.53 1010s 1 1 1 2 2 6 o 21.84 3.98 1010s 1 1 1 2 2 7 o 11.92 3.24 1010s 1 1 1 3 0 1 o 20.22 2.60 1010s 1 1 1 3 0 2 o 15.58 1.67 1010s 1 1 1 3 0 3 o 43.75 4.24 1010s 1 1 1 3 0 4 o 53.24 5.13 1010s 1 1 1 3 0 5 o 9.04 2.60 1010s 1 1 1 3 0 6 o 16.05 2.16 1010s 1 1 1 3 0 7 o 10.18 3.61 1010s 1 1 1 3 0 8 f 21.57 2.93 1010s 1 1 1 3 0 9 o 5.10 2.75 1010s 1 1 1 3 0 10 o 9.06 4.48 1010s 1 1 1 3 0 11 o 7.20 4.29 1010s 1 1 1 3 1 0 o 6.01 1.35 1010s 1 1 1 3 1 1 o 38.17 5.32 1010s 1 1 1 3 1 2 o 88.61 10.65 1010s 1 1 1 3 1 3 o 46.76 4.49 1010s 1 1 1 3 1 4 o 21.38 1.98 1010s 1 1 1 3 1 5 o 10.82 1.68 1010s 1 1 1 3 1 6 o 9.92 1.96 1010s 1 1 1 3 1 7 o 13.79 1.74 1010s 1 1 1 3 1 8 o 18.26 2.25 1010s 1 1 1 3 1 9 o 10.74 2.36 1010s 1 1 1 3 1 10 o 4.53 1.95 1010s 1 1 1 3 2 0 o 36.54 6.90 1010s 1 1 1 3 2 1 o 7.87 2.79 1010s 1 1 1 3 2 2 o 18.30 2.61 1010s 1 1 1 3 2 3 o 17.39 2.45 1010s 1 1 1 3 2 4 o 17.18 2.74 1010s 1 1 1 3 2 5 o 13.02 2.60 1010s 1 1 1 3 2 6 o 4.72 1.98 1010s 1 1 1 4 0 1 o 3.64 2.08 1010s 1 1 1 4 0 2 o 63.80 6.24 1010s 1 1 1 4 0 3 o 19.19 1.93 1010s 1 1 1 4 0 4 o 63.44 6.28 1010s 1 1 1 4 0 5 o 30.78 6.03 1010s 1 1 1 4 0 6 o 9.03 2.53 1010s 1 1 1 4 0 7 o 18.16 2.40 1010s 1 1 1 4 0 8 o 8.94 3.14 1010s 1 1 1 4 0 9 o 6.87 3.36 1010s 1 1 1 4 0 10 o 9.58 4.40 1010s 1 1 1 4 1 0 o 24.37 2.38 1010s 1 1 1 4 1 1 o 49.48 4.80 1010s 1 1 1 4 1 2 o 10.45 1.03 1010s 1 1 1 4 1 3 o 15.01 1.64 1010s 1 1 1 4 1 4 o 4.52 1.88 1010s 1 1 1 4 1 5 f 35.40 3.27 1010s 1 1 1 4 1 6 o 8.15 2.10 1010s 1 1 1 4 1 7 o 9.72 1.59 1010s 1 1 1 4 1 8 o 5.93 1.88 1010s 1 1 1 4 1 9 o 13.31 3.66 1010s 1 1 1 4 2 0 o 12.03 2.31 1010s 1 1 1 4 2 1 o 13.76 1.98 1010s 1 1 1 4 2 2 o 10.87 2.55 1010s 1 1 1 4 2 3 o 7.78 2.40 1010s 1 1 1 4 2 4 o 19.45 4.53 1010s 1 1 1 4 2 5 o 11.32 4.24 1010s 1 1 1 4 2 6 o 7.29 3.50 1010s 1 1 1 5 0 1 o 67.42 11.14 1010s 1 1 1 5 0 2 o 13.50 3.13 1010s 1 1 1 5 0 3 o 22.37 2.21 1010s 1 1 1 5 0 4 o 56.42 6.72 1010s 1 1 1 5 0 5 o 25.46 3.07 1010s 1 1 1 5 0 6 o 38.61 4.82 1010s 1 1 1 5 0 7 o 14.33 2.65 1010s 1 1 1 5 0 8 f 4.56 2.78 1010s 1 1 1 5 0 9 o 8.50 3.26 1010s 1 1 1 5 1 0 o 21.65 2.85 1010s 1 1 1 5 1 1 o 12.29 1.67 1010s 1 1 1 5 1 2 o 11.21 3.27 1010s 1 1 1 5 1 3 o 9.29 2.49 1010s 1 1 1 5 1 4 o 12.76 2.42 1010s 1 1 1 5 1 5 o 4.61 0.86 1010s 1 1 1 5 1 6 o 21.81 2.38 1010s 1 1 1 5 1 7 o 11.05 2.11 1010s 1 1 1 5 1 8 o 4.27 1.64 1010s 1 1 1 5 2 0 o 17.82 3.76 1010s 1 1 1 5 2 1 o 13.94 3.96 1010s 1 1 1 5 2 2 o 14.67 2.97 1010s 1 1 1 5 2 3 o 12.27 4.35 1010s 1 1 1 5 2 4 o 12.90 2.88 1010s 1 1 1 5 2 5 o 8.21 2.77 1010s 1 1 1 6 0 1 o 4.02 2.51 1010s 1 1 1 6 0 2 o 14.11 3.04 1010s 1 1 1 6 0 4 o 44.86 5.41 1010s 1 1 1 6 0 5 f 22.85 4.74 1010s 1 1 1 6 0 6 o 41.69 6.63 1010s 1 1 1 6 0 7 o 7.42 2.96 1010s 1 1 1 6 0 8 o 13.47 5.61 1010s 1 1 1 6 1 0 o 25.42 2.26 1010s 1 1 1 6 1 1 o 9.87 3.01 1010s 1 1 1 6 1 2 o 28.37 5.85 1010s 1 1 1 6 1 3 o 16.66 3.91 1010s 1 1 1 6 1 4 o 23.02 5.62 1010s 1 1 1 6 1 6 o 26.51 4.88 1010s 1 1 1 6 1 7 o 3.67 1.58 1010s 1 1 1 6 2 0 o 8.22 2.50 1010s 1 1 1 6 2 2 o 9.67 2.35 1010s 1 1 1 6 2 3 o 3.73 1.60 1010s 1 1 1 7 0 1 o 10.99 3.37 1010s 1 1 1 7 0 2 o 17.23 3.99 1010s 1 1 1 7 0 3 o 5.15 2.69 1010s 1 1 1 7 0 4 o 5.19 3.01 1010s 1 1 1 7 0 5 o 23.76 3.00 1010s 1 1 1 7 0 6 o 5.48 3.05 1010s 1 1 1 7 0 7 o 6.05 3.12 1010s 1 1 1 7 0 8 o 7.94 3.69 1010s 1 1 1 7 1 0 o 33.08 3.93 1010s 1 1 1 7 1 1 o 8.43 3.00 1010s 1 1 1 7 1 2 o 10.12 3.61 1010s 1 1 1 7 1 3 o 14.66 3.85 1010s 1 1 1 7 1 4 o 9.43 3.13 1010s 1 1 1 7 1 6 o 14.64 4.20 1010s 1 1 1 7 2 0 o 14.80 3.92 1010s 1 1 1 7 2 1 o 6.02 2.00 1010s 1 1 1 8 0 2 o 29.07 8.06 1010s 1 1 1 8 0 3 o 5.29 2.84 1010s 1 1 1 8 0 4 o 22.81 5.95 1010s 1 1 1 8 0 5 o 4.11 2.70 1010s 1 1 1 8 1 0 o 7.24 1.50 1010s 1 1 1 8 1 1 o 8.85 3.06 1010s 1 1 1 8 1 2 o 6.83 3.09 1010s 1 1 1 8 1 3 o 18.14 5.99 1010s 1 1 1 9 0 1 o 13.49 3.22 1010s 1 1 1 9 0 2 o 11.72 3.95 1010s 1 1 1 10 0 2 o 7.39 3.73 1010s 1 1 1 10 1 0 o 16.08 6.44 1010s #END OF REFLECTIONS 1010s 1010s Starting iotbx.fetch_pdb 1010s on Thu Mar 13 11:04:35 2025 by ubuntu 1010s =============================================================================== 1010s 1010s Processing files: 1010s ------------------------------------------------------------------------------- 1010s 1010s No files found 1010s 1010s Processing PHIL parameters: 1010s ------------------------------------------------------------------------------- 1010s 1010s Adding command-line PHIL: 1010s ------------------------- 1010s action=all 1010s 1010s Final processed PHIL parameters: 1010s ------------------------------------------------------------------------------- 1010s fetch { 1010s pdb_ids = "6yvd" 1010s action = model data sequence half_maps *all 1010s } 1010s 1010s 1010s Starting job 1010s =============================================================================== 1010s Validating inputs: 1010s 1010s Model in PDB format saved to /tmp/autopkgtest.PtYqHY/autopkgtest_tmp/python3.13/6yvd.pdb 1010s Model in mmCIF format saved to /tmp/autopkgtest.PtYqHY/autopkgtest_tmp/python3.13/6yvd.cif 1010s Couldn't download sf for 6yvd at https://files.rcsb.org/download/6yvd-sf.cif.gz. 1010s Cryo-EM map saved to /tmp/autopkgtest.PtYqHY/autopkgtest_tmp/python3.13/emd_10944.map.gz 1010s Cryo-EM half map 1 saved to /tmp/autopkgtest.PtYqHY/autopkgtest_tmp/python3.13/emd_10944_half_map_1.map.gz 1010s Cryo-EM half map 2 saved to /tmp/autopkgtest.PtYqHY/autopkgtest_tmp/python3.13/emd_10944_half_map_2.map.gz 1010s Sequence saved to /tmp/autopkgtest.PtYqHY/autopkgtest_tmp/python3.13/6yvd.fa 1010s 1010s =============================================================================== 1010s Job complete 1010s Total CPU time: 0.58 seconds 1010s Starting iotbx.fetch_pdb 1010s on Thu Mar 13 11:04:48 2025 by ubuntu 1010s =============================================================================== 1010s 1010s Processing files: 1010s ------------------------------------------------------------------------------- 1010s 1010s No files found 1010s 1010s Processing PHIL parameters: 1010s ------------------------------------------------------------------------------- 1010s 1010s Adding command-line PHIL: 1010s ------------------------- 1010s action=model 1010s 1010s Final processed PHIL parameters: 1010s ------------------------------------------------------------------------------- 1010s fetch { 1010s pdb_ids = "6yvd" 1010s } 1010s 1010s 1010s Starting job 1010s =============================================================================== 1010s Validating inputs: 1010s 1010s Model in PDB format saved to /tmp/autopkgtest.PtYqHY/autopkgtest_tmp/python3.13/6yvd.pdb 1010s Model in mmCIF format saved to /tmp/autopkgtest.PtYqHY/autopkgtest_tmp/python3.13/6yvd.cif 1010s 1010s =============================================================================== 1010s Job complete 1010s Total CPU time: 0.48 seconds 1010s Starting iotbx.fetch_pdb 1010s on Thu Mar 13 11:04:51 2025 by ubuntu 1010s =============================================================================== 1010s 1010s Processing files: 1010s ------------------------------------------------------------------------------- 1010s 1010s No files found 1010s 1010s Processing PHIL parameters: 1010s ------------------------------------------------------------------------------- 1010s 1010s Adding command-line PHIL: 1010s ------------------------- 1010s action=model 1010s 1010s Final processed PHIL parameters: 1010s ------------------------------------------------------------------------------- 1010s fetch { 1010s pdb_ids = "6yvd" 1010s } 1010s 1010s 1010s Starting job 1010s =============================================================================== 1010s Validating inputs: 1010s 1010s Model in PDB format saved to /tmp/autopkgtest.PtYqHY/autopkgtest_tmp/python3.13/6yvd.pdb 1010s Model in mmCIF format saved to /tmp/autopkgtest.PtYqHY/autopkgtest_tmp/python3.13/6yvd.cif 1010s 1010s =============================================================================== 1010s Job complete 1010s Total CPU time: 0.47 seconds 1010s Starting iotbx.fetch_pdb 1010s on Thu Mar 13 11:04:54 2025 by ubuntu 1010s =============================================================================== 1010s 1010s Processing files: 1010s ------------------------------------------------------------------------------- 1010s 1010s No files found 1010s 1010s Processing PHIL parameters: 1010s ------------------------------------------------------------------------------- 1010s 1010s Adding command-line PHIL: 1010s ------------------------- 1010s action=data 1010s 1010s Final processed PHIL parameters: 1010s ------------------------------------------------------------------------------- 1010s fetch { 1010s pdb_ids = "6yvd" 1010s action = model *data sequence half_maps all 1010s } 1010s 1010s 1010s Starting job 1010s =============================================================================== 1010s Validating inputs: 1010s 1010s Couldn't download sf for 6yvd at https://files.rcsb.org/download/6yvd-sf.cif.gz. 1010s Cryo-EM map saved to /tmp/autopkgtest.PtYqHY/autopkgtest_tmp/python3.13/emd_10944.map.gz 1010s 1010s =============================================================================== 1010s Job complete 1010s Total CPU time: 0.44 seconds 1010s Starting iotbx.fetch_pdb 1010s on Thu Mar 13 11:04:59 2025 by ubuntu 1010s =============================================================================== 1010s 1010s Processing files: 1010s ------------------------------------------------------------------------------- 1010s 1010s No files found 1010s 1010s Processing PHIL parameters: 1010s ------------------------------------------------------------------------------- 1010s 1010s Adding command-line PHIL: 1010s ------------------------- 1010s action=half_maps 1010s 1010s Final processed PHIL parameters: 1010s ------------------------------------------------------------------------------- 1010s fetch { 1010s pdb_ids = "6yvd" 1010s action = model data sequence *half_maps all 1010s } 1010s 1010s 1010s Starting job 1010s =============================================================================== 1010s Validating inputs: 1010s 1010s Cryo-EM half map 1 saved to /tmp/autopkgtest.PtYqHY/autopkgtest_tmp/python3.13/emd_10944_half_map_1.map.gz 1010s Cryo-EM half map 2 saved to /tmp/autopkgtest.PtYqHY/autopkgtest_tmp/python3.13/emd_10944_half_map_2.map.gz 1010s 1010s =============================================================================== 1010s Job complete 1010s Total CPU time: 0.54 seconds 1010s Starting iotbx.fetch_pdb 1010s on Thu Mar 13 11:05:04 2025 by ubuntu 1010s =============================================================================== 1010s 1010s Processing files: 1010s ------------------------------------------------------------------------------- 1010s 1010s No files found 1010s 1010s Processing PHIL parameters: 1010s ------------------------------------------------------------------------------- 1010s 1010s Adding command-line PHIL: 1010s ------------------------- 1010s action=sequence 1010s 1010s Final processed PHIL parameters: 1010s ------------------------------------------------------------------------------- 1010s fetch { 1010s pdb_ids = "6yvd" 1010s action = model data *sequence half_maps all 1010s } 1010s 1010s 1010s Starting job 1010s =============================================================================== 1010s Validating inputs: 1010s 1010s Sequence saved to /tmp/autopkgtest.PtYqHY/autopkgtest_tmp/python3.13/6yvd.fa 1010s 1010s =============================================================================== 1010s Job complete 1010s Total CPU time: 0.47 seconds 1010s Starting iotbx.fetch_pdb 1010s on Thu Mar 13 11:05:05 2025 by ubuntu 1010s =============================================================================== 1010s 1010s Processing files: 1010s ------------------------------------------------------------------------------- 1010s 1010s No files found 1010s 1010s Processing PHIL parameters: 1010s ------------------------------------------------------------------------------- 1010s 1010s Adding command-line PHIL: 1010s ------------------------- 1010s action=all 1010s 1010s Final processed PHIL parameters: 1010s ------------------------------------------------------------------------------- 1010s fetch { 1010s pdb_ids = "6yvd" 1010s action = model data sequence half_maps *all 1010s } 1010s 1010s 1010s Starting job 1010s =============================================================================== 1010s Validating inputs: 1010s 1010s Model in PDB format saved to /tmp/autopkgtest.PtYqHY/autopkgtest_tmp/python3.13/6yvd.pdb 1010s Model in mmCIF format saved to /tmp/autopkgtest.PtYqHY/autopkgtest_tmp/python3.13/6yvd.cif 1010s Couldn't download sf for 6yvd at https://files.rcsb.org/download/6yvd-sf.cif.gz. 1010s Cryo-EM map saved to /tmp/autopkgtest.PtYqHY/autopkgtest_tmp/python3.13/emd_10944.map.gz 1010s Cryo-EM half map 1 saved to /tmp/autopkgtest.PtYqHY/autopkgtest_tmp/python3.13/emd_10944_half_map_1.map.gz 1010s Cryo-EM half map 2 saved to /tmp/autopkgtest.PtYqHY/autopkgtest_tmp/python3.13/emd_10944_half_map_2.map.gz 1010s Sequence saved to /tmp/autopkgtest.PtYqHY/autopkgtest_tmp/python3.13/6yvd.fa 1010s 1010s =============================================================================== 1010s Job complete 1010s Total CPU time: 0.61 seconds 1010s OK 1010s u+s,u,s: 0.37 0.30 0.07 1012s libtbx.python "/usr/lib/python3/dist-packages/libtbx/easy_run.py" [OK] 2.2s 1012s Time: 2.18 1012s Return code: 0 1012s OKs: 1 1012s Standard out: 1012s OK 1012s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_containers.py" [OK] 0.0s 1012s Time: 0.03 1012s Return code: 0 1012s OKs: 1 1012s Standard out: 1012s OK 1012s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_path.py" [OK] 0.1s 1012s Time: 0.07 1012s Return code: 0 1012s OKs: 1 1012s Standard out: 1012s OK 1012s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_math_utils.py" [OK] 0.3s 1012s Time: 0.33 1012s Return code: 0 1012s OKs: 1 1012s Standard out: 1012s OK 1012s libtbx.python "/usr/lib/python3/dist-packages/libtbx/assert_utils.py" [OK] 0.2s 1012s Time: 0.16 1012s Return code: 0 1012s OKs: 1 1012s Standard out: 1012s OK 1013s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_str_utils.py" [OK] 0.3s 1013s Time: 0.31 1013s Return code: 0 1013s OKs: 1 1013s Standard out: 1013s OK 1013s libtbx.python "/usr/lib/python3/dist-packages/libtbx/table_utils.py" [OK] 0.0s 1013s Time: 0.04 1013s Return code: 0 1013s OKs: 1 1013s Standard out: 1013s OK 1015s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_dlite.py" [OK] 2.1s 1015s Time: 2.08 1015s Return code: 0 1015s OKs: 1 1015s Standard out: 1015s OK 1015s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_tokenizer.py" [OK] 0.1s 1015s Time: 0.08 1015s Return code: 0 1015s OKs: 1 1015s Standard out: 1015s OK 1015s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst.py" [OK] 0.3s 1015s Time: 0.26 1015s Return code: 0 1015s OKs: 1 1015s Standard out: 1015s OK 1015s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_experimental.py" [OK] 0.1s 1015s Time: 0.07 1015s Return code: 0 1015s OKs: 1 1015s Standard out: 1015s OK 1015s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_interface.py" [OK] 0.1s 1015s Time: 0.11 1015s Return code: 0 1015s OKs: 1 1015s Standard out: 1015s phenix module not available: skipping advanced tests 1015s phaser module not available: skipping advanced tests 1015s OK 1016s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_object_oriented_patterns.py" [OK] 0.1s 1016s Time: 0.10 1016s Return code: 0 1016s OKs: 0 1016s libtbx.python "/usr/lib/python3/dist-packages/libtbx/find_reference_cycles.py" [OK] 0.1s 1016s Time: 0.05 1016s Return code: 0 1016s OKs: 1 1016s Standard out: 1016s OK 1016s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_binary_search.py" [OK] 0.0s 1016s Time: 0.05 1016s Return code: 0 1016s OKs: 1 1016s Standard out: 1016s OK 1016s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_topological_sort.py" [OK] 0.0s 1016s Time: 0.05 1016s Return code: 0 1016s OKs: 1 1016s Standard out: 1016s OK 1016s libtbx.python "/usr/lib/python3/dist-packages/libtbx/clusterTests.py" [OK] 0.2s 1016s Time: 0.20 1016s Return code: 0 1016s OKs: 1 1016s Standard out: 1016s ---------------------------------------------------------------------- 1016s Ran 13 tests in 0.127s 1016s 1016s OK 1016s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_citations.py" [OK] 0.2s 1016s Time: 0.22 1016s Return code: 0 1016s OKs: 1 1016s Standard out: 1016s OK 1016s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_python_code_parsing.py" [OK] 0.1s 1016s Time: 0.05 1016s Return code: 0 1016s OKs: 1 1016s Standard out: 1016s OK 1016s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_representation.py" [OK] 0.0s 1016s Time: 0.03 1016s Return code: 0 1016s OKs: 0 1016s Standard out: 1016s 99999999999999950039963891867 1016s 99999999999999963917751699682 1016s 99999999999999977795539507496 1016s 99999999999999991673327315311 1016s 100000000000000005551115123125 1016s 100000000000000019428902930940 1016s 100000000000000033306690738754 1016s 100000000000000047184478546569 1016s 100000000000000061062266354383 1016s 100000000000000074940054162198 1016s 100000000000000088817841970012 1016s 100000000000000102695629777826 1016s 100000000000000116573417585641 1016s 100000000000000130451205393455 1016s 100000000000000144328993201270 1016s 100000000000000158206781009084 1016s 100000000000000172084568816899 1016s 100000000000000185962356624713 1016s 100000000000000199840144432528 1016s 100000000000000213717932240342 1016s 100000000000000227595720048157 1016s 100000000000000241473507855971 1016s 100000000000000255351295663786 1016s 100000000000000269229083471600 1016s 100000000000000283106871279414 1016s 100000000000000296984659087229 1016s 100000000000000310862446895043 1016s 100000000000000324740234702858 1016s 100000000000000338618022510672 1016s 100000000000000352495810318487 1016s BEst 450359962737049.6 1016s 900719925474099.2 1016s 55.32192809488736 1016s 56.32192809488736 1016s True 1016s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_find_unused_imports.py" [OK] 0.0s 1016s Time: 0.04 1016s Return code: 0 1016s OKs: 1 1016s Standard out: 1016s OK 1017s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_program_template.py" [OK] 0.3s 1017s Time: 0.32 1017s Return code: 0 1017s OKs: 0 1017s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_version.py" [OK] 0.1s 1017s Time: 0.08 1017s Return code: 0 1017s OKs: 0 1017s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_scheduling.py" [OK] 7.4s 1017s Time: 7.41 1017s Return code: 0 1017s OKs: 0 1017s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp_multicore.py" [OK] 0.3s 1017s Time: 0.35 1017s Return code: 0 1017s OKs: 0 1017s Standard out: 1017s [1] 1 1017s [2] 2 1017s [3] 6 1017s [4] 24 1017s [5] 120 1017s [6] 720 1017s [7] 5040 1019s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1019s 1 1019s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1019s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_xmlrpc_utils.py" [EXPECTED FAIL] 2.4s 1019s Time: 2.42 1019s Return code: 1 1019s OKs: 0 1019s Standard error: 1019s Traceback (most recent call last): 1019s File "/usr/lib/python3/dist-packages/libtbx/tst_xmlrpc_utils.py", line 42, in 1019s exercise() 1019s ~~~~~~~~^^ 1019s File "/usr/lib/python3/dist-packages/libtbx/tst_xmlrpc_utils.py", line 15, in exercise 1019s server = xmlrpc_utils.external_program_server(command=full_cmd, 1019s program_id="TEST", 1019s timeout=None, 1019s cache_requests=True, 1019s log=log) 1019s TypeError: external_program_server.__init__() got an unexpected keyword argument 'command' 1023s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1023s 139 1023s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1023s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_smoothing.py" [FAIL] 3.3s 1023s Time: 3.30 1023s Return code: 139 1023s OKs: 0 1023s Standard error: 1023s Segmentation fault (core dumped) 1024s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_runtime_utils.py" [OK] 6.8s 1024s Time: 6.81 1024s Return code: 0 1024s OKs: 1 1024s Standard out: 1024s OK 1026s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1026s 139 1026s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1026s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_genetic_algorithm_with_mp.py" [FAIL] 3.3s 1026s Time: 3.35 1026s Return code: 139 1026s OKs: 0 1026s Standard error: 1026s Segmentation fault (core dumped) 1026s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_1" [OK] 0.0s 1026s Time: 0.01 1026s Return code: 0 1026s OKs: 1 1026s Standard out: 1026s Total OK: 511 1026s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_2" [OK] 0.0s 1026s Time: 0.01 1026s Return code: 0 1026s OKs: 1 1026s Standard out: 1026s Total OK: 268 1026s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_3" [OK] 0.0s 1026s Time: 0.01 1026s Return code: 0 1026s OKs: 1 1026s Standard out: 1026s Total OK: 164 1026s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_4" [OK] 0.0s 1026s Time: 0.01 1026s Return code: 0 1026s OKs: 1 1026s Standard out: 1026s Total OK: 1420 1026s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_5" [OK] 0.0s 1026s Time: 0.01 1026s Return code: 0 1026s OKs: 1 1026s Standard out: 1026s Total OK: 23 1026s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_vec3" [OK] 0.0s 1026s Time: 0.00 1026s Return code: 0 1026s OKs: 1 1026s Standard out: 1026s Total OK: 83 1026s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_unsigned_float_arithmetic" [OK] 0.0s 1026s Time: 0.01 1026s Return code: 0 1026s OKs: 1 1026s Standard out: 1026s OK 1026s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_mat3" [OK] 0.0s 1026s Time: 0.00 1026s Return code: 0 1026s OKs: 1 1026s Standard out: 1026s Total OK: 129 1026s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_sym_mat3" [OK] 0.0s 1026s Time: 0.00 1026s Return code: 0 1026s OKs: 1 1026s Standard out: 1026s Total OK: 91 1026s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_ref_matrix_facet" [OK] 0.0s 1026s Time: 0.00 1026s Return code: 0 1026s OKs: 1 1026s Standard out: 1026s OK 1026s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_accessors" [OK] 0.0s 1026s Time: 0.00 1026s Return code: 0 1026s OKs: 1 1026s Standard out: 1026s Total OK: 1730 1026s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_optional_copy" [OK] 0.0s 1026s Time: 0.00 1026s Return code: 0 1026s OKs: 1 1026s Standard out: 1026s OK 1026s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_rectangular_full_packed" [OK] 0.0s 1026s Time: 0.00 1026s Return code: 0 1026s OKs: 0 1026s Standard out: 1026s Test of accessor for rectangular full packed format skipped 1026s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex_argument_passing.py" [OK] 0.1s 1026s Time: 0.15 1026s Return code: 0 1026s OKs: 1 1026s Standard out: 1026s OK 1027s "/usr/lib/cctbx/python3.13/scitbx/serialization/tst_base_256" [OK] 0.2s 1027s Time: 0.19 1027s Return code: 0 1027s OKs: 1 1027s Standard out: 1027s OK 1029s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1029s 139 1029s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1029s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_basic.py" [FAIL] 5.3s 1029s Time: 5.26 1029s Return code: 139 1029s OKs: 1 1029s Standard out: 1029s 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' 1029s Size of an empty container. 1029s Some of those containers store a pointer to a raw storage: 1029s the 'cumulative' entry refers to the total memory footprint 1029s whereas the other entry does not include the raw storage. 1029s 1029s int : 4 1029s af::ref : 32 1029s scitbx::auto_array : 8 1029s boost::shared_array : 16 1029s boost::ptr_vector : 24 1029s std::vector : 24 1029s af::shared : 16 1029s af::shared [cumulative] : 64 1029s std::valarray : 16 1029s af::versa : 24 1029s af::versa > : 280 1029s af::versa > [cumulative] : 328 1029s 1029s double : 8 1029s af::ref : 32 1029s scitbx::auto_array : 8 1029s boost::shared_array : 16 1029s boost::ptr_vector : 24 1029s std::vector : 24 1029s af::shared : 16 1029s af::shared [cumulative] : 64 1029s std::valarray : 16 1029s af::versa : 24 1029s af::versa > : 280 1029s af::versa > [cumulative] : 328 1029s 1029s OK 1029s Standard error: 1029s Segmentation fault (core dumped) 1032s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1032s 139 1032s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1032s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_minimum_covering_ellipsoid.py" [FAIL] 5.5s 1032s Time: 5.54 1032s Return code: 139 1032s OKs: 0 1032s Standard error: 1032s Segmentation fault (core dumped) 1035s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1035s 139 1035s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1035s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian_fit_1d_analytical.py" [FAIL] 6.0s 1035s Time: 6.02 1035s Return code: 139 1035s OKs: 0 1035s Standard error: 1035s Segmentation fault (core dumped) 1035s "/usr/lib/cctbx/python3.13/scitbx/math/tests/tst" [OK] 0.0s 1035s Time: 0.01 1035s Return code: 0 1035s OKs: 2 1035s Standard out: 1035s copysign(3.f, +0.f) = 3 instead of 0.f as per C99 1035s copysign(3.f, -0.f) = -3 instead of -0.f as per C99 1035s linear interpolation test OK 1035s OK 1035s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_givens" [OK] 0.0s 1035s Time: 0.00 1035s Return code: 0 1035s OKs: 1 1035s Standard out: 1035s OK 1035s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_householder" [OK] 0.0s 1035s Time: 0.01 1035s Return code: 0 1035s OKs: 1 1035s Standard out: 1035s OK 1035s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_svd" [OK] 0.0s 1035s Time: 0.01 1035s Return code: 0 1035s OKs: 1 1035s Standard out: 1035s OK 1035s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_cholesky" [OK] 0.1s 1035s Time: 0.11 1035s Return code: 0 1035s OKs: 1 1035s Standard out: 1035s Exercising sizes up to 100 1035s Hilbert 1035s Condition 1 1035s Condition 2 1035s Condition 3 1035s Condition 4 1035s OK 1035s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/tests/tst_row_echelon.py" [OK] 0.1s 1035s Time: 0.08 1035s Return code: 0 1035s OKs: 1 1035s Standard out: 1035s OK 1035s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/tests/tst_householder.py" [OK] 0.2s 1035s Time: 0.18 1035s Return code: 0 1035s OKs: 1 1035s Standard out: 1035s OK 1036s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_matrix.py" [OK] 0.2s 1036s Time: 0.19 1036s Return code: 0 1036s OKs: 1 1036s Standard out: 1036s OK 1038s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1038s 139 1038s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1038s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_cubic_equation.py" [FAIL] 5.9s 1038s Time: 5.88 1038s Return code: 139 1038s OKs: 0 1038s Standard error: 1038s Segmentation fault (core dumped) 1041s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1041s 139 1041s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1041s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_cholesky.py" [FAIL] 5.4s 1041s Time: 5.43 1041s Return code: 139 1041s OKs: 0 1041s Standard error: 1041s Segmentation fault (core dumped) 1044s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1044s 139 1044s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1044s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_svd.py" [FAIL] 6.0s 1044s Time: 5.99 1044s Return code: 139 1044s OKs: 0 1044s Standard error: 1044s Segmentation fault (core dumped) 1047s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1047s 139 1047s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1047s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_eigensystem.py" [FAIL] 5.8s 1047s Time: 5.84 1047s Return code: 139 1047s OKs: 0 1047s Standard error: 1047s Segmentation fault (core dumped) 1050s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1050s 139 1050s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1050s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_svd.py" [FAIL] 5.8s 1050s Time: 5.84 1050s Return code: 139 1050s OKs: 0 1050s Standard error: 1050s Segmentation fault (core dumped) 1050s libtbx.python "/usr/lib/python3/dist-packages/scitbx/error/tst_error.py" [OK] 0.1s 1050s Time: 0.08 1050s Return code: 0 1050s OKs: 1 1050s Standard out: 1050s OK 1050s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_map.py" [OK] 0.1s 1050s Time: 0.06 1050s Return code: 0 1050s OKs: 1 1050s Standard out: 1050s OK 1050s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_set.py" [OK] 0.1s 1050s Time: 0.06 1050s Return code: 0 1050s OKs: 1 1050s Standard out: 1050s OK 1050s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_vector.py" [OK] 0.1s 1050s Time: 0.06 1050s Return code: 0 1050s OKs: 1 1050s Standard out: 1050s OK 1053s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1053s 139 1053s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1053s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_dsyev.py" [FAIL] 5.7s 1053s Time: 5.69 1053s Return code: 139 1053s OKs: 0 1053s Standard error: 1053s Segmentation fault (core dumped) 1055s Standard error: 1055s Segmentation fault (core dumped) 1055s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1055s 139 1055s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1055s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/regression_test.py" [FAIL] 5.3s 1055s Time: 5.34 1055s Return code: 139 1055s OKs: 0 1059s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1059s 139 1059s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1059s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex.py" [FAIL] 5.9s 1059s Time: 5.89 1059s Return code: 139 1059s OKs: 0 1059s Standard error: 1059s Segmentation fault (core dumped) 1061s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1061s 139 1061s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1061s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_numpy_bridge.py" [FAIL] 5.9s 1061s Time: 5.88 1061s Return code: 139 1061s OKs: 0 1061s Standard error: 1061s Segmentation fault (core dumped) 1064s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1064s 139 1064s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1064s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_smart_selection.py" [FAIL] 5.6s 1064s Time: 5.59 1064s Return code: 139 1064s OKs: 0 1064s Standard error: 1064s Segmentation fault (core dumped) 1067s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1067s 139 1067s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1067s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_shared.py" [FAIL] 5.6s 1067s Time: 5.59 1067s Return code: 139 1067s OKs: 0 1067s Standard error: 1067s Segmentation fault (core dumped) 1069s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_cost_of_m_handle_in_af_shared.py" [OK] 2.2s 1069s Time: 2.22 1069s Return code: 0 1069s OKs: 1 1069s Standard out: 1069s Loop over af::shared: 1069s data_size=1000, n_repeats=30000 1069s size+begin inside loop: 0.16 s 1069s begin outside loop: 0.12 s 1069s size+begin outside loop: 0.09 s 1069s 1069s data_size=10000, n_repeats=3000 1069s size+begin inside loop: 0.16 s 1069s begin outside loop: 0.12 s 1069s size+begin outside loop: 0.09 s 1069s 1069s data_size=100000, n_repeats=300 1069s size+begin inside loop: 0.17 s 1069s begin outside loop: 0.12 s 1069s size+begin outside loop: 0.09 s 1069s 1069s data_size=1000000, n_repeats=30 1069s size+begin inside loop: 0.17 s 1069s begin outside loop: 0.12 s 1069s size+begin outside loop: 0.09 s 1069s 1069s data_size=10000000, n_repeats=3 1069s size+begin inside loop: 0.22 s 1069s begin outside loop: 0.12 s 1069s size+begin outside loop: 0.09 s 1069s 1069s OK 1069s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_cubicle_neighbors.py" [OK] 0.2s 1069s Time: 0.15 1069s Return code: 0 1069s OKs: 1 1069s Standard out: 1069s OK 1069s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_r3_utils.py" [OK] 0.2s 1069s Time: 0.17 1069s Return code: 0 1069s OKs: 1 1069s Standard out: 1069s OK 1070s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_regular_grid_on_unit_sphere.py" [OK] 0.5s 1070s Time: 0.54 1070s Return code: 0 1070s OKs: 0 1073s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1073s 139 1073s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1073s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/__init__.py" [FAIL] 3.1s 1073s Standard error: 1073s Segmentation fault (core dumped) 1073s Time: 3.12 1073s Return code: 139 1073s OKs: 0 1076s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1076s 139 1076s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1076s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_random_transform.py" [FAIL] 3.1s 1076s Time: 3.14 1076s Return code: 139 1076s OKs: 0 1076s Standard error: 1076s Segmentation fault (core dumped) 1076s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_graph.py" [OK] 0.1s 1076s Time: 0.06 1076s Return code: 0 1076s OKs: 1 1076s Standard out: 1076s OK 1076s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_robust.py" [OK] 0.1s 1076s Time: 0.14 1076s Return code: 0 1076s OKs: 1 1076s Standard out: 1076s OK 1079s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1079s 139 1079s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1079s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/superpose.py" [FAIL] 2.9s 1079s Time: 2.87 1079s Return code: 139 1079s OKs: 0 1079s Standard error: 1079s Segmentation fault (core dumped) 1081s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_integer_offsets_vs_pointers.py" [OK] 17.0s 1081s Time: 17.03 1081s Return code: 0 1081s OKs: 1 1081s Standard out: 1081s data_size = 1000 n_repeats = 30000 1081s use_pointers = False 1081s use_iterators = 0 time = 0.44 s overhead = 0.00 s (d[p[i]] -1.36424e-08) 1081s use_iterators = 1 time = 0.23 s overhead = 0.00 s (d[*p++] -1.36424e-08) 1081s use_pointers = True 1081s use_iterators = 0 time = 0.23 s overhead = 0.00 s (*dp[i] -1.36424e-08) 1081s use_iterators = 1 time = 0.49 s overhead = 0.00 s (**dpi++ -1.36424e-08) 1081s use_iterators = 2 time = 0.05 s overhead = 0.00 s (**dpp++ -1.36424e-08) 1081s data_size = 10000 n_repeats = 3000 1081s use_pointers = False 1081s use_iterators = 0 time = 0.42 s overhead = 0.00 s (d[p[i]] 2.1828e-08) 1081s use_iterators = 1 time = 0.22 s overhead = 0.00 s (d[*p++] 2.1828e-08) 1081s use_pointers = True 1081s use_iterators = 0 time = 0.23 s overhead = 0.00 s (*dp[i] 2.1828e-08) 1081s use_iterators = 1 time = 0.49 s overhead = 0.00 s (**dpi++ 2.1828e-08) 1081s use_iterators = 2 time = 0.05 s overhead = 0.00 s (**dpp++ 2.1828e-08) 1081s data_size = 100000 n_repeats = 300 1081s use_pointers = False 1081s use_iterators = 0 time = 0.42 s overhead = 0.00 s (d[p[i]] -1.30927e-08) 1081s use_iterators = 1 time = 0.26 s overhead = 0.00 s (d[*p++] -1.30927e-08) 1081s use_pointers = True 1081s use_iterators = 0 time = 0.23 s overhead = 0.00 s (*dp[i] -1.30927e-08) 1081s use_iterators = 1 time = 0.51 s overhead = 0.00 s (**dpi++ -1.30927e-08) 1081s use_iterators = 2 time = 0.06 s overhead = 0.00 s (**dpp++ -1.30927e-08) 1081s data_size = 1000000 n_repeats = 30 1081s use_pointers = False 1081s use_iterators = 0 time = 0.47 s overhead = 0.02 s (d[p[i]] -1.64131e-07) 1081s use_iterators = 1 time = 0.30 s overhead = 0.01 s (d[*p++] -1.64131e-07) 1081s use_pointers = True 1081s use_iterators = 0 time = 0.25 s overhead = 0.02 s (*dp[i] -1.64131e-07) 1081s use_iterators = 1 time = 0.88 s overhead = 0.02 s (**dpi++ -1.64131e-07) 1081s use_iterators = 2 time = 0.07 s overhead = 0.02 s (**dpp++ -1.64131e-07) 1081s data_size = 10000000 n_repeats = 3 1081s use_pointers = False 1081s use_iterators = 0 time = 1.99 s overhead = 0.22 s (d[p[i]] -1.70934e-08) 1081s use_iterators = 1 time = 1.29 s overhead = 0.20 s (d[*p++] -1.70934e-08) 1081s use_pointers = True 1081s use_iterators = 0 time = 1.01 s overhead = 0.20 s (*dp[i] -1.70934e-08) 1081s use_iterators = 1 time = 2.93 s overhead = 0.20 s (**dpi++ -1.70934e-08) 1081s use_iterators = 2 time = 0.39 s overhead = 0.20 s (**dpp++ -1.70934e-08) 1081s OK 1082s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1082s 139 1082s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1082s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/spe.py" [FAIL] 2.8s 1082s Time: 2.79 1082s Return code: 139 1082s OKs: 0 1082s Standard error: 1082s Segmentation fault (core dumped) 1086s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1086s 139 1086s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1086s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/incremental_SO3_sampling.py" [FAIL] 4.7s 1086s Time: 4.65 1086s Return code: 139 1086s OKs: 0 1086s Standard error: 1086s Segmentation fault (core dumped) 1089s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1089s 139 1089s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1089s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_curve_fitting.py" [FAIL] 6.6s 1089s Time: 6.56 1089s Return code: 139 1089s OKs: 0 1089s Standard error: 1089s Segmentation fault (core dumped) 1089s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_similarity_indices.py" [OK] 0.2s 1089s Time: 0.19 1089s Return code: 0 1089s OKs: 1 1089s Standard out: 1089s OK 1091s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1091s 139 1091s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1091s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_weighted_correlation.py" [FAIL] 5.5s 1091s Time: 5.51 1091s Return code: 139 1091s OKs: 0 1091s Standard error: 1091s Segmentation fault (core dumped) 1091s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_fit_quadratic_function.py" [OK] 0.2s 1091s Time: 0.20 1091s Return code: 0 1091s OKs: 1 1091s Standard out: 1091s OK 1092s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gcd.py" [OK] 0.5s 1092s Time: 0.54 1092s Return code: 0 1092s OKs: 1 1092s Standard out: 1092s compare_with_boost_rational_gcd(gcd_int_simple) 1092s compare_with_boost_rational_gcd(gcd_long_simple) 1092s compare_with_boost_rational_gcd(gcd_long_binary) 1092s gcd_int_boost 999 w=0.03 u+s=0.03 1092s gcd_int_simple 999 w=0.02 u+s=0.02 1092s gcd_long_boost 999 w=0.04 u+s=0.04 1092s gcd_long_simple 999 w=0.02 u+s=0.02 1092s gcd_unsigned_long_binary 999 w=0.09 u+s=0.09 1092s gcd_long_binary 999 w=0.09 u+s=0.09 1092s OK 1094s Standard error: 1094s 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/math/tests/tst_exp_functions.py" [FAIL] 5.4s 1094s Time: 5.45 1094s Return code: 139 1094s OKs: 0 1097s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_r3_rotation.py" [OK] 2.5s 1097s Time: 2.52 1097s Return code: 0 1097s OKs: 0 1097s Standard out: 1097s times unit quaternion <-> matrix 1097s py: 0.04 0.03 s 1097s c++: 0.04 0.04 s 1097s ratio: 1.00 0.73 1097s u+s,u,s: 2.47 2.44 0.03 1097s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1097s 139 1097s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1097s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_math.py" [FAIL] 5.2s 1097s Time: 5.18 1097s Return code: 139 1097s OKs: 0 1097s Standard error: 1097s Segmentation fault (core dumped) 1097s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_line_search.py" [OK] 0.2s 1097s Time: 0.19 1097s Return code: 0 1097s OKs: 1 1097s Standard out: 1097s OK 1100s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1100s 139 1100s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1100s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_resample.py" [FAIL] 3.1s 1100s Time: 3.11 1100s Return code: 139 1100s OKs: 0 1100s Standard error: 1100s Segmentation fault (core dumped) 1103s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1103s 139 1103s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1103s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian.py" [FAIL] 5.2s 1103s Time: 5.16 1103s Return code: 139 1103s OKs: 0 1103s Standard error: 1103s Segmentation fault (core dumped) 1103s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_bessel.py" [OK] 0.2s 1103s Time: 0.17 1103s Return code: 0 1103s OKs: 0 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/math/tests/tst_quadrature.py" [FAIL] 5.4s 1105s Time: 5.35 1105s Return code: 139 1105s OKs: 0 1105s Standard error: 1105s Segmentation fault (core dumped) 1106s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_euler_angles.py" [OK] 0.7s 1106s Time: 0.74 1106s Return code: 0 1106s OKs: 0 1106s Standard out: 1106s u+s,u,s: 0.70 0.68 0.02 1106s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_superpose.py" [OK] 0.2s 1106s Time: 0.23 1106s Return code: 0 1106s OKs: 1 1106s Standard out: 1106s OK 1106s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_uniform_rotation_matrix.py" [OK] 0.2s 1106s Time: 0.18 1106s Return code: 0 1106s OKs: 1 1106s Standard out: 1106s OK 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/math/tests/tst_halton.py" [FAIL] 5.2s 1108s Time: 5.16 1108s Return code: 139 1108s OKs: 0 1108s Standard error: 1108s Segmentation fault (core dumped) 1108s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike_mom.py" [OK] 0.2s 1108s Time: 0.17 1108s Return code: 0 1108s OKs: 1 1108s Standard out: 1108s OK 1108s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/sieve_of_eratosthenes.py" [OK] 0.0s 1108s Time: 0.03 1108s Return code: 0 1108s OKs: 1 1108s Standard out: 1108s OK 1108s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/besselk.py" [OK] 0.0s 1108s Time: 0.03 1108s Return code: 0 1108s OKs: 1 1108s Standard out: 1108s OK 1111s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1111s 139 1111s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1111s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/scale_curves.py" [FAIL] 2.9s 1111s Time: 2.93 1111s Return code: 139 1111s OKs: 0 1111s Standard error: 1111s Segmentation fault (core dumped) 1114s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1114s 139 1114s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1114s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_fit_peak.py" [FAIL] 3.1s 1114s Time: 3.08 1114s Return code: 139 1114s OKs: 0 1114s Standard error: 1114s Segmentation fault (core dumped) 1118s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1118s 139 1118s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1118s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike.py" [FAIL] 11.3s 1118s Time: 11.30 1118s Return code: 139 1118s OKs: 0 1118s Standard error: 1118s Segmentation fault (core dumped) 1118s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_orthonormal_basis.py" [OK] 0.2s 1118s Time: 0.17 1118s Return code: 0 1118s OKs: 1 1118s Standard out: 1118s OK 1118s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_g_function.py" [OK] 0.2s 1118s Time: 0.18 1118s Return code: 0 1118s OKs: 0 1118s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_angle_derivative.py" [OK] 0.2s 1118s Time: 0.17 1118s Return code: 0 1118s OKs: 1 1118s Standard out: 1118s OK 1120s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1120s 139 1120s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1120s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_clustering.py" [FAIL] 6.1s 1120s Time: 6.07 1120s Return code: 139 1120s OKs: 0 1120s Standard error: 1120s Segmentation fault (core dumped) 1123s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1123s 139 1123s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1123s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_periodogram.py" [FAIL] 4.7s 1123s Time: 4.73 1123s Return code: 139 1123s OKs: 0 1123s Standard error: 1123s Segmentation fault (core dumped) 1123s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_tetrahedron.py" [OK] 0.2s 1123s Time: 0.20 1123s Return code: 0 1123s OKs: 1 1123s Standard out: 1123s OK 1123s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_undirected_graph.py" [OK] 0.2s 1123s Time: 0.17 1123s Return code: 0 1123s OKs: 0 1124s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_so3_lie_algebra.py" [OK] 0.2s 1124s Time: 0.18 1124s Return code: 0 1124s OKs: 0 1124s libtbx.python "/usr/lib/python3/dist-packages/scitbx/minpack/tst.py" [OK] 0.2s 1124s Time: 0.17 1124s Return code: 0 1124s OKs: 1 1124s Standard out: 1124s OK 1124s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_ext.py" [OK] 0.2s 1124s Time: 0.15 1124s Return code: 0 1124s OKs: 1 1124s Standard out: 1124s OK 1126s Standard error: 1126s Segmentation fault (core dumped) 1126s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1126s 139 1126s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1126s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_error_propagation_matrix_inverse.py" [FAIL] 5.5s 1126s Time: 5.52 1126s Return code: 139 1126s OKs: 0 1129s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1129s 139 1129s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1129s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_curvatures.py" [FAIL] 4.7s 1129s Time: 4.71 1129s Return code: 139 1129s OKs: 0 1129s Standard error: 1129s Segmentation fault (core dumped) 1129s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_func_free_line_search.py" [OK] 0.2s 1129s Time: 0.16 1129s Return code: 0 1129s OKs: 1 1129s Standard out: 1129s The answer is: [2, -5, 500] 1129s The start value is: [-100, 203, 999] 1129s scitbx.lbfgs: use gradient_only line search: True 1129s scitbx.lbfgs: use gradient_only line search: False 1129s OK 1129s "/usr/lib/cctbx/python3.13/scitbx/lbfgs/tst_lbfgs" [OK] 0.0s 1129s Time: 0.01 1129s Return code: 0 1129s OKs: 0 1129s Standard out: 1129s n: 100 1129s m: 5 1129s xtol: 1e-16 1129s f: 254.065 gnorm: 325.365 1129s 1 2 0.000607303 1129s f: 207.819 gnorm: 54.5204 1129s 2 3 1 1129s f: 206.329 gnorm: 12.6873 1129s 3 4 1 1129s f: 206.158 gnorm: 12.9705 1129s 4 5 1 1129s f: 204.568 gnorm: 36.0649 1129s 5 6 1 1129s f: 201.009 gnorm: 69.9702 1129s 6 7 1 1129s f: 132.076 gnorm: 99.1014 1129s 7 11 2.30835 1129s f: 131.557 gnorm: 80.1033 1129s 8 13 0.152436 1129s f: 120.196 gnorm: 66.244 1129s 9 15 5 1129s f: 105.948 gnorm: 116.627 1129s 10 16 1 1129s f: 87.4002 gnorm: 17.1325 1129s 11 17 1 1129s f: 72.7773 gnorm: 32.6968 1129s 12 18 1 1129s f: 67.7306 gnorm: 49.5851 1129s 13 20 0.213662 1129s f: 60.0913 gnorm: 52.8678 1129s 14 21 1 1129s f: 45.9493 gnorm: 28.0796 1129s 15 22 1 1129s f: 37.3669 gnorm: 39.3487 1129s 16 23 1 1129s f: 23.0492 gnorm: 14.5867 1129s 17 24 1 1129s f: 19.8468 gnorm: 17.9762 1129s 18 26 0.156708 1129s f: 17.6677 gnorm: 48.6045 1129s 19 27 1 1129s f: 13.9465 gnorm: 22.2498 1129s 20 28 1 1129s f: 9.11604 gnorm: 28.0105 1129s 21 29 1 1129s f: 5.82159 gnorm: 10.2151 1129s 22 30 1 1129s f: 4.75971 gnorm: 28.511 1129s 23 32 0.436181 1129s f: 2.35807 gnorm: 22.65 1129s 24 33 1 1129s f: 1.55734 gnorm: 15.4752 1129s 25 34 1 1129s f: 0.810498 gnorm: 2.3865 1129s 26 36 0.404632 1129s f: 0.508703 gnorm: 9.94499 1129s 27 38 0.247512 1129s f: 0.363447 gnorm: 15.2129 1129s 28 39 1 1129s f: 0.167247 gnorm: 9.7728 1129s 29 40 1 1129s f: 0.0372373 gnorm: 1.32586 1129s 30 41 1 1129s f: 0.0098316 gnorm: 4.14194 1129s 31 42 1 1129s f: 0.000471098 gnorm: 0.567595 1129s 32 43 1 1129s f: 3.2788e-06 gnorm: 0.027547 1129s 33 44 1 1129s f: 2.34044e-08 gnorm: 0.00607363 1129s 34 45 1 1129s f: 2.09469e-13 gnorm: 1.31535e-05 1129s 35 46 1 1132s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1132s 139 1132s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1132s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgsb/boost_python/tst_lbfgsb.py" [FAIL] 3.0s 1132s Time: 3.02 1132s Return code: 139 1132s OKs: 0 1132s Standard error: 1132s Segmentation fault (core dumped) 1135s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1135s 139 1135s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1135s libtbx.python "/usr/lib/python3/dist-packages/scitbx/fftpack/boost_python/tst_fftpack.py" [FAIL] 3.0s 1135s Time: 3.02 1135s Return code: 139 1135s OKs: 0 1135s Standard error: 1135s Segmentation fault (core dumped) 1136s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" [OK] 10.7s 1136s Time: 10.69 1136s Return code: 0 1136s OKs: 1 1136s Standard out: 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 5 -1 0 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 5 -1 0 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 5 -1 0 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 4 -1 1 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 4 -1 1 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 4 -1 1 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 5 -1 2 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 5 -1 2 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 5 -1 2 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 5 -1 3 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 5 -1 3 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 5 -1 3 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 6 0 0 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 6 0 0 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 6 0 0 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 6 0 1 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 6 0 1 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 6 0 1 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 4 0 2 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 4 0 2 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 4 0 2 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 2 0 3 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 2 0 3 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 2 0 3 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 6 1 0 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 6 1 0 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 6 1 0 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 4 1 1 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 4 1 1 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 4 1 1 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 7 1 2 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 7 1 2 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 7 1 2 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 7 1 3 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 7 1 3 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 7 1 3 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 5 2 0 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 5 2 0 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 5 2 0 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 4 2 1 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 4 2 1 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 4 2 1 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 4 2 2 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 4 2 2 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 4 2 2 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 6 2 3 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 6 2 3 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 6 2 3 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 5 3 0 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 5 3 0 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 5 3 0 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 2 3 1 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 2 3 1 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 2 3 1 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 2 3 2 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 2 3 2 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 2 3 2 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 7 3 3 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 7 3 3 1136s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 7 3 3 1136s usr+sys time: 0.33 seconds 1136s wall clock time: 10.52 seconds 1136s OK 1137s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_array_loops.py" [OK] 0.1s 1137s Time: 0.13 1137s Return code: 0 1137s OKs: 1 1137s Standard out: 1137s 10.0 1137s 11.0 1137s 12.0 1137s 1137s 10.0 1137s 11.0 1137s 12.0 1137s 1137s 0 10.0 1137s 1 11.0 1137s 2 12.0 1137s 1137s 100.0 1137s 110.0 1137s 120.0 1137s 1137s 200.0 1137s 210.0 1137s 220.0 1137s 1137s OK 1137s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/principal_axes_of_inertia.py" [OK] 0.1s 1137s Time: 0.15 1137s Return code: 0 1137s OKs: 0 1137s Standard out: 1137s (7.796692307692308, 1.365076923076923, 8.357692307692307) 1137s (38.140037692307715, 97.02526753846156, 79.02221969230771, -19.808558307692305, 35.14258523076924, 7.662036692307694) 1137s [104.22746487361262, 97.26642591377531, 12.693634135689017] 1137s [-0.4390539716746839, 0.8222124337102901, -0.36221309171382476, 0.303721679623708, 0.515239851411788, 0.8014243799908461, 0.8455677094610694, 0.24185658843488292, -0.47594184450140553] 1137s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_recipe.py" [OK] 0.1s 1137s Time: 0.14 1137s Return code: 0 1137s OKs: 1 1137s Standard out: 1137s refinery 1137s compute_functional_and_gradients 1137s callback_after_step 1137s OK 1138s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1138s 139 1138s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1138s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_grid.py" [FAIL] 2.8s 1138s Time: 2.85 1138s Return code: 139 1138s OKs: 0 1138s Standard error: 1138s Segmentation fault (core dumped) 1140s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1140s 139 1140s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1140s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_linear_least_squares_fit.py" [FAIL] 3.4s 1140s Time: 3.37 1140s Return code: 139 1140s OKs: 0 1140s Standard error: 1140s Segmentation fault (core dumped) 1143s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1143s 139 1143s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1143s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/chebyshev_lsq_example.py" [FAIL] 5.3s 1143s Standard error: 1143s Time: 5.30 1143s Return code: 139 1143s OKs: 0 1143s Segmentation fault (core dumped) 1143s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/rigid_body_refinement_core.py" [OK] 0.2s 1143s Time: 0.15 1143s Return code: 0 1143s OKs: 1 1143s Standard out: 1143s an ea: [0.0, 0.0, 0.0] 1143s fd ea: [2.9856131013692537e-15, 8.482502921596884e-16, 3.956636706594845e-15] 1143s an lt: [-0.0, -0.0, -0.0] 1143s fd lt: [0.0, 0.0, 0.0] 1143s 1143s an ea: [1.4293798315070272, -4.7699199336056015, -3.2848275925325994] 1143s fd ea: [1.4293798327180696, -4.769919932368083, -3.284827593041939] 1143s an lt: [-2.6395370381698946, 3.8546779254822816, -3.7648774634679576] 1143s fd lt: [-2.639537036053241, 3.8546779261849906, -3.764877463563465] 1143s 1143s an ea: [-4.386454471339835, 2.1848899436111178, 5.0802158076235635] 1143s fd ea: [-4.386454468985335, 2.184889945411328, 5.080215810693289] 1143s an lt: [-4.688132824683539, -10.874759921610867, -1.9393316543209416] 1143s fd lt: [-4.688132825947378, -10.874759922785415, -1.939331655265164] 1143s 1143s an ea: [-5.097458993694191, 2.0225151159319297, 4.479103261227751] 1143s fd ea: [-5.097458993574833, 2.0225151207142744, 4.479103258958617] 1143s an lt: [-2.8154365578392593, -5.157085781215166, -17.014046644874668] 1143s fd lt: [-2.8154365576682494, -5.157085780638226, -17.014046648000658] 1143s 1143s OK 1146s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1146s 139 1146s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1146s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/immoptibox_ports.py" [FAIL] 5.6s 1146s Time: 5.56 1146s Return code: 139 1146s OKs: 0 1146s Standard error: 1146s Segmentation fault (core dumped) 1148s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1148s 139 1148s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1148s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/integrating_a_weighted_sinc_function.py" [FAIL] 5.4s 1148s Time: 5.41 1148s Return code: 139 1148s OKs: 0 1148s Standard error: 1148s Segmentation fault (core dumped) 1149s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_utils.py" [OK] 0.0s 1149s Time: 0.04 1149s Return code: 0 1149s OKs: 1 1149s Standard out: 1149s OK 1149s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/rigidity.py" [OK] 0.0s 1149s Time: 0.04 1149s Return code: 0 1149s OKs: 0 1149s Standard out: 1149s double banana 3D dof (method=integer): 7 1149s double banana 3D dof (method=float): 7 1149s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_rigidity.py" [OK] 0.2s 1149s Time: 0.25 1149s Return code: 0 1149s OKs: 0 1149s Standard out: 1149s repeat_log = {0: 85} 1149s u+s,u,s: 0.21 0.20 0.01 1149s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/rigidity_matrix_symbolic.py" [OK] 0.3s 1149s Time: 0.27 1149s Return code: 0 1149s OKs: 0 1149s Standard out: 1149s u+s,u,s: 0.24 0.24 0.00 1151s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1151s 139 1151s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1151s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/minimizer_comparisons.py" [FAIL] 5.4s 1151s Time: 5.40 1151s Return code: 139 1151s OKs: 0 1151s Standard error: 1151s Segmentation fault (core dumped) 1152s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree_find_paths.py" [OK] 2.5s 1152s Time: 2.53 1152s Return code: 0 1152s OKs: 1 1152s Standard out: 1152s OK 1152s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/test_cases_tardy_pdb.py" [OK] 0.1s 1152s Time: 0.06 1152s Return code: 0 1152s OKs: 0 1154s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1154s 139 1154s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1154s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree.py" [FAIL] 3.3s 1154s Time: 3.28 1154s Return code: 139 1154s OKs: 0 1154s Standard error: 1154s Segmentation fault (core dumped) 1157s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1157s 139 1157s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1157s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_basic.py" [FAIL] 5.6s 1157s Time: 5.58 1157s Return code: 139 1157s OKs: 0 1157s Standard error: 1157s Segmentation fault (core dumped) 1160s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1160s 139 1160s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1160s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_tardy.py" [FAIL] 5.5s 1160s Time: 5.49 1160s Return code: 139 1160s OKs: 0 1160s Standard error: 1160s Segmentation fault (core dumped) 1163s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1163s 139 1163s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1163s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_energy_plots.py" [FAIL] 5.5s 1163s Time: 5.54 1163s Return code: 139 1163s OKs: 0 1163s Standard error: 1163s Segmentation fault (core dumped) 1163s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/free_motion_reference_impl.py" [OK] 0.0s 1163s Time: 0.04 1163s Return code: 0 1163s OKs: 1 1163s Standard out: 1163s e_kin tot ang lin: 0.04066059413038476 0.012310594130384761 0.02835 1163s e_pot: 0.6403087877704161 1163s e_tot: 0.6809693819008009 1163s ang acc 3D: (0.4499405243671747, -0.22736369685250066, -0.6859763000328927) 1163s lin acc 3D: (0.2108121283092794, 0.3044814367238479, -0.7824311428947446) 1163s 1163s e_kin tot ang lin: 0.043334386720177365 0.012335145793951681 0.030999240926225684 1163s e_pot: 0.6375204431681878 1163s e_tot: 0.6808548298883652 1163s ang acc 3D: (0.4491523283824315, -0.2233952828755118, -0.688364609039924) 1163s lin acc 3D: (0.2063305410676703, 0.3022012812609254, -0.7827791077048256) 1163s 1163s e_kin tot ang lin: 0.04624491637806352 0.012390841212545118 0.0338540751655184 1163s e_pot: 0.6344966498401754 1163s e_tot: 0.6807415662182389 1163s ang acc 3D: (0.4482905223840879, -0.2193464063160701, -0.6906197519803725) 1163s lin acc 3D: (0.20168867739512958, 0.299808900299363, -0.7830079270607541) 1163s 1163s e_kin tot ang lin: 0.049389854602061224 0.01247763222642335 0.036912222375637876 1163s e_pot: 0.6312398275384674 1163s e_tot: 0.6806296821405287 1163s ang acc 3D: (0.44735466644443667, -0.21521902126722914, -0.692740958483326) 1163s lin acc 3D: (0.19688964121862268, 0.29730414639378616, -0.7831155604559972) 1163s 1163s e_kin tot ang lin: 0.05276668787891577 0.012595448079626585 0.04017123979928919 1163s e_pot: 0.6277525800757479 1163s e_tot: 0.6805192679546637 1163s ang acc 3D: (0.4463443200247767, -0.2110151239756078, -0.694727476553102) 1163s lin acc 3D: (0.1919366941490876, 0.29468687861617315, -0.783099948460292) 1163s 1163s e_kin tot ang lin: 0.05637271969939971 0.012744195480724368 0.043628524218675344 1163s e_pot: 0.6240376932449352 1163s e_tot: 0.6804104129443349 1163s ang acc 3D: (0.4452590426839754, -0.2067367517215091, -0.6965785731789051) 1163s lin acc 3D: (0.18683325327725137, 0.29195696483157874, -0.7829590159403469) 1163s 1163s e_kin tot ang lin: 0.060205072713709167 0.012923758676161239 0.04728131403754793 1163s e_pot: 0.6200981325993219 1163s e_tot: 0.680303205313031 1163s ang acc 3D: (0.44409839480429714, -0.20238598167333133, -0.6982935349568492) 1163s lin acc 3D: (0.18158288880693388, 0.2891142841060344, -0.7826906753299725) 1163s 1163s e_kin tot ang lin: 0.06426069102522652 0.013133999536143382 0.051126691489083144 1163s e_pot: 0.6159370410950341 1163s e_tot: 0.6801977321202606 1163s ang acc 3D: (0.4428619383337592, -0.1979649297164907, -0.6998716687235316) 1163s lin acc 3D: (0.17618932152521946, 0.2861587292410898, -0.7822928299444691) 1163s 1163s e_kin tot ang lin: 0.06853634262082685 0.013374757653013635 0.05516158496781321 1163s e_pot: 0.6115577365976127 1163s e_tot: 0.6800940792184396 1163s ang acc 3D: (0.4415492375442347, -0.1934757492571058, -0.7013123022002559) 1163s lin acc 3D: (0.17065642010895676, 0.2830902094290727, -0.7817633773339945) 1163s 1163s e_kin tot ang lin: 0.07302862193581516 0.013645850452066947 0.059382771483748216 1163s e_pot: 0.6069637092547071 1163s e_tot: 0.6799923311905223 1163s ang acc 3D: (0.44015985980451133, -0.18892063000069204, -0.702614784647033) 1163s lin acc 3D: (0.16498819826718966, 0.2799086530227533, -0.7811002126706817) 1163s 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/rigid_body/tst.py" [FAIL] 5.6s 1166s Time: 5.60 1166s Return code: 139 1166s OKs: 0 1166s Standard error: 1166s Segmentation fault (core dumped) 1168s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1168s 139 1168s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1168s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_featherstone.py" [FAIL] 5.7s 1168s Time: 5.66 1168s Return code: 139 1168s OKs: 0 1168s Standard error: 1168s Segmentation fault (core dumped) 1171s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1171s 139 1171s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1171s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion.py" [FAIL] 5.7s 1171s Time: 5.67 1171s Return code: 139 1171s OKs: 0 1171s Standard error: 1171s Segmentation fault (core dumped) 1174s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1174s 139 1174s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1174s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion_hard.py" [FAIL] 5.5s 1174s Time: 5.55 1174s Return code: 139 1174s OKs: 0 1174s Standard error: 1174s Segmentation fault (core dumped) 1177s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1177s 139 1177s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1177s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_joint_lib.py" [FAIL] 5.6s 1177s Time: 5.60 1177s Return code: 139 1177s OKs: 0 1177s Standard error: 1177s Segmentation fault (core dumped) 1177s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_spherical_refinement.py" [OK] 0.4s 1177s Time: 0.36 1177s Return code: 0 1177s OKs: 1 1177s Standard out: 1177s OK 1177s usr+sys time: 0.31 seconds 1177s wall clock time: 0.30 seconds 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/rigid_body/proto/tst_singular.py" [FAIL] 5.7s 1180s Time: 5.66 1180s Return code: 139 1180s OKs: 0 1180s Standard error: 1180s Segmentation fault (core dumped) 1182s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1182s 139 1182s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1182s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_molecules.py" [FAIL] 5.2s 1182s Time: 5.19 1182s Return code: 139 1182s OKs: 0 1182s Standard error: 1182s Segmentation fault (core dumped) 1185s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1185s 139 1185s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1185s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_sparse.py" [FAIL] 5.5s 1185s Time: 5.49 1185s Return code: 139 1185s OKs: 0 1185s Standard error: 1185s Segmentation fault (core dumped) 1188s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1188s 139 1188s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1188s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_lu_factorization.py" [FAIL] 5.5s 1188s Time: 5.51 1188s Return code: 139 1188s OKs: 0 1188s Standard error: 1188s Segmentation fault (core dumped) 1191s Standard error: 1191s Segmentation fault (core dumped) 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/iso_surface/tst_iso_surface.py" [FAIL] 5.5s 1191s Time: 5.45 1191s Return code: 139 1191s OKs: 0 1193s Standard error: 1193s Segmentation fault (core dumped) 1193s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1193s 139 1193s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1193s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/simplex.py" [FAIL] 5.5s 1193s Time: 5.47 1193s Return code: 139 1193s OKs: 0 1193s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/golden_section_search.py" [OK] 0.0s 1193s Time: 0.03 1193s Return code: 0 1193s OKs: 0 1196s Standard error: 1196s Segmentation fault (core dumped) 1196s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1196s 139 1196s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1196s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/differential_evolution.py" [FAIL] 5.4s 1196s Time: 5.37 1196s Return code: 139 1196s OKs: 0 1199s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1199s 139 1199s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1199s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/direct_search_simulated_annealing.py" [FAIL] 5.3s 1199s Time: 5.25 1199s Return code: 139 1199s OKs: 0 1199s Standard error: 1199s Segmentation fault (core dumped) 1202s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1202s 139 1202s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1202s libtbx.python "/usr/lib/python3/dist-packages/scitbx/random/tests/tst_random.py" [FAIL] 6.0s 1202s Time: 5.95 1202s Return code: 139 1202s OKs: 0 1202s Standard error: 1202s Segmentation fault (core dumped) 1202s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/test_problems.py" [OK] 0.2s 1202s Time: 0.17 1202s Return code: 0 1202s OKs: 0 1203s libtbx.python "/usr/lib/python3/dist-packages/scitbx/glmtbx/tests/tst.py" [OK] 0.9s 1203s Time: 0.85 1203s Return code: 0 1203s OKs: 2 1203s Standard out: 1203s OK 1203s OK 1205s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1205s 139 1205s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1205s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/tst_normal_equations.py" [FAIL] 6.0s 1205s Time: 6.01 1205s Return code: 139 1205s OKs: 0 1205s Standard error: 1205s Segmentation fault (core dumped) 1207s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1207s 139 1207s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1207s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_basic.py" [FAIL] 4.3s 1207s Time: 4.32 1207s Return code: 139 1207s OKs: 0 1207s Standard error: 1207s Segmentation fault (core dumped) 1210s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1210s 139 1210s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1210s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_booth.py" [FAIL] 5.2s 1210s Time: 5.20 1210s Return code: 139 1210s OKs: 0 1210s Standard error: 1210s Segmentation fault (core dumped) 1210s libtbx.python "/usr/lib/python3/dist-packages/scitbx/suffixtree/test/tst_single.py" [OK] 0.1s 1210s Time: 0.09 1210s Return code: 0 1210s OKs: 0 1213s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1213s 139 1213s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1213s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_twisted.py" [FAIL] 5.3s 1213s Time: 5.30 1213s Return code: 139 1213s OKs: 0 1213s Standard error: 1213s Segmentation fault (core dumped) 1216s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1216s 139 1216s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1216s libtbx.python "/usr/lib/python3/dist-packages/smtbx/absolute_structure/tests/tst_absolute_structure.py" --fix_random_seeds [FAIL] 5.8s 1216s Time: 5.80 1216s Return code: 139 1216s OKs: 0 1216s Standard error: 1216s Segmentation fault (core dumped) 1219s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1219s 139 1219s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1219s libtbx.python "/usr/lib/python3/dist-packages/smtbx/ab_initio/tests/tst_ab_initio_ext.py" [FAIL] 6.1s 1219s Time: 6.13 1219s Return code: 139 1219s OKs: 0 1219s Standard error: 1219s Segmentation fault (core dumped) 1222s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1222s 139 1222s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1222s 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] 6.0s 1222s Time: 6.01 1222s Return code: 139 1222s OKs: 0 1222s Standard error: 1222s Segmentation fault (core dumped) 1225s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1225s 139 1225s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1225s libtbx.python "/usr/lib/python3/dist-packages/smtbx/masks/tests/tst_masks.py" [FAIL] 6.3s 1225s Time: 6.33 1225s Return code: 139 1225s OKs: 0 1225s Standard error: 1225s Segmentation fault (core dumped) 1228s Standard error: 1228s Segmentation fault (core dumped) 1228s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1228s 139 1228s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1228s libtbx.python "/usr/lib/python3/dist-packages/smtbx/structure_factors/direct/tests/tst_standard_xray.py" [FAIL] 6.5s 1228s Time: 6.46 1228s Return code: 139 1228s OKs: 0 1231s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1231s 139 1231s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1231s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_weighting_schemes.py" --fix_random_seeds [FAIL] 6.3s 1231s Time: 6.27 1231s Return code: 139 1231s OKs: 0 1231s Standard error: 1231s Segmentation fault (core dumped) 1231s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_reparametrisation" [OK] 0.0s 1231s Time: 0.01 1231s Return code: 0 1231s OKs: 1 1231s Standard out: 1231s sizeof(parameter) = 32 1231s OK 1235s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1235s 139 1235s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1235s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_lbfgs.py" [FAIL] 6.3s 1235s Time: 6.30 1235s Return code: 139 1235s OKs: 0 1235s Standard error: 1235s Segmentation fault (core dumped) 1235s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens" [OK] 0.0s 1235s Time: 0.01 1235s Return code: 0 1235s OKs: 1 1235s Standard out: 1235s OK 1238s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1238s 139 1238s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1238s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_occupancies.py" [FAIL] 6.6s 1238s Time: 6.60 1238s Return code: 139 1238s OKs: 0 1238s Standard error: 1238s Segmentation fault (core dumped) 1238s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_special_position" [OK] 0.0s 1238s Time: 0.01 1238s Return code: 0 1238s OKs: 1 1238s Standard out: 1238s OK 1241s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1241s 139 1241s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1241s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_same_group.py" [FAIL] 6.6s 1241s Time: 6.58 1241s Return code: 139 1241s OKs: 0 1241s Standard error: 1241s Segmentation fault (core dumped) 1244s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1244s 139 1244s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1244s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_reparametrisation.py" [FAIL] 6.4s 1244s Time: 6.37 1244s Return code: 139 1244s OKs: 0 1244s Standard error: 1244s Segmentation fault (core dumped) 1247s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1247s 139 1247s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1247s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=naive [FAIL] 6.3s 1247s Time: 6.26 1247s Return code: 139 1247s OKs: 0 1247s Standard error: 1247s 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/smtbx/refinement/constraints/tests/tst_disorder.py" [FAIL] 6.3s 1251s Time: 6.29 1251s Return code: 139 1251s OKs: 0 1251s Standard error: 1251s 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/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=levenberg-marquardt [FAIL] 3.2s 1251s Time: 3.22 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/smtbx/refinement/constraints/tests/tst_rigid.py" [FAIL] 3.4s 1254s Time: 3.42 1254s Return code: 139 1254s OKs: 0 1254s Standard error: 1254s Segmentation fault (core dumped) 1257s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1257s 139 1257s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1257s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_direction.py" [FAIL] 6.5s 1257s Time: 6.50 1257s Return code: 139 1257s OKs: 0 1257s Standard error: 1257s Segmentation fault (core dumped) 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/smtbx/refinement/restraints/tests/tst_adp_restraints.py" [FAIL] 6.2s 1260s Time: 6.17 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/smtbx/refinement/restraints/tests/tst_manager.py" [FAIL] 6.2s 1263s Time: 6.22 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/smtbx/refinement/restraints/tests/tst_restraints.py" --verbose --scatterers=5 --resolution=0.2 [FAIL] 6.3s 1266s Time: 6.28 1266s Return code: 139 1266s OKs: 0 1266s Standard error: 1266s Segmentation fault (core dumped) 1270s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1270s 139 1270s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1270s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_refine.py" [FAIL] 6.4s 1270s Time: 6.43 1270s Return code: 139 1270s OKs: 0 1270s Standard error: 1270s Segmentation fault (core dumped) 1275s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1275s 1 1275s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1275s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py" [FAIL] 8.7s 1275s Time: 8.75 1275s Return code: 1 1275s OKs: 0 1275s Standard out: 1275s 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 1275s Standard error: 1275s Traceback (most recent call last): 1275s File "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py", line 37, in 1275s run() 1275s ~~~^^ 1275s File "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py", line 27, in run 1275s run_buf.raise_if_errors() 1275s ~~~~~~~~~~~~~~~~~~~~~~~^^ 1275s File "/usr/lib/python3/dist-packages/libtbx/easy_run.py", line 46, in raise_if_errors 1275s raise Error(msg) 1275s RuntimeError: child process stderr output: 1275s 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' 1275s Segmentation fault (core dumped) 1276s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1276s 139 1276s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1276s libtbx.python "/usr/lib/python3/dist-packages/smtbx/tests/tst_utils.py" [FAIL] 6.3s 1276s Time: 6.33 1276s Return code: 139 1276s OKs: 0 1276s Standard error: 1276s Segmentation fault (core dumped) 1279s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1279s 139 1279s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1279s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_least_squares.py" [EXPECTED UNSTABLE] 4.0s 1279s Standard error: 1279s Segmentation fault (core dumped) 1279s Time: 3.97 1279s Return code: 139 1279s OKs: 0 1279s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_predict.py" [OK] 0.2s 1279s Time: 0.23 1279s Return code: 0 1279s OKs: 1 1279s Standard out: 1279s OK 1280s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_ewald_sphere.py" [OK] 0.2s 1280s Time: 0.21 1280s Return code: 0 1280s OKs: 1 1280s Standard out: 1280s OK 1280s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_partial_derivatives.py" [OK] 0.2s 1280s Time: 0.20 1280s Return code: 0 1280s OKs: 1 1280s Standard out: 1280s OK 1282s Standard error: 1282s Segmentation fault (core dumped) 1282s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1282s 139 1282s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1282s libtbx.python "/usr/lib/python3/dist-packages/rstbx/dps_core/tst_iotbx_converter.py" [FAIL] 5.9s 1282s Time: 5.95 1282s Return code: 139 1282s OKs: 0 1285s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1285s 139 1285s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1285s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/fastbragg/tst_bragg_minimal.py" [FAIL] 5.4s 1285s Time: 5.39 1285s Return code: 139 1285s OKs: 0 1285s Standard error: 1285s Segmentation fault (core dumped) 1288s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1288s 139 1288s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1288s libtbx.python "/usr/lib/python3/dist-packages/rstbx/sublattice_support/tst_sublattice.py" [FAIL] 6.0s 1288s Time: 5.99 1288s Return code: 139 1288s OKs: 0 1288s Standard error: 1288s Segmentation fault (core dumped) 1288s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/core_toolbox/boost_python/tst_small_image.py" [OK] 0.4s 1288s Time: 0.40 1288s Return code: 0 1288s OKs: 1 1288s Standard out: 1288s OK 1289s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/diffraction/geometry.py" [OK] 0.2s 1289s Time: 0.18 1289s Return code: 0 1289s OKs: 1 1289s Standard out: 1289s OK 1289s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/math_support/sphere_formulae.py" [OK] 0.0s 1289s Time: 0.03 1289s Return code: 0 1289s OKs: 1 1289s Standard out: 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 -c "from rstbx.run_tests import run; run()" [FAIL] 4.4s 1290s Time: 4.36 1290s Return code: 139 1290s OKs: 0 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s ================================================================================ 1290s 1290s Tests finished. Elapsed time: 975.54s 1290s 1290s Distribution of test runtimes: 1290s 0.0s - 4.4s: 284 1290s 4.4s - 8.9s: 252 1290s 8.9s - 13.3s: 7 1290s 13.3s - 17.8s: 1 1290s 17.8s - 22.2s: 0 1290s 22.2s - 26.7s: 1 1290s 26.7s - 31.1s: 0 1290s 31.1s - 35.5s: 0 1290s 35.5s - 40.0s: 0 1290s 40.0s - 44.4s: 1 1290s 1290s 1290s Warning: the following are 5 longest jobs: 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_fetch.py": 44.4s 1290s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_thread_utils.py": 23.5s 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_integer_offsets_vs_pointers.py": 17.0s 1290s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_separate_files.py": 13.3s 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike.py": 11.3s 1290s Please try to reduce overall runtime - consider splitting up these tests. 1290s 1290s 1290s Error: the following jobs returned non-zero exit codes or suspicious stderr output: 1290s 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sf_low_res_accuracy.py" [FAIL] 3.8s 1290s Standard error: 1290s Time: 3.85 1290s Return code: 139 1290s OKs: 0 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Traceback (most recent call last): 1290s File "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py", line 140, in 1290s exercise() 1290s ~~~~~~~~^^ 1290s File "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py", line 126, in exercise 1290s assert not easy_run.call(cmd) 1290s ^^^^^^^^^^^^^^^^^^^^^^ 1290s AssertionError 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_double_step_filtration.py" [FAIL] 4.3s 1290s Time: 4.26 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_is_periodic.py" [FAIL] 6.2s 1290s Time: 6.16 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_reindexing.py" [FAIL] 6.0s 1290s Time: 6.00 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_data_manipulation.py" [FAIL] 5.8s 1290s Time: 5.78 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_bfgs.py" [FAIL] 6.0s 1290s Time: 5.98 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_dev.py" P31 [FAIL] 6.0s 1290s Time: 5.98 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry/tests/tst_geometry.py" [FAIL] 6.2s 1290s Time: 6.23 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/covariance/tests/tst_covariance.py" [FAIL] 6.3s 1290s Time: 6.31 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_goodness_of_symmetry.py" [FAIL] 6.2s 1290s Time: 6.21 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_from_map.py" P312 [FAIL] 6.1s 1290s Time: 6.09 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_xray.py" [FAIL] 5.6s 1290s Time: 5.61 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray.py" I41/acd [FAIL] 6.5s 1290s Time: 6.45 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_r1.py" [FAIL] 6.2s 1290s Time: 6.25 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_shelxl_wght_ls.py" [FAIL] 6.1s 1290s Time: 6.08 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_f_model.py" [FAIL] 6.1s 1290s Time: 6.14 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/array_family/boost_python/tst_flex.py" [FAIL] 6.2s 1290s Time: 6.19 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_uctbx.py" [FAIL] 6.1s 1290s Time: 6.12 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_crystal_orientation.py" [FAIL] 6.1s 1290s Time: 6.06 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_sgtbx.py" [FAIL] 6.3s 1290s Time: 6.30 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_ext.py" [FAIL] 6.2s 1290s Time: 6.21 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_distance_based_connectivity.py" [FAIL] 6.1s 1290s Time: 6.13 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_super_cell.py" [FAIL] 6.9s 1290s Time: 6.92 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adptbx/boost_python/tst_adptbx.py" [FAIL] 7.2s 1290s Time: 7.17 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/boost_python/tst_miller.py" [FAIL] 6.6s 1290s Time: 6.63 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_xray_scattering.py" [FAIL] 6.7s 1290s Time: 6.65 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_formula.py" [FAIL] 5.8s 1290s Time: 5.81 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_attenuation_coefficient.py" [FAIL] 6.2s 1290s Time: 6.18 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/boost_python/tst_maptbx.py" [FAIL] 6.1s 1290s Time: 6.14 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_bcr.py" [FAIL] 6.9s 1290s Time: 6.93 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_loft.py" [FAIL] 6.8s 1290s Time: 6.80 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/dmtbx/boost_python/tst_dmtbx.py" [FAIL] 6.0s 1290s Time: 6.02 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/translation_search/boost_python/tst_translation_search.py" [FAIL] 5.9s 1290s Time: 5.95 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_ext.py" [FAIL] 6.3s 1290s Time: 6.30 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_angle_derivs.py" [FAIL] 4.7s 1290s Time: 4.68 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adp_restraints/tst_ext.py" [FAIL] 5.9s 1290s Time: 5.91 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_krivy_gruber.py" --Quick [FAIL] 6.1s 1290s Time: 6.10 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx.py" [FAIL] 6.1s 1290s Time: 6.06 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_space_group_type_tidy_cb_op_t.py" [FAIL] 6.1s 1290s Time: 6.13 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_denominators.py" P31 [FAIL] 6.4s 1290s Time: 6.36 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_subgroups.py" [FAIL] 6.4s 1290s Time: 6.38 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_lattice_symmetry.py" [FAIL] 6.5s 1290s Time: 6.54 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints.py" P3 [FAIL] 6.6s 1290s Time: 6.56 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints_cartesian.py" [FAIL] 6.5s 1290s Time: 6.51 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reflection_statistics.py" [FAIL] 6.0s 1290s Time: 6.03 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_harker.py" [FAIL] 6.5s 1290s Time: 6.54 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_special_op_simplifier.py" [FAIL] 6.8s 1290s Time: 6.80 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_twin_target.py" [FAIL] 6.9s 1290s Time: 6.94 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/symbol_confidence.py" [FAIL] 6.8s 1290s Time: 6.80 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/bravais_types.py" [FAIL] 6.7s 1290s Time: 6.68 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_lookup_utils.py" [FAIL] 6.9s 1290s Time: 6.86 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal.py" I41/acd [FAIL] 7.1s 1290s Time: 7.07 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_direct_space_asu.py" I41/acd [FAIL] 7.1s 1290s Time: 7.09 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pair_asu_table.py" [FAIL] 7.1s 1290s Time: 7.12 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_asu_clusters.py" [FAIL] 6.8s 1290s Time: 6.78 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_close_packing.py" R-3mr [FAIL] 6.4s 1290s Time: 6.41 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fourier_transform_real_part_at_x.py" P31 [FAIL] 6.8s 1290s Time: 6.78 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller.py" P31 [FAIL] 7.0s 1290s Time: 6.97 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem.py" [FAIL] 7.3s 1290s Time: 7.26 1290s Retur Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Traceback (most recent call last): 1290s File "/usr/lib/python3.13/urllib/request.py", line 1541, in ftp_open 1290s fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout) 1290s File "/usr/lib/python3.13/urllib/request.py", line 1561, in connect_ftp 1290s return ftpwrapper(user, passwd, host, port, dirs, timeout, 1290s persistent=False) 1290s File "/usr/lib/python3.13/urllib/request.py", line 2409, in __init__ 1290s self.init() 1290s ~~~~~~~~~^^ 1290s File "/usr/lib/python3.13/urllib/request.py", line 2418, in init 1290s self.ftp.connect(self.host, self.port, self.timeout) 1290s ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1290s File "/usr/lib/python3.13/ftplib.py", line 158, in connect 1290s self.sock = socket.create_connection((self.host, self.port), self.timeout, 1290s ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1290s source_address=self.source_address) 1290s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1290s File "/usr/lib/python3.13/socket.py", line 864, in create_connection 1290s raise exceptions[0] 1290s File "/usr/lib/python3.13/socket.py", line 849, in create_connection 1290s sock.connect(sa) 1290s ~~~~~~~~~~~~^^^^ 1290s ConnectionRefusedError: [Errno 111] Connection refused 1290s 1290s The above exception was the direct cause of the following exception: 1290s 1290s Traceback (most recent call last): 1290s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 327, in 1290s exercise(sys.argv[1:]) 1290s ~~~~~~~~^^^^^^^^^^^^^^ 1290s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 26, in exercise 1290s exercise_validation() 1290s ~~~~~~~~~~~~~~~~~~~^^ 1290s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 29, in exercise_validation 1290s cd = validation.smart_load_dictionary(name="cif_core.dic") 1290s File "/usr/lib/python3/dist-packages/iotbx/cif/validation.py", line 111, in smart_load_dictionary 1290s url = locate_dictionary(name, registry_location=registry_location) 1290s File "/usr/lib/python3/dist-packages/iotbx/cif/validation.py", line 129, in locate_dictionary 1290s cm = cif.reader(file_object=urlopen(registry_location)).model() 1290s ~~~~~~~^^^^^^^^^^^^^^^^^^^ 1290s File "/usr/lib/python3.13/urllib/request.py", line 189, in urlopen 1290s return opener.open(url, data, timeout) 1290s ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1290s File "/usr/lib/python3.13/urllib/request.py", line 489, in open 1290s response = self._open(req, data) 1290s File "/usr/lib/python3.13/urllib/request.py", line 506, in _open 1290s result = self._call_chain(self.handle_open, protocol, protocol + 1290s '_open', req) 1290s File "/usr/lib/python3.13/urllib/request.py", line 466, in _call_chain 1290s result = func(*args) 1290s File "/usr/lib/python3.13/urllib/request.py", line 1558, in ftp_open 1290s raise URLError(exp) from exp 1290s urllib.error.URLError: 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s *** buffer overflow detected ***: terminated 1290s Aborted (core dumped) 1290s Standard error: 1290s *** buffer overflow detected ***: terminated 1290s Aborted (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s *** buffer overflow detected ***: terminated 1290s Aborted (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s /usr/lib/python3/dist-packages/ccp4io_adaptbx/__init__.py:25: UserWarning: ccp4io_adaptbx: cannot locate syminfo.lib 1290s warnings.warn("ccp4io_adaptbx: cannot locate syminfo.lib") 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s n code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reciprocal_space_asu.py" P312 [FAIL] 6.4s 1290s Time: 6.44 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_triplet_generator.py" P41 [FAIL] 6.6s 1290s Time: 6.62 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_emma.py" P31 [FAIL] 7.0s 1290s Time: 6.97 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_expand_to_p1.py" P31 [FAIL] 6.9s 1290s Time: 6.88 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_change_basis.py" P31 [FAIL] 6.5s 1290s Time: 6.47 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wilson_plot.py" P31 [FAIL] 6.6s 1290s Time: 6.62 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_derivatives.py" P31 [FAIL] 6.7s 1290s Time: 6.71 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_fast_gradients.py" P31 [FAIL] 6.7s 1290s Time: 6.69 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F P31 [FAIL] 6.3s 1290s Time: 6.30 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F_sq P31 [FAIL] 3.0s 1290s Time: 3.01 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_weights_for_symmetry_summation.py" Pmmm [FAIL] 3.4s 1290s Time: 3.39 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_structure_factors.py" P31 [FAIL] 6.6s 1290s Time: 6.58 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_real_space_refinement_simple.py" [FAIL] 6.4s 1290s Time: 6.41 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation.py" [FAIL] 6.2s 1290s Time: 6.23 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation_2.py" [FAIL] 6.2s 1290s Time: 6.17 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_loc_res.py" [FAIL] 7.3s 1290s Time: 7.33 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_target_and_gradients.py" [FAIL] 7.4s 1290s Time: 7.43 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_merge_equivalents.py" P31 [FAIL] 6.6s 1290s Time: 6.58 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grouped_data.py" P31 [FAIL] 6.7s 1290s Time: 6.67 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_fft_map.py" P31 [FAIL] 6.8s 1290s Time: 6.75 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sampled_model_density.py" P31 [FAIL] 6.6s 1290s Time: 6.59 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fast_nv1995.py" F222 [FAIL] 6.4s 1290s Time: 6.37 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_lbfgs.py" [FAIL] 5.9s 1290s Time: 5.90 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_2.py" [FAIL] 7.0s 1290s Time: 7.05 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_french_wilson.py" [FAIL] 6.2s 1290s Time: 6.19 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/make_cns_input.py" P31 [FAIL] 6.1s 1290s Time: 6.13 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pointgroup_tools.py" [FAIL] 5.4s 1290s Time: 5.41 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/sub_lattice_tools.py" [FAIL] 6.2s 1290s Time: 6.16 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/rational_matrices_point_groups.py" [FAIL] 6.1s 1290s Time: 6.11 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/cosets.py" [FAIL] 5.9s 1290s Time: 5.86 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_pg_tools.py" [FAIL] 6.0s 1290s Time: 6.01 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_twin_laws.py" [FAIL] 6.6s 1290s Time: 6.57 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_find_best_cell.py" [FAIL] 6.5s 1290s Time: 6.47 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_amplitude_normalisation.py" [FAIL] 6.2s 1290s Time: 6.23 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_statistics_graphs.py" [FAIL] 6.4s 1290s Time: 6.41 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_web_change_basis.py" [FAIL] 6.5s 1290s Time: 6.52 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/direct_space_asu/proto/tst_asu.py" [FAIL] 6.3s 1290s Time: 6.31 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_tidy_pickling.py" [FAIL] 6.3s 1290s Time: 6.26 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/masks/tests/tst_flood_fill.py" [FAIL] 6.2s 1290s Time: 6.24 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_r_free_utils.py" [FAIL] 6.1s 1290s Time: 6.14 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_ccp.py" [FAIL] 6.3s 1290s Time: 6.27 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_mask.py" [FAIL] 6.9s 1290s Time: 6.93 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_map_peak_3d_as_2d.py" [FAIL] 6.8s 1290s Time: 6.85 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_asymmetric_map.py" [FAIL] 6.7s 1290s Time: 6.74 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_peak_volume_estimate.py" [FAIL] 6.8s 1290s Time: 6.78 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_resolution_from_map_and_model.py" [FAIL] 6.8s 1290s Time: 6.82 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_curves.py" [FAIL] 6.9s 1290s Time: 6.87 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_radius_as_central_peak_width.py" [FAIL] 6.7s 1290s Time: 6.72 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_get_percentile_cutoffs.py" [FAIL] 6.8s 1290s Time: 6.82 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sphericity.py" [FAIL] 5.6s 1290s Time: 5.57 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_statistics.py" [FAIL] 7.0s 1290s Time: 6.98 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity.py" [FAIL] 6.3s 1290s Time: 6.34 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity_allsym.py" [FAIL] 6.7s 1290s Time: 6.65 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py" [FAIL] 9.2s 1290s Time: 9.22 1290s Return code: 1 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_prepare_map_for_docking.py" [FAIL] 7.0s 1290s Time: 6.96 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/cma_es/tst_cma_es.py" [FAIL] 5.9s 1290s Time: 5.85 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mrc_io.py" [FAIL] 3.6s 1290s Time: 3.56 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/gui_tools/tst.py" [FAIL] 3.8s 1290s Time: 3.84 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phil.py" [FAIL] 4.7s 1290s Time: 4.74 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_manager.py" [FAIL] 7.1s 1290s Time: 7.07 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager_wrapping.py" [FAIL] 7.3s 1290s Time: 7.34 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager.py" [FAIL] 6.6s 1290s Time: 6.60 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry.py" [FAIL] 4.8s 1290s Time: 4.83 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry_cif.py" [FAIL] 8.6s 1290s Time: 8.62 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_tools.py" [FAIL] 6.5s 1290s Time: 6.45 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_atom_selections_10k.py" [FAIL] 6.1s 1290s Time: 6.10 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_crystal_symmetry_from_any.py" [FAIL] 6.6s 1290s Time: 6.56 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/kriber/tst_strudat.py" [FAIL] 6.3s 1290s Time: 6.30 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_geometry.py" [FAIL] 6.2s 1290s Time: 6.24 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_lex_parse_build.py" [FAIL] 6.6s 1290s Time: 6.57 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model.py" [FAIL] 6.6s 1290s Time: 6.58 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py" [FAIL] 2.5s 1290s Time: 2.48 1290s Return code: 1 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_restraints.py" [FAIL] 6.5s 1290s Time: 6.52 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_hklf.py" [FAIL] 3.6s 1290s Time: 3.56 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_lex_parse_build.py" [FAIL] 6.9s 1290s Time: 6.90 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_writer.py" [FAIL] 6.5s 1290s Time: 6.51 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_fvar_encoding.py" [FAIL] 6.2s 1290s Time: 6.25 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_pdb.py" [FAIL] 6.4s 1290s Time: 6.38 1290s Return code: 134 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy.py" [FAIL] 7.0s 1290s Time: 7.05 1290s Return code: 134 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy.py" [FAIL] 4.0s 1290s Time: 3.96 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_ext.py" [FAIL] 6.2s 1290s Time: 6.16 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection.py" [FAIL] 6.5s 1290s Time: 6.47 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation.py" [FAIL] 5.5s 1290s Time: 5.53 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection_string.py" [FAIL] 6.1s 1290s Time: 6.09 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_utils.py" [FAIL] 5.5s 1290s Time: 5.53 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_truncate_to_ala/tst.py" [FAIL] 3.7s 1290s Time: 3.69 1290s Return code: 134 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_examples.py" [FAIL] 6.7s 1290s Time: 6.70 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/space_group_symbols.py" [FAIL] 6.7s 1290s Time: 6.65 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/tst_cns.py" [FAIL] 5.8s 1290s Time: 5.82 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_merge.py" P31 [FAIL] 5.9s 1290s Time: 5.90 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/no_merge_original_index.py" [FAIL] 5.8s 1290s Time: 5.80 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/ccp4_map/tst.py" [FAIL] 5.9s 1290s Time: 5.85 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_ext.py" [FAIL] 6.4s 1290s Time: 6.44 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_extract_from_symmetry_lib.py" [FAIL] 6.6s 1290s Time: 6.63 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_dano.py" [FAIL] 6.1s 1290s Time: 6.08 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst.py" P31 [FAIL] 5.5s 1290s Time: 5.55 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_utils.py" [FAIL] 6.3s 1290s Time: 6.26 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xplor/tst_xplormap.py" [FAIL] 6.2s 1290s Time: 6.20 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phases.py" P31 [FAIL] 6.1s 1290s Time: 6.12 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py" [FAIL] 8.5s 1290s Time: 8.50 1290s Return code: 1 1290s OKs: 0 1290s Standard error: 1290s Traceback (most recent call last): 1290s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 477, in 1290s exercise(sys.argv[1:]) 1290s ~~~~~~~~^^^^^^^^^^^^^^ 1290s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 22, in exercise 1290s run_and_compare( 1290s ~~~~~~~~~~~~~~~^ 1290s ['iotbx.lattice_symmetry' 1290s ^^^^^^^^^^^^^^^^^^^^^^^^^ 1290s ...<31 lines>... 1290s 1290s 1290s """) 1290s ^^^^ 1290s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 17, in run_and_compare 1290s command=command).raise_if_errors().stdout_lines 1290s ~~~~~~~~~~~~~~~^^ 1290s File "/usr/lib/python3/dist-packages/libtbx/easy_run.py", line 46, in raise_if_errors 1290s raise Error(msg) 1290s RuntimeError: child process stderr output: 1290s command: 'iotbx.lattice_symmetry --unit_cell="12.7923,12.8923,29.4356,102.846,103.846,22.7475"' 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s *** buffer overflow detected ***: terminated 1290s Aborted (core dumped) 1290s Traceback (most recent call last): 1290s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py", line 138, in 1290s exercise() 1290s ~~~~~~~~^^ 1290s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py", line 48, in exercise 1290s assert not easy_run.call("iotbx.pdb.box_around_molecule %s.pdb" % ( 1290s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1290s prefix)) 1290s ^^^^^^^^ 1290s AssertionError 1290s Standard error: 1290s *** buffer overflow detected ***: terminated 1290s Aborted (core dumped) 1290s Standard error: 1290s *** buffer overflow detected ***: terminated 1290s Aborted (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Traceback (most recent call last): 1290s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py", line 60, in 1290s exercise() 1290s ~~~~~~~~^^ 1290s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py", line 48, in exercise 1290s assert (len(out.stdout_lines) == 2) and (len(out.stderr_lines) == 0) 1290s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1290s AssertionError 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_statistics.py" Fdd2 P31m [FAIL] 6.7s 1290s Time: 6.74 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_file_reader.py" [FAIL] 4.3s 1290s Time: 4.30 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py" [FAIL] 9.4s 1290s Time: 9.41 1290s Return code: 1 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_segids.py" [FAIL] 7.1s 1290s Time: 7.07 1290s Return code: 134 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_forward_compatible_pdb.py" [FAIL] 3.7s 1290s Time: 3.68 1290s Return code: 134 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_symmetry.py" [FAIL] 4.9s 1290s Time: 4.91 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_editor.py" [FAIL] 5.7s 1290s Time: 5.74 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py" [FAIL] 8.2s 1290s Time: 8.24 1290s Return code: 1 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_map_coefficients.py" [FAIL] 5.3s 1290s Time: 5.25 1290s Return code: 139 1290s OKs: 0 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Traceback (most recent call last): 1290s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py", line 815, in 1290s exercise_1() 1290s ~~~~~~~~~~^^ 1290s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py", line 806, in exercise_1 1290s assert not easy_run.call(cmd) 1290s ^^^^^^^^^^^^^^^^^^^^^^ 1290s AssertionError 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py" [FAIL] 6.8s 1290s Time: 6.80 1290s Return code: 1 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_integrate_hkl.py" [FAIL] 7.0s 1290s Time: 7.01 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_no_merge_original_index.py" [FAIL] 3.7s 1290s Time: 3.70 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_export_scalepack_unmerged.py" [FAIL] 6.2s 1290s Time: 6.20 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/dsn6/tst.py" P31 [FAIL] 6.2s 1290s Time: 6.24 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_ligs.py" [FAIL] 5.4s 1290s Time: 5.40 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_broken_chain.py" [FAIL] 6.6s 1290s Time: 6.56 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_shortcut_1.py" [FAIL] 6.6s 1290s Time: 6.59 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_groups_preprocessing.py" [FAIL] 7.3s 1290s Time: 7.33 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_input.py" [FAIL] 7.4s 1290s Time: 7.39 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_user_selections.py" [FAIL] 6.7s 1290s Time: 6.70 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs.py" [FAIL] 7.4s 1290s Time: 7.38 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_without_validation.py" [FAIL] 7.2s 1290s Time: 7.19 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_read_mtrix_records_from_cif.py" [FAIL] 6.9s 1290s Time: 6.93 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_show_systematic_absences.py" [FAIL] 7.0s 1290s Time: 7.04 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_miller_sort_asu.py" [FAIL] 6.2s 1290s Time: 6.22 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_xray_scale.py" [FAIL] 6.5s 1290s Time: 6.46 1290s Return code: 134 1290s OKs: 0 1290s Standard error: 1290s *** buffer overflow detected ***: terminated 1290s Aborted (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Traceback (most recent call last): 1290s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py", line 395, in 1290s tst_1() 1290s ~~~~~^^ 1290s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py", line 370, in tst_1 1290s assert os.path.isfile('%s.cif_%s_000.mtz' % (prefix, bn)) 1290s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1290s AssertionError 1290s Standard error: 1290s *** buffer overflow detected ***: terminated 1290s Aborted (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_as_pdb_1atom.py" [FAIL] 6.6s 1290s Time: 6.63 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_1.py" [FAIL] 7.8s 1290s Time: 7.81 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py" [FAIL] 10.1s 1290s Time: 10.07 1290s Return code: 1 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_all_chain_ids.py" [FAIL] 8.1s 1290s Time: 8.10 1290s Return code: 134 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_extract_xtal_data.py" [FAIL] 5.2s 1290s Time: 5.20 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cli_parser.py" [FAIL] 7.5s 1290s Time: 7.47 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_occupancies_rounding.py" [FAIL] 6.5s 1290s Time: 6.53 1290s Return code: 134 1290s OKs: 0 1290s Standard error: 1290s *** buffer overflow detected ***: terminated 1290s Aborted (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_debug_write.py" [FAIL] 3.1s 1290s Time: 3.13 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_smoothing.py" [FAIL] 3.3s 1290s Time: 3.30 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_genetic_algorithm_with_mp.py" [FAIL] 3.3s 1290s Time: 3.35 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_basic.py" [FAIL] 5.3s 1290s Time: 5.26 1290s Return code: 139 1290s OKs: 1 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_minimum_covering_ellipsoid.py" [FAIL] 5.5s 1290s Time: 5.54 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian_fit_1d_analytical.py" [FAIL] 6.0s 1290s Time: 6.02 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_cubic_equation.py" [FAIL] 5.9s 1290s Time: 5.88 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_cholesky.py" [FAIL] 5.4s 1290s Time: 5.43 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_svd.py" [FAIL] 6.0s 1290s Time: 5.99 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_eigensystem.py" [FAIL] 5.8s 1290s Time: 5.84 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_svd.py" [FAIL] 5.8s 1290s Time: 5.84 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_dsyev.py" [FAIL] 5.7s 1290s Time: 5.69 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/regression_test.py" [FAIL] 5.3s 1290s Time: 5.34 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex.py" [FAIL] 5.9s 1290s Time: 5.89 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_numpy_bridge.py" [FAIL] 5.9s 1290s Time: 5.88 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_smart_selection.py" [FAIL] 5.6s 1290s Time: 5.59 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_shared.py" [FAIL] 5.6s 1290s Time: 5.59 1290s Return code: 139 1290s OKs: 0 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/__init__.py" [FAIL] 3.1s 1290s Time: 3.12 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_random_transform.py" [FAIL] 3.1s 1290s Time: 3.14 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/superpose.py" [FAIL] 2.9s 1290s Time: 2.87 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/spe.py" [FAIL] 2.8s 1290s Time: 2.79 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/incremental_SO3_sampling.py" [FAIL] 4.7s 1290s Time: 4.65 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_curve_fitting.py" [FAIL] 6.6s 1290s Time: 6.56 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_weighted_correlation.py" [FAIL] 5.5s 1290s Time: 5.51 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_exp_functions.py" [FAIL] 5.4s 1290s Time: 5.45 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_math.py" [FAIL] 5.2s 1290s Time: 5.18 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_resample.py" [FAIL] 3.1s 1290s Time: 3.11 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian.py" [FAIL] 5.2s 1290s Time: 5.16 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_quadrature.py" [FAIL] 5.4s 1290s Time: 5.35 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_halton.py" [FAIL] 5.2s 1290s Time: 5.16 1290s Return code: 139 1290s OKs: 0 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/scale_curves.py" [FAIL] 2.9s 1290s Time: 2.93 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_fit_peak.py" [FAIL] 3.1s 1290s Time: 3.08 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike.py" [FAIL] 11.3s 1290s Time: 11.30 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_clustering.py" [FAIL] 6.1s 1290s Time: 6.07 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_periodogram.py" [FAIL] 4.7s 1290s Time: 4.73 1290s Return code: 139 1290s OKs: 0 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Traceback (most recent call last): 1290s File "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py", line 37, in 1290s run() 1290s ~~~^^ 1290s File "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py", line 27, in run 1290s run_buf.raise_if_errors() 1290s ~~~~~~~~~~~~~~~~~~~~~~~^^ 1290s File "/usr/lib/python3/dist-packages/libtbx/easy_run.py", line 46, in raise_if_errors 1290s raise Error(msg) 1290s RuntimeError: child process stderr output: 1290s 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' 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s Standard error: 1290s Segmentation fault (core dumped) 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_error_propagation_matrix_inverse.py" [FAIL] 5.5s 1290s Time: 5.52 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_curvatures.py" [FAIL] 4.7s 1290s Time: 4.71 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgsb/boost_python/tst_lbfgsb.py" [FAIL] 3.0s 1290s Time: 3.02 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/fftpack/boost_python/tst_fftpack.py" [FAIL] 3.0s 1290s Time: 3.02 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_grid.py" [FAIL] 2.8s 1290s Time: 2.85 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_linear_least_squares_fit.py" [FAIL] 3.4s 1290s Time: 3.37 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/chebyshev_lsq_example.py" [FAIL] 5.3s 1290s Time: 5.30 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/immoptibox_ports.py" [FAIL] 5.6s 1290s Time: 5.56 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/integrating_a_weighted_sinc_function.py" [FAIL] 5.4s 1290s Time: 5.41 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/minimizer_comparisons.py" [FAIL] 5.4s 1290s Time: 5.40 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree.py" [FAIL] 3.3s 1290s Time: 3.28 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_basic.py" [FAIL] 5.6s 1290s Time: 5.58 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_tardy.py" [FAIL] 5.5s 1290s Time: 5.49 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_energy_plots.py" [FAIL] 5.5s 1290s Time: 5.54 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/tst.py" [FAIL] 5.6s 1290s Time: 5.60 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_featherstone.py" [FAIL] 5.7s 1290s Time: 5.66 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion.py" [FAIL] 5.7s 1290s Time: 5.67 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion_hard.py" [FAIL] 5.5s 1290s Time: 5.55 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_joint_lib.py" [FAIL] 5.6s 1290s Time: 5.60 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_singular.py" [FAIL] 5.7s 1290s Time: 5.66 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_molecules.py" [FAIL] 5.2s 1290s Time: 5.19 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_sparse.py" [FAIL] 5.5s 1290s Time: 5.49 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_lu_factorization.py" [FAIL] 5.5s 1290s Time: 5.51 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/iso_surface/tst_iso_surface.py" [FAIL] 5.5s 1290s Time: 5.45 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/simplex.py" [FAIL] 5.5s 1290s Time: 5.47 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/differential_evolution.py" [FAIL] 5.4s 1290s Time: 5.37 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/direct_search_simulated_annealing.py" [FAIL] 5.3s 1290s Time: 5.25 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/random/tests/tst_random.py" [FAIL] 6.0s 1290s Time: 5.95 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/tst_normal_equations.py" [FAIL] 6.0s 1290s Time: 6.01 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_basic.py" [FAIL] 4.3s 1290s Time: 4.32 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_booth.py" [FAIL] 5.2s 1290s Time: 5.20 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_twisted.py" [FAIL] 5.3s 1290s Time: 5.30 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/smtbx/absolute_structure/tests/tst_absolute_structure.py" --fix_random_seeds [FAIL] 5.8s 1290s Time: 5.80 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/smtbx/ab_initio/tests/tst_ab_initio_ext.py" [FAIL] 6.1s 1290s Time: 6.13 1290s Return code: 139 1290s OKs: 0 1290s 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] 6.0s 1290s Time: 6.01 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/smtbx/masks/tests/tst_masks.py" [FAIL] 6.3s 1290s Time: 6.33 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/smtbx/structure_factors/direct/tests/tst_standard_xray.py" [FAIL] 6.5s 1290s Time: 6.46 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_weighting_schemes.py" --fix_random_seeds [FAIL] 6.3s 1290s Time: 6.27 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_lbfgs.py" [FAIL] 6.3s 1290s Time: 6.30 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_occupancies.py" [FAIL] 6.6s 1290s Time: 6.60 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_same_group.py" [FAIL] 6.6s 1290s Time: 6.58 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_reparametrisation.py" [FAIL] 6.4s 1290s Time: 6.37 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=naive [FAIL] 6.3s 1290s Time: 6.26 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_disorder.py" [FAIL] 6.3s 1290s Time: 6.29 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=levenberg-marquardt [FAIL] 3.2s 1290s Time: 3.22 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_rigid.py" [FAIL] 3.4s 1290s Time: 3.42 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_direction.py" [FAIL] 6.5s 1290s Time: 6.50 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_adp_restraints.py" [FAIL] 6.2s 1290s Time: 6.17 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_manager.py" [FAIL] 6.2s 1290s Time: 6.22 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_restraints.py" --verbose --scatterers=5 --resolution=0.2 [FAIL] 6.3s 1290s Time: 6.28 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_refine.py" [FAIL] 6.4s 1290s Time: 6.43 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py" [FAIL] 8.7s 1290s Time: 8.75 1290s Return code: 1 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/smtbx/tests/tst_utils.py" [FAIL] 6.3s 1290s Time: 6.33 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/rstbx/dps_core/tst_iotbx_converter.py" [FAIL] 5.9s 1290s Time: 5.95 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/fastbragg/tst_bragg_minimal.py" [FAIL] 5.4s 1290s Time: 5.39 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python "/usr/lib/python3/dist-packages/rstbx/sublattice_support/tst_sublattice.py" [FAIL] 6.0s 1290s Time: 5.99 1290s Return code: 139 1290s OKs: 0 1290s libtbx.python -c "from rstbx.run_tests import run; run()" [FAIL] 4.4s 1290s Time: 4.36 1290s Return code: 139 1290s OKs: 0 1290s 1290s Please verify these tests manually. 1290s 1290s Summary: 1290s Tests run : 546 1290s Failures : 284 1290s Warnings (possible failures) : 0 1290s Known Failures ( 4) : 4 1290s Known Unstable ( 3) : 2 1290s Stderr output (discouraged) : 291 1290s 1290s See run_tests_parallel_zlog for full output. 1290s 1290s 1290s ******************************************************************************** 1290s ERROR: 284 TEST FAILURES. PLEASE FIX BEFORE COMMITTING CODE. 1290s ******************************************************************************** 1290s 1290s autopkgtest [11:09:57]: test cctbx: -----------------------] 1291s autopkgtest [11:09:58]: test cctbx: - - - - - - - - - - results - - - - - - - - - - 1291s cctbx FAIL non-zero exit status 1 1291s autopkgtest [11:09:58]: test dxtbx: preparing testbed 1343s autopkgtest [11:10:50]: testbed dpkg architecture: amd64 1343s autopkgtest [11:10:50]: testbed apt version: 2.9.31ubuntu1 1343s autopkgtest [11:10:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup 1344s autopkgtest [11:10:51]: testbed release detected to be: plucky 1344s autopkgtest [11:10:51]: updating testbed package index (apt update) 1345s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 1345s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 1345s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 1345s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 1345s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [11.5 kB] 1346s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [43.9 kB] 1346s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [396 kB] 1346s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [47.7 kB] 1347s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [61.3 kB] 1347s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [162 kB] 1347s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [348 kB] 1347s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [3536 B] 1347s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [7592 B] 1347s Fetched 1192 kB in 2s (571 kB/s) 1347s Reading package lists... 1348s Reading package lists... 1348s Building dependency tree... 1348s Reading state information... 1349s Calculating upgrade... 1349s Calculating upgrade... 1349s The following package was automatically installed and is no longer required: 1349s libnl-genl-3-200 1349s Use 'sudo apt autoremove' to remove it. 1349s The following NEW packages will be installed: 1349s libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-7 1349s linux-headers-6.14.0-7-generic linux-image-6.14.0-7-generic 1349s linux-modules-6.14.0-7-generic linux-modules-extra-6.14.0-7-generic 1349s linux-tools-6.14.0-7 linux-tools-6.14.0-7-generic pnp.ids 1349s The following packages will be upgraded: 1349s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 1349s curl dosfstools exfatprogs fwupd gcc-15-base gir1.2-girepository-2.0 1349s gir1.2-glib-2.0 htop hwdata initramfs-tools initramfs-tools-bin 1349s initramfs-tools-core libapparmor1 libapt-pkg7.0 libassuan9 libatomic1 1349s libaudit-common libaudit1 libbinutils libbrotli1 libc-bin libc-dev-bin libc6 1349s libc6-dev libcap-ng0 libctf-nobfd0 libctf0 libcurl3t64-gnutls libcurl4t64 1349s libestr0 libftdi1-2 libfwupd3 libgcc-s1 libgirepository-1.0-1 1349s libglib2.0-0t64 libglib2.0-data libgpgme11t64 libgprofng0 libjemalloc2 1349s liblz4-1 liblzma5 libncurses6 libncursesw6 libnewt0.52 libnl-3-200 1349s libnl-genl-3-200 libnl-route-3-200 libnss-systemd libpam-systemd 1349s libparted2t64 libpci3 libpython3-stdlib libseccomp2 libselinux1 1349s libsemanage-common libsemanage2 libsframe1 libsqlite3-0 libstdc++6 1349s libsystemd-shared libsystemd0 libtinfo6 libudev1 libxml2 linux-firmware 1349s linux-generic linux-headers-generic linux-headers-virtual 1349s linux-image-generic linux-image-virtual linux-libc-dev linux-tools-common 1349s linux-virtual locales media-types ncurses-base ncurses-bin ncurses-term 1349s parted pci.ids pciutils python-apt-common python3 python3-apt python3-bcrypt 1349s python3-cffi-backend python3-dbus python3-gi python3-lazr.uri 1349s python3-markupsafe python3-minimal python3-newt python3-rpds-py 1349s python3-systemd python3-yaml rsync rsyslog systemd systemd-cryptsetup 1349s systemd-resolved systemd-sysv systemd-timesyncd ubuntu-kernel-accessories 1349s ubuntu-minimal ubuntu-standard udev whiptail xz-utils 1349s 114 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 1349s Need to get 818 MB of archives. 1349s After this operation, 325 MB of additional disk space will be used. 1349s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 1349s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 1349s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 1350s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 1350s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 1350s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 1350s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-7.7 [1723 kB] 1350s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250222-0ubuntu1 [10.4 kB] 1350s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250222-0ubuntu1 [53.4 kB] 1350s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250222-0ubuntu1 [77.8 kB] 1350s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250222-0ubuntu1 [798 kB] 1350s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 1350s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 1350s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 1350s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 1350s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.3-1ubuntu3 [595 kB] 1350s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.3-1ubuntu3 [199 kB] 1350s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.3-1ubuntu3 [11.9 kB] 1350s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.3-1ubuntu3 [345 kB] 1350s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.3-1ubuntu3 [302 kB] 1350s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.3-1ubuntu3 [2371 kB] 1350s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.3-1ubuntu3 [3052 kB] 1350s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.3-1ubuntu3 [42.1 kB] 1350s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.3-1ubuntu3 [124 kB] 1350s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.3-1ubuntu3 [1404 kB] 1350s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.3-1ubuntu3 [215 kB] 1350s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 1350s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 1350s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 1350s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu6 [53.5 kB] 1350s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 1350s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 1350s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.32ubuntu1 [1138 kB] 1350s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.32ubuntu1 [1439 kB] 1350s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.32ubuntu1 [222 kB] 1350s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 1350s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 1350s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 1350s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 1350s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 1350s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2.1build1 [7268 B] 1350s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2.1build1 [106 kB] 1350s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 1351s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 1351s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 1351s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.2-2 [43.1 kB] 1351s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 1351s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 1351s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 1351s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 1351s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 1351s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 1351s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-newt amd64 0.52.24-4ubuntu2 [21.1 kB] 1351s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libnewt0.52 amd64 0.52.24-4ubuntu2 [55.7 kB] 1351s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 1351s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 1351s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 1351s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 1351s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 1351s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 1351s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 1351s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 1351s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 1351s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 1351s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 whiptail amd64 0.52.24-4ubuntu2 [19.1 kB] 1351s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-minimal amd64 1.549 [11.5 kB] 1351s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 1351s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 1351s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 1351s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 1351s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 1351s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 parted amd64 3.6-5 [53.9 kB] 1351s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libparted2t64 amd64 3.6-5 [158 kB] 1351s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 1351s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 1351s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 1351s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 1351s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-standard amd64 1.549 [11.5 kB] 1351s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 1351s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 1351s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 1351s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 1351s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 1351s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 1351s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 1351s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 1351s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 1351s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 1351s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 1351s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 exfatprogs amd64 1.2.8-1 [76.3 kB] 1351s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 1351s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 1351s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 1351s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 1351s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 1351s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 1351s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 1376s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools all 0.146ubuntu1 [7920 B] 1376s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-core all 0.146ubuntu1 [51.9 kB] 1376s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-bin amd64 0.146ubuntu1 [26.2 kB] 1377s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 1377s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libftdi1-2 amd64 1.5-8build1 [30.2 kB] 1377s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu2 [155 kB] 1377s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 1377s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-7-generic amd64 6.14.0-7.7 [41.2 MB] 1379s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-7-generic amd64 6.14.0-7.7 [15.3 MB] 1379s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-7-generic amd64 6.14.0-7.7 [120 MB] 1382s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-7.7+1 [1736 B] 1382s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-7.7+1 [11.1 kB] 1382s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-7.7+1 [1724 B] 1382s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-7.7+1 [11.1 kB] 1382s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-7.7+1 [1648 B] 1382s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-7 all 6.14.0-7.7 [14.2 MB] 1383s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-7-generic amd64 6.14.0-7.7 [3859 kB] 1383s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-7.7+1 [11.0 kB] 1383s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-7.7 [521 kB] 1383s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-7 amd64 6.14.0-7.7 [6147 kB] 1383s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-7-generic amd64 6.14.0-7.7 [1612 B] 1383s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 1383s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 1383s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu2 [278 kB] 1383s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 1383s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-kernel-accessories amd64 1.549 [11.2 kB] 1383s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bcrypt amd64 4.2.0-2.1build1 [221 kB] 1384s Preconfiguring packages ... 1384s Fetched 818 MB in 34s (24.0 MB/s) 1384s (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 ... 109140 files and directories currently installed.) 1384s Preparing to unpack .../ncurses-bin_6.5+20250216-2_amd64.deb ... 1384s Unpacking ncurses-bin (6.5+20250216-2) over (6.5+20250216-1) ... 1384s Setting up ncurses-bin (6.5+20250216-2) ... 1384s (Reading database ... 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binutils-x86-64-linux-gnu (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 1393s Preparing to unpack .../36-libbinutils_2.44-3ubuntu1_amd64.deb ... 1393s Unpacking libbinutils:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 1393s Preparing to unpack .../37-binutils_2.44-3ubuntu1_amd64.deb ... 1393s Unpacking binutils (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 1393s Preparing to unpack .../38-binutils-common_2.44-3ubuntu1_amd64.deb ... 1393s Unpacking binutils-common:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 1393s Preparing to unpack .../39-libsframe1_2.44-3ubuntu1_amd64.deb ... 1393s Unpacking libsframe1:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 1393s Preparing to unpack .../40-libbrotli1_1.1.0-2build4_amd64.deb ... 1393s Unpacking libbrotli1:amd64 (1.1.0-2build4) over (1.1.0-2build3) ... 1393s Preparing to unpack .../41-curl_8.12.1-3ubuntu1_amd64.deb ... 1393s Unpacking curl (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ... 1393s Preparing to unpack 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linux-modules-6.14.0-7-generic (6.14.0-7.7) ... 1406s Setting up ubuntu-kernel-accessories (1.549) ... 1406s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 1406s Setting up pci.ids (0.0~2025.03.09-1) ... 1406s Setting up libnewt0.52:amd64 (0.52.24-4ubuntu2) ... 1406s Setting up apt-utils (2.9.32ubuntu1) ... 1406s Setting up libdebuginfod-common (0.192-4) ... 1406s Setting up exfatprogs (1.2.8-1) ... 1406s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 1406s Setting up libestr0:amd64 (0.1.11-2) ... 1406s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 1406s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 1406s Setting up dosfstools (4.2-1.2) ... 1406s Setting up rsyslog (8.2412.0-2ubuntu2) ... 1406s info: The user `syslog' is already a member of `adm'. 1407s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 1407s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 1407s Setting up linux-libc-dev:amd64 (6.14.0-7.7) ... 1407s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 1407s Setting up systemd (257.3-1ubuntu3) ... 1407s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 1407s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 1408s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 1408s Setting up libparted2t64:amd64 (3.6-5) ... 1408s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 1408s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 1408s Setting up libjemalloc2:amd64 (5.3.0-3) ... 1408s Setting up locales (2.41-1ubuntu1) ... 1408s Installing new version of config file /etc/locale.alias ... 1409s Generating locales (this might take a while)... 1410s en_US.UTF-8... done 1410s Generation complete. 1410s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 1410s Setting up linux-modules-extra-6.14.0-7-generic (6.14.0-7.7) ... 1412s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 1412s Installing new version of config file /etc/apparmor.d/fusermount3 ... 1412s Installing new version of config file /etc/apparmor.d/lsusb ... 1412s Installing new version of config file /etc/apparmor.d/openvpn ... 1413s Reloading AppArmor profiles 1415s Setting up libftdi1-2:amd64 (1.5-8build1) ... 1415s Setting up libglib2.0-data (2.84.0-1) ... 1415s Setting up systemd-cryptsetup (257.3-1ubuntu3) ... 1415s Setting up linux-headers-6.14.0-7 (6.14.0-7.7) ... 1415s Setting up libncurses6:amd64 (6.5+20250216-2) ... 1415s Setting up xz-utils (5.6.4-1) ... 1415s Setting up linux-image-6.14.0-7-generic (6.14.0-7.7) ... 1417s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 1417s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 1417s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-7-generic 1417s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-7-generic 1417s Setting up systemd-timesyncd (257.3-1ubuntu3) ... 1417s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 1417s Setting up libatomic1:amd64 (15-20250222-0ubuntu1) ... 1417s Setting up udev (257.3-1ubuntu3) ... 1418s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 1418s Setting up libpci3:amd64 (1:3.13.0-2) ... 1418s Setting up whiptail (0.52.24-4ubuntu2) ... 1418s Setting up python-apt-common (2.9.9build1) ... 1418s Setting up pnp.ids (0.393-3) ... 1418s Setting up libnl-3-200:amd64 (3.7.0-1) ... 1418s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu2) ... 1418s Setting up linux-image-virtual (6.14.0-7.7+1) ... 1418s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 1418s Setting up libc-dev-bin (2.41-1ubuntu1) ... 1418s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 1418s Setting up rsync (3.4.1+ds1-3) ... 1419s rsync.service is a disabled or a static unit not running, not starting it. 1419s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 1419s Setting up systemd-resolved (257.3-1ubuntu3) ... 1419s Setting up initramfs-tools-bin (0.146ubuntu1) ... 1419s Setting up ncurses-term (6.5+20250216-2) ... 1419s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 1419s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 1419s Setting up linux-image-generic (6.14.0-7.7+1) ... 1419s Setting up systemd-sysv (257.3-1ubuntu3) ... 1419s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 1419s Setting up htop (3.4.0-2) ... 1419s Setting up linux-headers-6.14.0-7-generic (6.14.0-7.7) ... 1419s Setting up parted (3.6-5) ... 1419s Setting up libnss-systemd:amd64 (257.3-1ubuntu3) ... 1419s Setting up python3 (3.13.2-2) ... 1419s Setting up linux-headers-generic (6.14.0-7.7+1) ... 1419s Setting up python3-newt:amd64 (0.52.24-4ubuntu2) ... 1420s Setting up python3-markupsafe (2.1.5-1build4) ... 1420s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 1420s Setting up hwdata (0.393-3) ... 1420s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 1420s No schema files found: doing nothing. 1420s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 1420s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 1420s Setting up pciutils (1:3.13.0-2) ... 1420s Setting up python3-rpds-py (0.21.0-2ubuntu2) ... 1420s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 1420s Setting up libpam-systemd:amd64 (257.3-1ubuntu3) ... 1420s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 1420s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 1420s Setting up curl (8.12.1-3ubuntu1) ... 1420s Setting up initramfs-tools-core (0.146ubuntu1) ... 1420s Setting up linux-tools-common (6.14.0-7.7) ... 1420s Setting up python3-systemd (235-1build6) ... 1420s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 1420s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 1420s Setting up python3-dbus (1.3.2-5build5) ... 1420s Setting up initramfs-tools (0.146ubuntu1) ... 1420s Installing new version of config file /etc/kernel/postinst.d/initramfs-tools ... 1420s Installing new version of config file /etc/kernel/postrm.d/initramfs-tools ... 1420s update-initramfs: deferring update (trigger activated) 1420s Setting up linux-headers-virtual (6.14.0-7.7+1) ... 1420s Setting up linux-generic (6.14.0-7.7+1) ... 1420s Setting up ubuntu-minimal (1.549) ... 1420s Setting up python3-apt (2.9.9build1) ... 1420s Setting up python3-bcrypt (4.2.0-2.1build1) ... 1420s Setting up python3-yaml (6.0.2-1build2) ... 1421s Setting up libfwupd3:amd64 (2.0.6-4) ... 1421s Setting up python3-lazr.uri (1.0.6-6) ... 1421s Setting up binutils (2.44-3ubuntu1) ... 1421s Setting up ubuntu-standard (1.549) ... 1421s Setting up linux-virtual (6.14.0-7.7+1) ... 1421s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 1421s Setting up python3-gi (3.50.0-4build1) ... 1421s Setting up linux-tools-6.14.0-7 (6.14.0-7.7) ... 1421s Setting up linux-tools-6.14.0-7-generic (6.14.0-7.7) ... 1421s Setting up fwupd (2.0.6-4) ... 1421s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 1421s fwupd.service is a disabled or a static unit not running, not starting it. 1421s Processing triggers for man-db (2.13.0-1) ... 1423s Processing triggers for dbus (1.16.2-1ubuntu1) ... 1423s Processing triggers for shared-mime-info (2.4-5) ... 1423s Warning: program compiled against libxml 212 using older 209 1423s Processing triggers for libc-bin (2.41-1ubuntu1) ... 1423s Processing triggers for linux-image-6.14.0-7-generic (6.14.0-7.7) ... 1423s /etc/kernel/postinst.d/initramfs-tools: 1423s update-initramfs: Generating /boot/initrd.img-6.14.0-7-generic 1423s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 1433s /etc/kernel/postinst.d/zz-update-grub: 1433s Sourcing file `/etc/default/grub' 1433s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 1433s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 1433s Generating grub configuration file ... 1433s Found linux image: /boot/vmlinuz-6.14.0-7-generic 1433s Found initrd image: /boot/initrd.img-6.14.0-7-generic 1434s Found linux image: /boot/vmlinuz-6.12.0-16-generic 1434s Found initrd image: /boot/initrd.img-6.12.0-16-generic 1434s Found linux image: /boot/vmlinuz-6.11.0-8-generic 1434s Found initrd image: /boot/initrd.img-6.11.0-8-generic 1434s Warning: os-prober will not be executed to detect other bootable partitions. 1434s Systems on them will not be added to the GRUB boot configuration. 1434s Check GRUB_DISABLE_OS_PROBER documentation entry. 1434s Adding boot menu entry for UEFI Firmware Settings ... 1434s done 1434s Processing triggers for initramfs-tools (0.146ubuntu1) ... 1434s update-initramfs: Generating /boot/initrd.img-6.14.0-7-generic 1434s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 1444s Reading package lists... 1445s Building dependency tree... 1445s Reading state information... 1445s Solving dependencies... 1445s The following packages will be REMOVED: 1445s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 1445s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 1445s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 1445s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 1445s 0 upgraded, 0 newly installed, 11 to remove and 0 not upgraded. 1445s After this operation, 225 MB disk space will be freed. 1445s (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 ... 148650 files and directories currently installed.) 1445s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 1445s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 1445s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 1445s Removing libpython3.12t64:amd64 (3.12.9-1) ... 1445s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 1445s Removing libnsl2:amd64 (1.3.0-3build3) ... 1445s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 1446s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 1446s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 1448s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 1448s /etc/kernel/postrm.d/initramfs-tools: 1448s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 1448s /etc/kernel/postrm.d/zz-update-grub: 1448s Sourcing file `/etc/default/grub' 1448s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 1448s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 1448s Generating grub configuration file ... 1449s Found linux image: /boot/vmlinuz-6.14.0-7-generic 1449s Found initrd image: /boot/initrd.img-6.14.0-7-generic 1449s Found linux image: /boot/vmlinuz-6.12.0-16-generic 1449s Found initrd image: /boot/initrd.img-6.12.0-16-generic 1449s Warning: os-prober will not be executed to detect other bootable partitions. 1449s Systems on them will not be added to the GRUB boot configuration. 1449s Check GRUB_DISABLE_OS_PROBER documentation entry. 1449s Adding boot menu entry for UEFI Firmware Settings ... 1449s done 1449s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 1449s Processing triggers for libc-bin (2.41-1ubuntu1) ... 1449s (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 ... 115819 files and directories currently installed.) 1449s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 1449s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 1449s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 1450s autopkgtest [11:12:37]: upgrading testbed (apt dist-upgrade and autopurge) 1450s Reading package lists... 1450s Building dependency tree... 1450s Reading state information... 1450s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 1450s Starting 2 pkgProblemResolver with broken count: 0 1450s Done 1451s Entering ResolveByKeep 1451s 1451s Calculating upgrade... 1451s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1452s Reading package lists... 1452s Building dependency tree... 1452s Reading state information... 1452s Starting pkgProblemResolver with broken count: 0 1452s Starting 2 pkgProblemResolver with broken count: 0 1452s Done 1452s Solving dependencies... 1453s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1453s autopkgtest [11:12:40]: rebooting testbed after setup commands that affected boot 1479s Reading package lists... 1479s Building dependency tree... 1479s Reading state information... 1480s Starting pkgProblemResolver with broken count: 0 1480s Starting 2 pkgProblemResolver with broken count: 0 1480s Done 1480s The following NEW packages will be installed: 1480s adwaita-icon-theme at-spi2-common bitshuffle blt dconf-gsettings-backend 1480s dconf-service fontconfig fontconfig-config fonts-dejavu-core 1480s fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lyx 1480s gtk-update-icon-cache hicolor-icon-theme libaec0 libamd-comgr2 libamdhip64-5 1480s libann-cctbx-dev libann-cctbx0 libantlr3c-3.4-0 libasan8 1480s libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 libavahi-client3 1480s libavahi-common-data libavahi-common3 libblas3 libboost-numpy1.83.0 1480s libboost-python-dev libboost-python1.83-dev libboost-python1.83.0 1480s libboost-thread1.83.0 libboost-timer1.83.0 libboost1.83-dev 1480s libcairo-gobject2 libcairo2 libcbf1t64 libccp4-data libccp4-dev libccp4c0t64 1480s libccp4f0t64 libcctbx-dev libcctbx0 libcolord2 libcups2t64 libdatrie1 1480s libdconf1 libdeflate0 libdouble-conversion3 libdrm-intel1 libegl-mesa0 1480s libegl1 libepoxy0 libevent-pthreads-2.1-7t64 libexpat1-dev libfabric1 1480s libfontconfig1 libgbm1 libgcc-14-dev libgdk-pixbuf-2.0-0 1480s libgdk-pixbuf2.0-common libgfortran5 libgl1 libgl1-mesa-dri libglew2.2 1480s libglu1-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 1480s libgtk-3-0t64 libgtk-3-common libharfbuzz0b libhdf5-310 libhdf5-hl-310 1480s libhdf5-openmpi-310 libhsa-runtime64-1 libhsakmt1 libhwasan0 1480s libhwloc-plugins libhwloc15 libibmad5 libibumad3 libice6 libimagequant0 1480s libinput-bin libinput10 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 1480s libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 1480s liblbfgsb0 liblcms2-2 liblerc4 libllvm17t64 liblsan0 liblzf1 libmd4c0 1480s libmmdb2-0 libmtdev1t64 libmunge2 libnetcdf22 libnotify4 libopengl0 1480s libopenjp2-7 libopenmpi40 libpango-1.0-0 libpangocairo-1.0-0 1480s libpangoft2-1.0-0 libpciaccess0 libpcre2-16-0 libpcre2-32-0 libpixman-1-0 1480s libpmix2t64 libpsm-infinipath1 libpsm2-2 libpython3-dev libpython3.13-dev 1480s libqhull-r8.0 libqt5core5t64 libqt5dbus5t64 libqt5designer5 libqt5gui5t64 1480s libqt5help5 libqt5network5t64 libqt5opengl5t64 libqt5printsupport5t64 1480s libqt5sql5t64 libqt5test5t64 libqt5widgets5t64 libqt5xml5t64 libquadmath0 1480s libraqm0 librdmacm1t64 libsharpyuv0 libsm6 libssm2 libstdc++-14-dev libsz2 1480s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libtsan2 libubsan1 libucx0 1480s libvulkan1 libwacom-common libwacom9 libwayland-client0 libwayland-cursor0 1480s libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 libwebpmux3 1480s libwxbase3.2-1t64 libwxgtk-gl3.2-1t64 libwxgtk3.2-1t64 libx11-xcb1 1480s libxcb-dri3-0 libxcb-glx0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 1480s libxcb-present0 libxcb-randr0 libxcb-render-util0 libxcb-render0 1480s libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-util1 libxcb-xfixes0 1480s libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxcomposite1 libxcursor1 1480s libxdamage1 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon-x11-0 1480s libxnvctrl0 libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1 libxtst6 1480s libxxf86vm1 mesa-libgallium ocl-icd-libopencl1 pymol-data 1480s python-matplotlib-data python3-all python3-brotli python3-cctbx 1480s python3-contourpy python3-cycler python3-dateutil python3-decorator 1480s python3-dev python3-dials-data python3-flexcache python3-flexparser 1480s python3-fonttools python3-fs python3-h5py python3-h5py-serial 1480s python3-hdf5plugin python3-importlib-resources python3-iniconfig 1480s python3-kiwisolver python3-legacy-cgi python3-lxml python3-lz4 1480s python3-matplotlib python3-mpmath python3-mrcfile python3-natsort 1480s python3-numpy python3-numpy-dev python3-nxmx python3-opengl 1480s python3-ordered-set python3-packaging python3-pil python3-pil.imagetk 1480s python3-pint python3-platformdirs python3-pluggy python3-procrunner 1480s python3-pycbf python3-pymol python3-pyqt5 python3-pyqt5.qtopengl 1480s python3-pyqt5.sip python3-pytest python3-pytest-datadir python3-pytest-mock 1480s python3-pytest-regressions python3-scipy python3-six python3-sympy 1480s python3-tk python3-tqdm python3-ufolib2 python3-wxgtk4.0 python3.12-tk 1480s python3.13-dev python3.13-tk sphinx-rtd-theme-common tk8.6-blt2.5 1480s unicode-data x11-common zlib1g-dev 1480s 0 upgraded, 268 newly installed, 0 to remove and 0 not upgraded. 1480s Need to get 270 MB of archives. 1480s After this operation, 1291 MB of additional disk space will be used. 1480s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-lato all 2.015-1 [2781 kB] 1481s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-4 [148 kB] 1481s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 1481s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB] 1481s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 1481s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:2.2.3+ds-4 [5702 kB] 1482s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [8004 B] 1482s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 1482s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 1482s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 1482s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 1482s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 1482s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 1482s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 1482s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 1482s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [161 kB] 1482s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 gtk-update-icon-cache amd64 4.17.5+ds-3ubuntu1 [54.0 kB] 1483s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 hicolor-icon-theme all 0.18-2 [13.3 kB] 1483s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 adwaita-icon-theme all 48~beta-3 [578 kB] 1483s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 at-spi2-common all 2.55.90-1 [9072 B] 1483s Get:21 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 1483s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 1483s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-310 amd64 1.14.5+repack-3 [1519 kB] 1483s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [62.6 kB] 1483s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 1483s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py-serial amd64 3.13.0-1 [1230 kB] 1483s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py all 3.13.0-1 [7978 B] 1483s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 1483s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [7966 B] 1484s Get:30 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3build1 [178 kB] 1484s Get:31 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 1484s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 librdmacm1t64 amd64 55.0-1ubuntu1 [71.5 kB] 1484s Get:33 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfabric1 amd64 1.17.0-3.1 [789 kB] 1484s Get:34 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc15 amd64 2.12.0-1 [194 kB] 1484s Get:35 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmunge2 amd64 0.5.16-1 [16.5 kB] 1484s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 1484s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 1484s Get:38 http://ftpmaster.internal/ubuntu plucky/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1build1 [38.5 kB] 1484s Get:39 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc-plugins amd64 2.12.0-1 [16.0 kB] 1484s Get:40 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpmix2t64 amd64 5.0.6-5 [714 kB] 1484s Get:41 http://ftpmaster.internal/ubuntu plucky/universe amd64 libllvm17t64 amd64 1:17.0.6-21 [26.0 MB] 1486s Get:42 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build2 [14.4 MB] 1487s Get:43 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsakmt1 amd64 5.7.0-1build1 [62.9 kB] 1487s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsa-runtime64-1 amd64 5.7.1-2build1 [491 kB] 1487s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamdhip64-5 amd64 5.7.1-5 [9643 kB] 1488s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libibumad3 amd64 55.0-1ubuntu1 [29.7 kB] 1488s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libibmad5 amd64 55.0-1ubuntu1 [42.7 kB] 1488s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 libucx0 amd64 1.18.1+ds-2 [1293 kB] 1488s Get:49 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmpi40 amd64 5.0.7-1 [2526 kB] 1488s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-openmpi-310 amd64 1.14.5+repack-3 [1584 kB] 1488s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 bitshuffle amd64 0.5.2-1build2 [154 kB] 1488s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 1488s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 1489s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 1489s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 1489s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 1489s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 1489s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 1489s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 1489s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 1489s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 1489s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [694 kB] 1489s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-8 [4824 B] 1489s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libdconf1 amd64 0.40.0-5 [39.8 kB] 1489s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 dconf-service amd64 0.40.0-5 [28.4 kB] 1489s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [22.7 kB] 1489s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB] 1489s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 1490s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.3-1 [171 kB] 1490s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 libann-cctbx0 amd64 1.1.2+doc-9build1 [32.7 kB] 1490s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 libann-cctbx-dev amd64 1.1.2+doc-9build1 [45.1 kB] 1490s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 libantlr3c-3.4-0 amd64 3.4+dfsg-4build2 [44.9 kB] 1490s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 15-20250222-0ubuntu1 [3055 kB] 1490s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libatk1.0-0t64 amd64 2.55.90-1 [55.3 kB] 1490s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libxi6 amd64 2:1.8.2-1 [32.4 kB] 1490s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libatspi2.0-0t64 amd64 2.55.90-1 [91.1 kB] 1490s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libatk-bridge2.0-0t64 amd64 2.55.90-1 [69.0 kB] 1490s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common-data amd64 0.8-16ubuntu1 [30.9 kB] 1491s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common3 amd64 0.8-16ubuntu1 [23.6 kB] 1491s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-client3 amd64 0.8-16ubuntu1 [27.5 kB] 1491s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-python1.83.0 amd64 1.83.0-4.1ubuntu1 [325 kB] 1491s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 libboost-numpy1.83.0 amd64 1.83.0-4.1ubuntu1 [242 kB] 1491s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 15-20250222-0ubuntu1 [28.6 kB] 1491s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 15-20250222-0ubuntu1 [1355 kB] 1491s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 15-20250222-0ubuntu1 [2756 kB] 1491s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 15-20250222-0ubuntu1 [1205 kB] 1491s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 15-20250222-0ubuntu1 [1677 kB] 1491s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 15-20250222-0ubuntu1 [152 kB] 1491s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-17ubuntu3 [2816 kB] 1492s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-17ubuntu3 [2486 kB] 1492s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost1.83-dev amd64 1.83.0-4.1ubuntu1 [10.7 MB] 1492s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1-dev amd64 2.6.4-1 [148 kB] 1492s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 1492s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-dev amd64 3.13.2-1 [5501 kB] 1493s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-dev amd64 3.13.2-2 [10.7 kB] 1493s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-dev amd64 3.13.2-1 [508 kB] 1493s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 1493s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 1493s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 8.1.3-4 [30.9 kB] 1493s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dev amd64 3.13.2-2 [26.7 kB] 1493s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 libboost-python1.83-dev amd64 1.83.0-4.1ubuntu1 [338 kB] 1493s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 libboost-python-dev amd64 1.83.0.2ubuntu1 [4516 B] 1493s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-thread1.83.0 amd64 1.83.0-4.1ubuntu1 [278 kB] 1493s Get:104 http://ftpmaster.internal/ubuntu plucky/universe amd64 libboost-timer1.83.0 amd64 1.83.0-4.1ubuntu1 [241 kB] 1493s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 1494s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 1494s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 1494s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 1494s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo-gobject2 amd64 1.18.2-2 [127 kB] 1494s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcbf1t64 amd64 0.9.7+dfsg1-5build1 [361 kB] 1494s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccp4-data all 8.0.0-4 [65.2 kB] 1494s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccp4c0t64 amd64 8.0.0-4 [104 kB] 1494s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmmdb2-0 amd64 2.0.22-1 [363 kB] 1495s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccp4f0t64 amd64 8.0.0-4 [228 kB] 1495s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccp4-dev amd64 8.0.0-4 [42.4 kB] 1495s Get:116 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libcctbx0 amd64 2024.10+ds2+~3.22.1+ds1-4build2 [2077 kB] 1495s Get:117 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libcctbx-dev amd64 2024.10+ds2+~3.22.1+ds1-4build2 [1192 kB] 1495s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 1495s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 libcolord2 amd64 1.4.7-3 [155 kB] 1495s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 libcups2t64 amd64 2.4.11-0ubuntu2 [292 kB] 1495s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 1495s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 libdouble-conversion3 amd64 3.3.1-1 [41.7 kB] 1495s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 libdrm-intel1 amd64 2.4.123-1 [68.8 kB] 1495s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-server0 amd64 1.23.1-3 [37.2 kB] 1496s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [7944 B] 1496s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-dri3-0 amd64 1.17.0-2 [7508 B] 1496s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-present0 amd64 1.17.0-2 [6064 B] 1496s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-randr0 amd64 1.17.0-2 [17.9 kB] 1496s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-sync1 amd64 1.17.0-2 [9312 B] 1496s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xfixes0 amd64 1.17.0-2 [10.2 kB] 1496s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 libxshmfence1 amd64 1.3-1build5 [4764 B] 1496s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 mesa-libgallium amd64 25.0.1-2ubuntu1 [12.1 MB] 1497s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 libgbm1 amd64 25.0.1-2ubuntu1 [33.4 kB] 1497s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-client0 amd64 1.23.1-3 [29.7 kB] 1497s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 libegl-mesa0 amd64 25.0.1-2ubuntu1 [136 kB] 1497s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 libepoxy0 amd64 1.5.10-2 [218 kB] 1497s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 libvulkan1 amd64 1.4.304.0-1 [147 kB] 1497s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 libgl1-mesa-dri amd64 25.0.1-2ubuntu1 [35.7 kB] 1497s Get:139 http://ftpmaster.internal/ubuntu plucky/main amd64 libglvnd0 amd64 1.7.0-1build1 [69.6 kB] 1497s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-glx0 amd64 1.17.0-2 [24.8 kB] 1497s Get:141 http://ftpmaster.internal/ubuntu plucky/main amd64 libxxf86vm1 amd64 1:1.1.4-1build4 [9282 B] 1497s Get:142 http://ftpmaster.internal/ubuntu plucky/main amd64 libglx-mesa0 amd64 25.0.1-2ubuntu1 [146 kB] 1497s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 libglx0 amd64 1.7.0-1build1 [38.6 kB] 1498s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 libgl1 amd64 1.7.0-1build1 [102 kB] 1498s Get:145 http://ftpmaster.internal/ubuntu plucky/universe amd64 libglew2.2 amd64 2.2.0-4build1 [187 kB] 1498s Get:146 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 1498s Get:147 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 1498s Get:148 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 1498s Get:149 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 1498s Get:150 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.1-1 [255 kB] 1498s Get:151 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [52.6 kB] 1498s Get:152 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [29.1 kB] 1498s Get:153 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-cursor0 amd64 1.23.1-3 [10.9 kB] 1498s Get:154 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-egl1 amd64 1.23.1-3 [6168 B] 1498s Get:155 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcomposite1 amd64 1:0.4.6-1 [6642 B] 1498s Get:156 http://ftpmaster.internal/ubuntu plucky/main amd64 libxfixes3 amd64 1:6.0.0-2build1 [10.8 kB] 1499s Get:157 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcursor1 amd64 1:1.2.3-1 [23.1 kB] 1499s Get:158 http://ftpmaster.internal/ubuntu plucky/main amd64 libxdamage1 amd64 1:1.1.6-1build1 [6150 B] 1499s Get:159 http://ftpmaster.internal/ubuntu plucky/main amd64 libxinerama1 amd64 2:1.1.4-3build1 [6396 B] 1499s Get:160 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrandr2 amd64 2:1.5.4-1 [19.6 kB] 1499s Get:161 http://ftpmaster.internal/ubuntu plucky/main amd64 libgtk-3-common all 3.24.48-3ubuntu1 [1424 kB] 1499s Get:162 http://ftpmaster.internal/ubuntu plucky/main amd64 libgtk-3-0t64 amd64 3.24.48-3ubuntu1 [3169 kB] 1499s Get:163 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 1499s Get:164 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 1499s Get:165 http://ftpmaster.internal/ubuntu plucky/main amd64 libwacom-common all 2.14.0-1 [103 kB] 1499s Get:166 http://ftpmaster.internal/ubuntu plucky/main amd64 libwacom9 amd64 2.14.0-1 [27.3 kB] 1499s Get:167 http://ftpmaster.internal/ubuntu plucky/main amd64 libinput-bin amd64 1.27.1-1 [23.4 kB] 1499s Get:168 http://ftpmaster.internal/ubuntu plucky/main amd64 libmtdev1t64 amd64 1.1.7-1 [16.3 kB] 1499s Get:169 http://ftpmaster.internal/ubuntu plucky/main amd64 libinput10 amd64 1.27.1-1 [155 kB] 1500s Get:170 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 1500s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 1501s Get:172 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmd4c0 amd64 0.5.2-2 [50.1 kB] 1501s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnetcdf22 amd64 1:4.9.3-1 [574 kB] 1502s Get:174 http://ftpmaster.internal/ubuntu plucky/main amd64 libnotify4 amd64 0.8.4-1 [26.9 kB] 1502s Get:175 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-16-0 amd64 10.45-1 [268 kB] 1502s Get:176 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-32-0 amd64 10.45-1 [251 kB] 1502s Get:177 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 1502s Get:178 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5core5t64 amd64 5.15.15+dfsg-4ubuntu1 [2038 kB] 1502s Get:179 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5dbus5t64 amd64 5.15.15+dfsg-4ubuntu1 [221 kB] 1502s Get:180 http://ftpmaster.internal/ubuntu plucky/main amd64 libegl1 amd64 1.7.0-1build1 [28.7 kB] 1502s Get:181 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5network5t64 amd64 5.15.15+dfsg-4ubuntu1 [725 kB] 1502s Get:182 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 1502s Get:183 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-icccm4 amd64 0.4.2-1 [11.1 kB] 1502s Get:184 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-util1 amd64 0.4.1-1 [11.2 kB] 1502s Get:185 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-image0 amd64 0.4.0-2build1 [10.8 kB] 1503s Get:186 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-keysyms1 amd64 0.4.1-1 [8738 B] 1503s Get:187 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render-util0 amd64 0.3.10-1 [10.8 kB] 1503s Get:188 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shape0 amd64 1.17.0-2 [6092 B] 1503s Get:189 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xinerama0 amd64 1.17.0-2 [5412 B] 1503s Get:190 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xinput0 amd64 1.17.0-2 [33.2 kB] 1503s Get:191 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xkb1 amd64 1.17.0-2 [32.3 kB] 1503s Get:192 http://ftpmaster.internal/ubuntu plucky/main amd64 libxkbcommon-x11-0 amd64 1.7.0-2 [15.2 kB] 1503s Get:193 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5gui5t64 amd64 5.15.15+dfsg-4ubuntu1 [3791 kB] 1503s Get:194 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5widgets5t64 amd64 5.15.15+dfsg-4ubuntu1 [2560 kB] 1503s Get:195 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5xml5t64 amd64 5.15.15+dfsg-4ubuntu1 [124 kB] 1504s Get:196 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5designer5 amd64 5.15.15-6build1 [2827 kB] 1504s Get:197 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5sql5t64 amd64 5.15.15+dfsg-4ubuntu1 [122 kB] 1504s Get:198 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5help5 amd64 5.15.15-6build1 [162 kB] 1504s Get:199 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5opengl5t64 amd64 5.15.15+dfsg-4ubuntu1 [150 kB] 1504s Get:200 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5printsupport5t64 amd64 5.15.15+dfsg-4ubuntu1 [208 kB] 1504s Get:201 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5test5t64 amd64 5.15.15+dfsg-4ubuntu1 [149 kB] 1504s Get:202 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 1504s Get:203 http://ftpmaster.internal/ubuntu plucky/universe amd64 libssm2 amd64 1.4.0-2build1 [87.7 kB] 1504s Get:204 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 1504s Get:205 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 1505s Get:206 http://ftpmaster.internal/ubuntu plucky/universe amd64 libwxbase3.2-1t64 amd64 3.2.6+dfsg-2ubuntu1 [980 kB] 1505s Get:207 http://ftpmaster.internal/ubuntu plucky/main amd64 libxtst6 amd64 2:1.2.5-1 [13.0 kB] 1505s Get:208 http://ftpmaster.internal/ubuntu plucky/universe amd64 libwxgtk3.2-1t64 amd64 3.2.6+dfsg-2ubuntu1 [4967 kB] 1505s Get:209 http://ftpmaster.internal/ubuntu plucky/universe amd64 libwxgtk-gl3.2-1t64 amd64 3.2.6+dfsg-2ubuntu1 [53.9 kB] 1506s Get:210 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu2 [175 kB] 1506s Get:211 http://ftpmaster.internal/ubuntu plucky/universe amd64 pymol-data all 3.0.0+dfsg-3build2 [1394 kB] 1506s Get:212 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-7build1 [2934 kB] 1507s Get:213 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.13.2-2 [884 B] 1507s Get:214 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build4 [367 kB] 1507s Get:215 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-legacy-cgi all 2.6.2-1 [16.6 kB] 1507s Get:216 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pycbf amd64 0.9.7+dfsg1-5build1 [166 kB] 1507s Get:217 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-hdf5plugin all 5.0.0-1 [23.1 kB] 1507s Get:218 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 1507s Get:219 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu3 [217 kB] 1507s Get:220 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 11.1.0-5build1 [583 kB] 1507s Get:221 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.9-1 [116 kB] 1507s Get:222 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.2-1 [107 kB] 1507s Get:223 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.13.1-1 [9770 B] 1507s Get:224 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 11.1.0-5build1 [9828 B] 1507s Get:225 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.1-1build1 [218 kB] 1507s Get:226 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 1508s Get:227 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-platformdirs all 4.3.6-1 [16.8 kB] 1508s Get:228 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-7 [90.8 kB] 1508s Get:229 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.1-1build1 [1408 kB] 1508s Get:230 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.4.0+dfsg-1build1 [27.0 kB] 1508s Get:231 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 1508s Get:232 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.14.1-4ubuntu2 [18.7 MB] 1509s Get:233 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 1509s Get:234 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-5 [4229 kB] 1509s Get:235 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 1509s Get:236 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 1509s Get:237 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.55.3-2build1 [1536 kB] 1510s Get:238 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-importlib-resources all 6.5.2-1 [24.5 kB] 1510s Get:239 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-3build1 [55.6 kB] 1510s Get:240 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 1510s Get:241 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-7build1 [17.4 MB] 1510s Get:242 http://ftpmaster.internal/ubuntu plucky/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 1510s Get:243 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mrcfile all 1.5.4-2 [116 kB] 1510s Get:244 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-natsort all 8.0.2-2 [33.8 kB] 1511s Get:245 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-flexcache all 0.3-2 [13.4 kB] 1511s Get:246 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-flexparser all 0.4-1 [43.8 kB] 1511s Get:247 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pint all 0.24.4-1 [203 kB] 1511s Get:248 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-nxmx all 0.0.4-1 [16.4 kB] 1511s Get:249 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ordered-set all 4.1.0-1 [9778 B] 1511s Get:250 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-procrunner all 2.3.3-2 [12.0 kB] 1511s Get:251 http://ftpmaster.internal/ubuntu plucky/main amd64 libopengl0 amd64 1.7.0-1build1 [32.8 kB] 1511s Get:252 http://ftpmaster.internal/ubuntu plucky/main amd64 libglu1-mesa amd64 9.0.2-1.1build1 [152 kB] 1511s Get:253 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-opengl all 3.1.7+dfsg-1 [612 kB] 1511s Get:254 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyqt5.sip amd64 12.17.0-1build1 [76.5 kB] 1511s Get:255 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyqt5 amd64 5.15.11+dfsg-2 [2725 kB] 1511s Get:256 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyqt5.qtopengl amd64 5.15.11+dfsg-2 [128 kB] 1512s Get:257 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pymol amd64 3.0.0+dfsg-3build2 [4131 kB] 1512s Get:258 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.17.0-1 [13.2 kB] 1512s Get:259 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-tqdm all 4.67.1-2 [92.5 kB] 1512s Get:260 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-wxgtk4.0 amd64 4.2.2+dfsg-3build1 [7838 kB] 1512s Get:261 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-cctbx amd64 2024.10+ds2+~3.22.1+ds1-4build2 [29.0 MB] 1513s Get:262 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 1513s Get:263 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 1513s Get:264 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.4-1 [252 kB] 1514s Get:265 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-dials-data all 2.4.0-2 [110 kB] 1514s Get:266 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-datadir all 1.4.1+ds-1 [5386 B] 1514s Get:267 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-mock all 3.14.0-2 [11.7 kB] 1514s Get:268 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-regressions all 2.5.0+ds-2 [39.2 kB] 1514s Fetched 270 MB in 33s (8083 kB/s) 1514s Selecting previously unselected package fonts-lato. 1515s (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 ... 115816 files and directories currently installed.) 1515s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ... 1515s Unpacking fonts-lato (2.015-1) ... 1515s Selecting previously unselected package python3-numpy-dev:amd64. 1515s Preparing to unpack .../001-python3-numpy-dev_1%3a2.2.3+ds-4_amd64.deb ... 1515s Unpacking python3-numpy-dev:amd64 (1:2.2.3+ds-4) ... 1515s Selecting previously unselected package libblas3:amd64. 1515s Preparing to unpack .../002-libblas3_3.12.1-2_amd64.deb ... 1515s Unpacking libblas3:amd64 (3.12.1-2) ... 1515s Selecting previously unselected package libgfortran5:amd64. 1515s Preparing to unpack .../003-libgfortran5_15-20250222-0ubuntu1_amd64.deb ... 1515s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ... 1515s Selecting previously unselected package liblapack3:amd64. 1515s Preparing to unpack .../004-liblapack3_3.12.1-2_amd64.deb ... 1515s Unpacking liblapack3:amd64 (3.12.1-2) ... 1515s Selecting previously unselected package python3-numpy. 1515s Preparing to unpack .../005-python3-numpy_1%3a2.2.3+ds-4_amd64.deb ... 1515s Unpacking python3-numpy (1:2.2.3+ds-4) ... 1515s Selecting previously unselected package libgdk-pixbuf2.0-common. 1515s Preparing to unpack .../006-libgdk-pixbuf2.0-common_2.42.12+dfsg-2_all.deb ... 1515s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... 1515s Selecting previously unselected package libjpeg-turbo8:amd64. 1515s Preparing to unpack .../007-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 1515s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 1515s Selecting previously unselected package libjpeg8:amd64. 1515s Preparing to unpack .../008-libjpeg8_8c-2ubuntu11_amd64.deb ... 1515s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 1515s Selecting previously unselected package libdeflate0:amd64. 1515s Preparing to unpack .../009-libdeflate0_1.23-1_amd64.deb ... 1515s Unpacking libdeflate0:amd64 (1.23-1) ... 1515s Selecting previously unselected package libjbig0:amd64. 1515s Preparing to unpack .../010-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 1515s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 1515s Selecting previously unselected package liblerc4:amd64. 1515s Preparing to unpack .../011-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 1515s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 1516s Selecting previously unselected package libsharpyuv0:amd64. 1516s Preparing to unpack .../012-libsharpyuv0_1.5.0-0.1_amd64.deb ... 1516s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 1516s Selecting previously unselected package libwebp7:amd64. 1516s Preparing to unpack .../013-libwebp7_1.5.0-0.1_amd64.deb ... 1516s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 1516s Selecting previously unselected package libtiff6:amd64. 1516s Preparing to unpack .../014-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 1516s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 1516s Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. 1516s Preparing to unpack .../015-libgdk-pixbuf-2.0-0_2.42.12+dfsg-2_amd64.deb ... 1516s Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... 1516s Selecting previously unselected package gtk-update-icon-cache. 1516s Preparing to unpack .../016-gtk-update-icon-cache_4.17.5+ds-3ubuntu1_amd64.deb ... 1516s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 1516s 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. 1516s Unpacking gtk-update-icon-cache (4.17.5+ds-3ubuntu1) ... 1516s Selecting previously unselected package hicolor-icon-theme. 1516s Preparing to unpack .../017-hicolor-icon-theme_0.18-2_all.deb ... 1516s Unpacking hicolor-icon-theme (0.18-2) ... 1516s Selecting previously unselected package adwaita-icon-theme. 1516s Preparing to unpack .../018-adwaita-icon-theme_48~beta-3_all.deb ... 1516s Unpacking adwaita-icon-theme (48~beta-3) ... 1516s Selecting previously unselected package at-spi2-common. 1516s Preparing to unpack .../019-at-spi2-common_2.55.90-1_all.deb ... 1516s Unpacking at-spi2-common (2.55.90-1) ... 1516s Selecting previously unselected package libaec0:amd64. 1516s Preparing to unpack .../020-libaec0_1.1.3-1_amd64.deb ... 1516s Unpacking libaec0:amd64 (1.1.3-1) ... 1516s Selecting previously unselected package libsz2:amd64. 1516s Preparing to unpack .../021-libsz2_1.1.3-1_amd64.deb ... 1516s Unpacking libsz2:amd64 (1.1.3-1) ... 1516s Selecting previously unselected package libhdf5-310:amd64. 1516s Preparing to unpack .../022-libhdf5-310_1.14.5+repack-3_amd64.deb ... 1516s Unpacking libhdf5-310:amd64 (1.14.5+repack-3) ... 1516s Selecting previously unselected package libhdf5-hl-310:amd64. 1516s Preparing to unpack .../023-libhdf5-hl-310_1.14.5+repack-3_amd64.deb ... 1516s Unpacking libhdf5-hl-310:amd64 (1.14.5+repack-3) ... 1516s Selecting previously unselected package liblzf1:amd64. 1516s Preparing to unpack .../024-liblzf1_3.6-4_amd64.deb ... 1516s Unpacking liblzf1:amd64 (3.6-4) ... 1516s Selecting previously unselected package python3-h5py-serial. 1516s Preparing to unpack .../025-python3-h5py-serial_3.13.0-1_amd64.deb ... 1516s Unpacking python3-h5py-serial (3.13.0-1) ... 1516s Selecting previously unselected package python3-h5py. 1516s Preparing to unpack .../026-python3-h5py_3.13.0-1_all.deb ... 1516s Unpacking python3-h5py (3.13.0-1) ... 1516s Selecting previously unselected package libgomp1:amd64. 1516s Preparing to unpack .../027-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 1516s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 1516s Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. 1516s Preparing to unpack .../028-libevent-pthreads-2.1-7t64_2.1.12-stable-10_amd64.deb ... 1516s Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 1516s Selecting previously unselected package libpsm-infinipath1. 1516s Preparing to unpack .../029-libpsm-infinipath1_3.3+20.604758e7-6.3build1_amd64.deb ... 1516s Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 1516s Selecting previously unselected package libpsm2-2. 1516s Preparing to unpack .../030-libpsm2-2_11.2.185-2.1_amd64.deb ... 1516s Unpacking libpsm2-2 (11.2.185-2.1) ... 1516s Selecting previously unselected package librdmacm1t64:amd64. 1516s Preparing to unpack .../031-librdmacm1t64_55.0-1ubuntu1_amd64.deb ... 1516s Unpacking librdmacm1t64:amd64 (55.0-1ubuntu1) ... 1516s Selecting previously unselected package libfabric1:amd64. 1516s Preparing to unpack .../032-libfabric1_1.17.0-3.1_amd64.deb ... 1516s Unpacking libfabric1:amd64 (1.17.0-3.1) ... 1516s Selecting previously unselected package libhwloc15:amd64. 1516s Preparing to unpack .../033-libhwloc15_2.12.0-1_amd64.deb ... 1516s Unpacking libhwloc15:amd64 (2.12.0-1) ... 1516s Selecting previously unselected package libmunge2:amd64. 1516s Preparing to unpack .../034-libmunge2_0.5.16-1_amd64.deb ... 1516s Unpacking libmunge2:amd64 (0.5.16-1) ... 1517s Selecting previously unselected package libpciaccess0:amd64. 1517s Preparing to unpack .../035-libpciaccess0_0.17-3build1_amd64.deb ... 1517s Unpacking libpciaccess0:amd64 (0.17-3build1) ... 1517s Selecting previously unselected package libxnvctrl0:amd64. 1517s Preparing to unpack .../036-libxnvctrl0_510.47.03-0ubuntu4_amd64.deb ... 1517s Unpacking libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 1517s Selecting previously unselected package ocl-icd-libopencl1:amd64. 1517s Preparing to unpack .../037-ocl-icd-libopencl1_2.3.2-1build1_amd64.deb ... 1517s Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 1517s Selecting previously unselected package libhwloc-plugins:amd64. 1517s Preparing to unpack .../038-libhwloc-plugins_2.12.0-1_amd64.deb ... 1517s Unpacking libhwloc-plugins:amd64 (2.12.0-1) ... 1517s Selecting previously unselected package libpmix2t64:amd64. 1517s Preparing to unpack .../039-libpmix2t64_5.0.6-5_amd64.deb ... 1517s Unpacking libpmix2t64:amd64 (5.0.6-5) ... 1517s Selecting previously unselected package libllvm17t64:amd64. 1517s Preparing to unpack .../040-libllvm17t64_1%3a17.0.6-21_amd64.deb ... 1517s Unpacking libllvm17t64:amd64 (1:17.0.6-21) ... 1517s Selecting previously unselected package libamd-comgr2:amd64. 1517s Preparing to unpack .../041-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_amd64.deb ... 1517s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 1517s Selecting previously unselected package libhsakmt1:amd64. 1517s Preparing to unpack .../042-libhsakmt1_5.7.0-1build1_amd64.deb ... 1517s Unpacking libhsakmt1:amd64 (5.7.0-1build1) ... 1517s Selecting previously unselected package libhsa-runtime64-1. 1517s Preparing to unpack .../043-libhsa-runtime64-1_5.7.1-2build1_amd64.deb ... 1517s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 1517s Selecting previously unselected package libamdhip64-5. 1518s Preparing to unpack .../044-libamdhip64-5_5.7.1-5_amd64.deb ... 1518s Unpacking libamdhip64-5 (5.7.1-5) ... 1518s Selecting previously unselected package libibumad3:amd64. 1518s Preparing to unpack .../045-libibumad3_55.0-1ubuntu1_amd64.deb ... 1518s Unpacking libibumad3:amd64 (55.0-1ubuntu1) ... 1518s Selecting previously unselected package libibmad5:amd64. 1518s Preparing to unpack .../046-libibmad5_55.0-1ubuntu1_amd64.deb ... 1518s Unpacking libibmad5:amd64 (55.0-1ubuntu1) ... 1518s Selecting previously unselected package libucx0:amd64. 1518s Preparing to unpack .../047-libucx0_1.18.1+ds-2_amd64.deb ... 1518s Unpacking libucx0:amd64 (1.18.1+ds-2) ... 1518s Selecting previously unselected package libopenmpi40:amd64. 1518s Preparing to unpack .../048-libopenmpi40_5.0.7-1_amd64.deb ... 1518s Unpacking libopenmpi40:amd64 (5.0.7-1) ... 1518s Selecting previously unselected package libhdf5-openmpi-310:amd64. 1518s Preparing to unpack .../049-libhdf5-openmpi-310_1.14.5+repack-3_amd64.deb ... 1518s Unpacking libhdf5-openmpi-310:amd64 (1.14.5+repack-3) ... 1518s Selecting previously unselected package bitshuffle. 1518s Preparing to unpack .../050-bitshuffle_0.5.2-1build2_amd64.deb ... 1518s Unpacking bitshuffle (0.5.2-1build2) ... 1518s Selecting previously unselected package libtcl8.6:amd64. 1518s Preparing to unpack .../051-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 1518s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 1518s Selecting previously unselected package fonts-dejavu-mono. 1518s Preparing to unpack .../052-fonts-dejavu-mono_2.37-8_all.deb ... 1518s Unpacking fonts-dejavu-mono (2.37-8) ... 1518s Selecting previously unselected package fonts-dejavu-core. 1518s Preparing to unpack .../053-fonts-dejavu-core_2.37-8_all.deb ... 1518s Unpacking fonts-dejavu-core (2.37-8) ... 1518s Selecting previously unselected package fontconfig-config. 1518s Preparing to unpack .../054-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 1518s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 1518s Selecting previously unselected package libfontconfig1:amd64. 1518s Preparing to unpack .../055-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 1518s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 1518s Selecting previously unselected package libxrender1:amd64. 1518s Preparing to unpack .../056-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 1518s Unpacking libxrender1:amd64 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previously unselected package libcairo2:amd64. 1523s Preparing to unpack .../107-libcairo2_1.18.2-2_amd64.deb ... 1523s Unpacking libcairo2:amd64 (1.18.2-2) ... 1523s Selecting previously unselected package libcairo-gobject2:amd64. 1523s Preparing to unpack .../108-libcairo-gobject2_1.18.2-2_amd64.deb ... 1523s Unpacking libcairo-gobject2:amd64 (1.18.2-2) ... 1523s Selecting previously unselected package libcbf1t64:amd64. 1523s Preparing to unpack .../109-libcbf1t64_0.9.7+dfsg1-5build1_amd64.deb ... 1523s Unpacking libcbf1t64:amd64 (0.9.7+dfsg1-5build1) ... 1523s Selecting previously unselected package libccp4-data. 1523s Preparing to unpack .../110-libccp4-data_8.0.0-4_all.deb ... 1523s Unpacking libccp4-data (8.0.0-4) ... 1523s Selecting previously unselected package libccp4c0t64:amd64. 1523s Preparing to unpack .../111-libccp4c0t64_8.0.0-4_amd64.deb ... 1523s Unpacking libccp4c0t64:amd64 (8.0.0-4) ... 1523s Selecting previously unselected package libmmdb2-0:amd64. 1523s Preparing to unpack .../112-libmmdb2-0_2.0.22-1_amd64.deb ... 1523s Unpacking libmmdb2-0:amd64 (2.0.22-1) ... 1523s Selecting previously unselected package libccp4f0t64:amd64. 1523s Preparing to unpack .../113-libccp4f0t64_8.0.0-4_amd64.deb ... 1523s Unpacking libccp4f0t64:amd64 (8.0.0-4) ... 1523s Selecting previously unselected package libccp4-dev:amd64. 1523s Preparing to unpack .../114-libccp4-dev_8.0.0-4_amd64.deb ... 1523s Unpacking libccp4-dev:amd64 (8.0.0-4) ... 1523s Selecting previously unselected package libcctbx0. 1523s Preparing to unpack .../115-libcctbx0_2024.10+ds2+~3.22.1+ds1-4build2_amd64.deb ... 1523s Unpacking libcctbx0 (2024.10+ds2+~3.22.1+ds1-4build2) ... 1523s Selecting previously unselected package libcctbx-dev. 1523s Preparing to unpack .../116-libcctbx-dev_2024.10+ds2+~3.22.1+ds1-4build2_amd64.deb ... 1523s Unpacking libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4build2) ... 1523s Selecting previously unselected package liblcms2-2:amd64. 1523s Preparing to unpack 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previously unselected package libglvnd0:amd64. 1524s Preparing to unpack .../138-libglvnd0_1.7.0-1build1_amd64.deb ... 1524s Unpacking libglvnd0:amd64 (1.7.0-1build1) ... 1524s Selecting previously unselected package libxcb-glx0:amd64. 1524s Preparing to unpack .../139-libxcb-glx0_1.17.0-2_amd64.deb ... 1524s Unpacking libxcb-glx0:amd64 (1.17.0-2) ... 1524s Selecting previously unselected package libxxf86vm1:amd64. 1524s Preparing to unpack .../140-libxxf86vm1_1%3a1.1.4-1build4_amd64.deb ... 1524s Unpacking libxxf86vm1:amd64 (1:1.1.4-1build4) ... 1524s Selecting previously unselected package libglx-mesa0:amd64. 1524s Preparing to unpack .../141-libglx-mesa0_25.0.1-2ubuntu1_amd64.deb ... 1524s Unpacking libglx-mesa0:amd64 (25.0.1-2ubuntu1) ... 1525s Selecting previously unselected package libglx0:amd64. 1525s Preparing to unpack .../142-libglx0_1.7.0-1build1_amd64.deb ... 1525s Unpacking libglx0:amd64 (1.7.0-1build1) ... 1525s Selecting previously unselected package libgl1:amd64. 1525s 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libpcre2-16-0:amd64. 1526s Preparing to unpack .../174-libpcre2-16-0_10.45-1_amd64.deb ... 1526s Unpacking libpcre2-16-0:amd64 (10.45-1) ... 1526s Selecting previously unselected package libpcre2-32-0:amd64. 1526s Preparing to unpack .../175-libpcre2-32-0_10.45-1_amd64.deb ... 1526s Unpacking libpcre2-32-0:amd64 (10.45-1) ... 1526s Selecting previously unselected package libqhull-r8.0:amd64. 1526s Preparing to unpack .../176-libqhull-r8.0_2020.2-6build1_amd64.deb ... 1526s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 1526s Selecting previously unselected package libqt5core5t64:amd64. 1526s Preparing to unpack .../177-libqt5core5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 1526s Unpacking libqt5core5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1526s Selecting previously unselected package libqt5dbus5t64:amd64. 1526s Preparing to unpack .../178-libqt5dbus5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 1526s Unpacking libqt5dbus5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1526s Selecting previously unselected package libegl1:amd64. 1526s Preparing to unpack .../179-libegl1_1.7.0-1build1_amd64.deb ... 1526s Unpacking libegl1:amd64 (1.7.0-1build1) ... 1526s Selecting previously unselected package libqt5network5t64:amd64. 1526s Preparing to unpack .../180-libqt5network5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 1526s Unpacking libqt5network5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1526s Selecting previously unselected package libsm6:amd64. 1526s Preparing to unpack .../181-libsm6_2%3a1.2.4-1_amd64.deb ... 1526s Unpacking libsm6:amd64 (2:1.2.4-1) ... 1526s Selecting previously unselected package libxcb-icccm4:amd64. 1526s Preparing to unpack .../182-libxcb-icccm4_0.4.2-1_amd64.deb ... 1526s Unpacking libxcb-icccm4:amd64 (0.4.2-1) ... 1526s Selecting previously unselected package libxcb-util1:amd64. 1526s Preparing to unpack .../183-libxcb-util1_0.4.1-1_amd64.deb ... 1526s Unpacking libxcb-util1:amd64 (0.4.1-1) ... 1526s Selecting previously unselected package libxcb-image0:amd64. 1526s 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unpack .../189-libxcb-xinput0_1.17.0-2_amd64.deb ... 1526s Unpacking libxcb-xinput0:amd64 (1.17.0-2) ... 1526s Selecting previously unselected package libxcb-xkb1:amd64. 1526s Preparing to unpack .../190-libxcb-xkb1_1.17.0-2_amd64.deb ... 1526s Unpacking libxcb-xkb1:amd64 (1.17.0-2) ... 1527s Selecting previously unselected package libxkbcommon-x11-0:amd64. 1527s Preparing to unpack .../191-libxkbcommon-x11-0_1.7.0-2_amd64.deb ... 1527s Unpacking libxkbcommon-x11-0:amd64 (1.7.0-2) ... 1527s Selecting previously unselected package libqt5gui5t64:amd64. 1527s Preparing to unpack .../192-libqt5gui5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 1527s Unpacking libqt5gui5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1527s Selecting previously unselected package libqt5widgets5t64:amd64. 1527s Preparing to unpack .../193-libqt5widgets5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 1527s Unpacking libqt5widgets5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1527s Selecting previously unselected package libqt5xml5t64:amd64. 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Selecting previously unselected package libqt5printsupport5t64:amd64. 1527s Preparing to unpack .../199-libqt5printsupport5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 1527s Unpacking libqt5printsupport5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1527s Selecting previously unselected package libqt5test5t64:amd64. 1527s Preparing to unpack .../200-libqt5test5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 1527s Unpacking libqt5test5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1527s Selecting previously unselected package libraqm0:amd64. 1527s Preparing to unpack .../201-libraqm0_0.10.2-1_amd64.deb ... 1527s Unpacking libraqm0:amd64 (0.10.2-1) ... 1527s Selecting previously unselected package libssm2:amd64. 1527s Preparing to unpack .../202-libssm2_1.4.0-2build1_amd64.deb ... 1527s Unpacking libssm2:amd64 (1.4.0-2build1) ... 1527s Selecting previously unselected package libwebpdemux2:amd64. 1527s Preparing to unpack .../203-libwebpdemux2_1.5.0-0.1_amd64.deb ... 1527s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 1527s Selecting previously unselected package libwebpmux3:amd64. 1527s Preparing to unpack .../204-libwebpmux3_1.5.0-0.1_amd64.deb ... 1527s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 1527s Selecting previously unselected package libwxbase3.2-1t64:amd64. 1527s Preparing to unpack .../205-libwxbase3.2-1t64_3.2.6+dfsg-2ubuntu1_amd64.deb ... 1527s Unpacking libwxbase3.2-1t64:amd64 (3.2.6+dfsg-2ubuntu1) ... 1527s Selecting previously unselected package libxtst6:amd64. 1527s Preparing to unpack .../206-libxtst6_2%3a1.2.5-1_amd64.deb ... 1527s Unpacking libxtst6:amd64 (2:1.2.5-1) ... 1527s Selecting previously unselected package libwxgtk3.2-1t64:amd64. 1527s Preparing to unpack .../207-libwxgtk3.2-1t64_3.2.6+dfsg-2ubuntu1_amd64.deb ... 1527s Unpacking libwxgtk3.2-1t64:amd64 (3.2.6+dfsg-2ubuntu1) ... 1527s Selecting previously unselected package libwxgtk-gl3.2-1t64:amd64. 1527s Preparing to unpack .../208-libwxgtk-gl3.2-1t64_3.2.6+dfsg-2ubuntu1_amd64.deb ... 1527s Unpacking libwxgtk-gl3.2-1t64:amd64 (3.2.6+dfsg-2ubuntu1) ... 1527s Selecting previously unselected package libxslt1.1:amd64. 1527s Preparing to unpack .../209-libxslt1.1_1.1.39-0exp1ubuntu2_amd64.deb ... 1527s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu2) ... 1528s Selecting previously unselected package pymol-data. 1528s Preparing to unpack .../210-pymol-data_3.0.0+dfsg-3build2_all.deb ... 1528s Unpacking pymol-data (3.0.0+dfsg-3build2) ... 1528s Selecting previously unselected package python-matplotlib-data. 1528s Preparing to unpack .../211-python-matplotlib-data_3.8.3-7build1_all.deb ... 1528s Unpacking python-matplotlib-data (3.8.3-7build1) ... 1528s Selecting previously unselected package python3-all. 1528s Preparing to unpack .../212-python3-all_3.13.2-2_amd64.deb ... 1528s Unpacking python3-all (3.13.2-2) ... 1528s Selecting previously unselected package python3-brotli. 1528s Preparing to unpack .../213-python3-brotli_1.1.0-2build4_amd64.deb ... 1528s Unpacking python3-brotli 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previously unselected package python3-pil:amd64. 1528s Preparing to unpack .../219-python3-pil_11.1.0-5build1_amd64.deb ... 1528s Unpacking python3-pil:amd64 (11.1.0-5build1) ... 1528s Selecting previously unselected package python3.12-tk. 1528s Preparing to unpack .../220-python3.12-tk_3.12.9-1_amd64.deb ... 1528s Unpacking python3.12-tk (3.12.9-1) ... 1528s Selecting previously unselected package python3.13-tk. 1528s Preparing to unpack .../221-python3.13-tk_3.13.2-1_amd64.deb ... 1528s Unpacking python3.13-tk (3.13.2-1) ... 1528s Selecting previously unselected package python3-tk:amd64. 1528s Preparing to unpack .../222-python3-tk_3.13.1-1_amd64.deb ... 1528s Unpacking python3-tk:amd64 (3.13.1-1) ... 1528s Selecting previously unselected package python3-pil.imagetk:amd64. 1528s Preparing to unpack .../223-python3-pil.imagetk_11.1.0-5build1_amd64.deb ... 1528s Unpacking python3-pil.imagetk:amd64 (11.1.0-5build1) ... 1528s Selecting previously unselected package python3-contourpy. 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(25.0.1-2ubuntu1) ... 1543s Setting up libqt5network5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1543s Setting up libavahi-common3:amd64 (0.8-16ubuntu1) ... 1543s Setting up libqt5xml5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1543s Setting up dconf-service (0.40.0-5) ... 1543s Setting up libqt5test5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1543s Setting up libhwloc-plugins:amd64 (2.12.0-1) ... 1543s Setting up libccp4f0t64:amd64 (8.0.0-4) ... 1543s Setting up libinput-bin (1.27.1-1) ... 1543s Setting up python3-pint (0.24.4-1) ... 1543s Setting up libthai0:amd64 (0.1.29-2build1) ... 1543s Setting up libegl-mesa0:amd64 (25.0.1-2ubuntu1) ... 1543s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 1543s Setting up libraqm0:amd64 (0.10.2-1) ... 1543s Setting up libpython3.13-dev:amd64 (3.13.2-1) ... 1543s Setting up libpmix2t64:amd64 (5.0.6-5) ... 1543s Setting up python3-numpy (1:2.2.3+ds-4) ... 1544s Setting up libjs-sphinxdoc (8.1.3-4) ... 1544s Setting up libhdf5-310:amd64 (1.14.5+repack-3) ... 1544s Setting up python3-pytest-mock (3.14.0-2) ... 1544s Setting up python3-lxml:amd64 (5.3.1-1build1) ... 1545s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 1545s Setting up libwayland-cursor0:amd64 (1.23.1-3) ... 1545s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 1545s Setting up libegl1:amd64 (1.7.0-1build1) ... 1545s Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... 1545s Setting up python3-contourpy (1.3.1-1build1) ... 1545s Setting up libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 1545s Setting up libgcc-14-dev:amd64 (14.2.0-17ubuntu3) ... 1545s Setting up python3-dials-data (2.4.0-2) ... 1545s Setting up libstdc++-14-dev:amd64 (14.2.0-17ubuntu3) ... 1545s Setting up libsm6:amd64 (2:1.2.4-1) ... 1545s Setting up libavahi-client3:amd64 (0.8-16ubuntu1) ... 1545s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 1545s Setting up python3-mrcfile (1.5.4-2) ... 1545s Setting up libatk-bridge2.0-0t64:amd64 (2.55.90-1) ... 1545s Setting up libinput10:amd64 (1.27.1-1) ... 1545s Setting up gtk-update-icon-cache (4.17.5+ds-3ubuntu1) ... 1545s Setting up libhdf5-hl-310:amd64 (1.14.5+repack-3) ... 1545s Setting up fontconfig (2.15.0-2ubuntu1) ... 1547s Regenerating fonts cache... done. 1547s Setting up libxft2:amd64 (2.3.6-1build1) ... 1547s Setting up libboost1.83-dev:amd64 (1.83.0-4.1ubuntu1) ... 1547s Setting up libglx-mesa0:amd64 (25.0.1-2ubuntu1) ... 1547s Setting up python3-scipy (1.14.1-4ubuntu2) ... 1550s Setting up libpython3-dev:amd64 (3.13.2-2) ... 1550s Setting up libcbf1t64:amd64 (0.9.7+dfsg1-5build1) ... 1550s Setting up libglx0:amd64 (1.7.0-1build1) ... 1550s Setting up dconf-gsettings-backend:amd64 (0.40.0-5) ... 1550s Setting up libccp4-dev:amd64 (8.0.0-4) ... 1550s Setting up python3.13-dev (3.13.2-1) ... 1550s Setting up libtk8.6:amd64 (8.6.16-1) ... 1550s Setting up libpango-1.0-0:amd64 (1.56.1-1) ... 1550s Setting up python3.12-tk (3.12.9-1) ... 1550s Setting up libnetcdf22:amd64 (1:4.9.3-1) ... 1550s Setting up python3-h5py-serial (3.13.0-1) ... 1550s Setting up libcairo2:amd64 (1.18.2-2) ... 1550s Setting up python3.13-tk (3.13.2-1) ... 1550s Setting up python3-pil:amd64 (11.1.0-5build1) ... 1551s Setting up libgl1:amd64 (1.7.0-1build1) ... 1551s Setting up libamdhip64-5 (5.7.1-5) ... 1551s Setting up python3-pytest-regressions (2.5.0+ds-2) ... 1551s Setting up adwaita-icon-theme (48~beta-3) ... 1551s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 1551s Setting up libnotify4:amd64 (0.8.4-1) ... 1551s Setting up python3-dev (3.13.2-2) ... 1551s Setting up libboost-python1.83-dev (1.83.0-4.1ubuntu1) ... 1551s Setting up python3-pycbf (0.9.7+dfsg1-5build1) ... 1551s Setting up python3-h5py (3.13.0-1) ... 1551s Setting up libglew2.2:amd64 (2.2.0-4build1) ... 1551s Setting up python3-hdf5plugin (5.0.0-1) ... 1551s Setting up libcairo-gobject2:amd64 (1.18.2-2) ... 1551s Setting up libpangoft2-1.0-0:amd64 (1.56.1-1) ... 1551s Setting up python3-nxmx (0.0.4-1) ... 1551s Setting up libcups2t64:amd64 (2.4.11-0ubuntu2) ... 1551s Setting up libgtk-3-common (3.24.48-3ubuntu1) ... 1551s Setting up libpangocairo-1.0-0:amd64 (1.56.1-1) ... 1551s Setting up libcctbx0 (2024.10+ds2+~3.22.1+ds1-4build2) ... 1551s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 1551s Setting up libucx0:amd64 (1.18.1+ds-2) ... 1551s Setting up blt (2.5.3+dfsg-8) ... 1551s Setting up python3-tk:amd64 (3.13.1-1) ... 1551s Setting up python3-opengl (3.1.7+dfsg-1) ... 1552s /usr/lib/python3/dist-packages/OpenGL/GL/AMD/vertex_shader_tessellator.py:1: SyntaxWarning: invalid escape sequence '\ ' 1552s '''OpenGL extension AMD.vertex_shader_tessellator 1553s Setting up libboost-python-dev (1.83.0.2ubuntu1) ... 1553s Setting up libqt5gui5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1553s Setting up python3-pil.imagetk:amd64 (11.1.0-5build1) ... 1553s Setting up libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4build2) ... 1553s Setting up libopenmpi40:amd64 (5.0.7-1) ... 1553s Setting up libqt5widgets5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1553s Setting up libhdf5-openmpi-310:amd64 (1.14.5+repack-3) ... 1553s Setting up libqt5help5:amd64 (5.15.15-6build1) ... 1553s Setting up libqt5opengl5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1553s Setting up libqt5printsupport5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1553s Setting up bitshuffle (0.5.2-1build2) ... 1553s Setting up libqt5designer5:amd64 (5.15.15-6build1) ... 1553s Setting up python3-pyqt5 (5.15.11+dfsg-2) ... 1553s Setting up python3-pyqt5.qtopengl (5.15.11+dfsg-2) ... 1553s Setting up python3-pymol (3.0.0+dfsg-3build2) ... 1554s Setting up python3-fonttools (4.55.3-2build1) ... 1555s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 1555s Setting up python3-matplotlib (3.8.3-7build1) ... 1556s Processing triggers for libc-bin (2.41-1ubuntu1) ... 1556s Processing triggers for man-db (2.13.0-1) ... 1558s Processing triggers for libglib2.0-0t64:amd64 (2.84.0-1) ... 1558s Setting up libgtk-3-0t64:amd64 (3.24.48-3ubuntu1) ... 1558s Processing triggers for udev (257.3-1ubuntu3) ... 1558s Setting up libwxgtk3.2-1t64:amd64 (3.2.6+dfsg-2ubuntu1) ... 1558s Setting up libwxgtk-gl3.2-1t64:amd64 (3.2.6+dfsg-2ubuntu1) ... 1558s Setting up python3-wxgtk4.0 (4.2.2+dfsg-3build1) ... 1559s Setting up python3-cctbx (2024.10+ds2+~3.22.1+ds1-4build2) ... 1562s /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:8: SyntaxWarning: invalid escape sequence '\{' 1562s """ Iterator to generate strings of length n_chars, using upper-case, 1562s /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:46: SyntaxWarning: invalid escape sequence '\/' 1562s special_characters = """[]_,.;:"&<>()\/\{}'`~!@#$%*|+-""" 1571s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:724: SyntaxWarning: invalid escape sequence '\o' 1571s width=pairwise_differences_db, label='$\omega_{hkl}$' 1571s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:739: SyntaxWarning: invalid escape sequence '\o' 1571s axes[0].set_ylabel('Distribution of $\omega_{hbk}$') 1571s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:740: SyntaxWarning: invalid escape sequence '\o' 1571s axes[0].set_xlabel('Normalized PD ($\omega_{hbk}$)') 1571s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:759: SyntaxWarning: invalid escape sequence '\o' 1571s axes[1].set_xlabel('Sorted Normalized PD ($\omega_{hbk}$)') 1571s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:778: SyntaxWarning: invalid escape sequence '\s' 1571s axes[2].set_ylabel('Standard Deviation of $I_{hbk}/\sigma_{hbk}$') 1571s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:807: SyntaxWarning: invalid escape sequence '\m' 1571s axes_sadd.set_ylabel('$s_{\mathrm{fac}}^2 \\times s_{\mathrm{add}}^2$') 1571s Processing triggers for libc-bin (2.41-1ubuntu1) ... 1592s autopkgtest [11:14:59]: test dxtbx: [----------------------- 1592s Testing dxtbx with python3.13: 1595s Fatal Python error: Segmentation fault 1595s 1595s Current thread 0x0000766dc1702100 (most recent call first): 1595s File "/usr/lib/python3/dist-packages/cctbx/sgtbx/__init__.py", line 102 in __init__ 1595s File "/usr/lib/python3/dist-packages/cctbx/crystal/__init__.py", line 75 in __init__ 1595s File "/tmp/autopkgtest.PtYqHY/autopkgtest_tmp/tests/test_crystal_model_equivalence.py", line 28 in 1595s File "/usr/lib/python3/dist-packages/_pytest/assertion/rewrite.py", line 184 in exec_module 1595s File "", line 935 in _load_unlocked 1595s File "", line 1331 in _find_and_load_unlocked 1595s File "", line 1360 in _find_and_load 1595s File "", line 1387 in _gcd_import 1595s File "/usr/lib/python3.13/importlib/__init__.py", line 88 in import_module 1595s File "/usr/lib/python3/dist-packages/_pytest/pathlib.py", line 587 in import_path 1595s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 493 in importtestmodule 1595s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 546 in _getobj 1595s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 284 in obj 1595s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 562 in _register_setup_module_fixture 1595s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 549 in collect 1595s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389 in collect 1595s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341 in from_call 1595s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 391 in pytest_make_collect_report 1595s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall 1595s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec 1595s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ 1595s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 567 in collect_one_node 1595s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 835 in _collect_one_node 1595s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 970 in genitems 1595s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 975 in genitems 1595s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 975 in genitems 1595s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 809 in perform_collect 1595s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 347 in pytest_collection 1595s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall 1595s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec 1595s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ 1595s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 336 in _main 1595s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 283 in wrap_session 1595s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 330 in pytest_cmdline_main 1595s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall 1595s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec 1595s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ 1595s File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 175 in main 1595s File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 201 in console_main 1595s File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 9 in 1595s File "", line 88 in _run_code 1595s File "", line 198 in _run_module_as_main 1595s 1595s 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) 1600s Segmentation fault (core dumped) 1600s autopkgtest [11:15:07]: test dxtbx: -----------------------] 1601s autopkgtest [11:15:08]: test dxtbx: - - - - - - - - - - results - - - - - - - - - - 1601s dxtbx FAIL non-zero exit status 139 1601s autopkgtest [11:15:08]: @@@@@@@@@@@@@@@@@@@@ summary 1601s cctbx FAIL non-zero exit status 1 1601s dxtbx FAIL non-zero exit status 139 1734s nova [W] Skipping flock for amd64 1734s Creating nova instance adt-plucky-amd64-cctbx-20250313-104827-juju-7f2275-prod-proposed-migration-environment-2-314e3a55-3596-445d-bddb-4b6ab1470d91 from image adt/ubuntu-plucky-amd64-server-20250304.img (UUID 9c7d4da5-d95f-4c85-ac1f-51eb37e75c4c)... 1734s nova [W] Timed out waiting for bad003f6-04d8-4279-a3f4-ed663bd36fc9 to get deleted. 1734s nova [W] Skipping flock for amd64 1734s Creating nova instance adt-plucky-amd64-cctbx-20250313-104827-juju-7f2275-prod-proposed-migration-environment-2-314e3a55-3596-445d-bddb-4b6ab1470d91 from image adt/ubuntu-plucky-amd64-server-20250304.img (UUID 9c7d4da5-d95f-4c85-ac1f-51eb37e75c4c)... 1734s nova [W] Timed out waiting for 398b27d5-9608-48ad-a466-c862b45c1888 to get deleted.