0s autopkgtest [13:06:02]: starting date and time: 2025-03-22 13:06:02+0000 0s autopkgtest [13:06:02]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [13:06:02]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5z3bokbl/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:cctbx --apt-upgrade cctbx --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=cctbx/2024.10+ds2+~3.22.1+ds1-4build2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-1.secgroup --name adt-plucky-amd64-cctbx-20250322-130601-juju-7f2275-prod-proposed-migration-environment-2-58a8511e-b12f-41e9-8c33-dcebd5980839 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 61s autopkgtest [13:07:03]: testbed dpkg architecture: amd64 61s autopkgtest [13:07:03]: testbed apt version: 2.9.31ubuntu1 61s autopkgtest [13:07:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup 61s autopkgtest [13:07:03]: testbed release detected to be: None 61s autopkgtest [13:07:03]: updating testbed package index (apt update) 61s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 61s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 61s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 61s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 61s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [11.5 kB] 61s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [29.9 kB] 61s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [288 kB] 62s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [1232 B] 62s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [36.9 kB] 62s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [43.5 kB] 62s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1320 B] 62s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [1256 B] 62s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 62s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [196 kB] 62s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [102 kB] 62s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [12.4 kB] 62s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [7592 B] 62s Get:18 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [3536 B] 62s Get:19 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [424 B] 63s Fetched 862 kB in 0s (3048 kB/s) 64s Reading package lists... 64s autopkgtest [13:07:06]: upgrading testbed (apt dist-upgrade and autopurge) 65s Reading package lists... 65s Building dependency tree... 65s Reading state information... 65s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 65s Starting 2 pkgProblemResolver with broken count: 0 65s Done 66s Entering ResolveByKeep 66s 66s Calculating upgrade... 66s The following packages were automatically installed and are no longer required: 66s libnl-genl-3-200 python3.12-gdbm 66s Use 'sudo apt autoremove' to remove them. 67s The following NEW packages will be installed: 67s linux-headers-6.14.0-11 linux-headers-6.14.0-11-generic 67s linux-image-6.14.0-11-generic linux-modules-6.14.0-11-generic 67s linux-modules-extra-6.14.0-11-generic pnp.ids 67s The following packages will be upgraded: 67s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 67s cloud-init cloud-init-base cron cron-daemon-common curl dbus dbus-bin 67s dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session 67s dhcpcd-base diffutils dosfstools dpkg dpkg-dev fwupd gcc-14-base gcc-15-base 67s gir1.2-girepository-2.0 gir1.2-glib-2.0 grub-common grub-efi-amd64-bin 67s grub-efi-amd64-signed grub-efi-amd64-unsigned grub-pc grub-pc-bin 67s grub2-common htop hwdata ibverbs-providers libapparmor1 libapt-pkg7.0 67s libatomic1 libaudit-common libaudit1 libbinutils libbrotli1 libc-bin 67s libc-dev-bin libc6 libc6-dev libcap-ng0 libctf-nobfd0 libctf0 67s libcurl3t64-gnutls libcurl4t64 libdbus-1-3 libdpkg-perl libdw1t64 libelf1t64 67s libestr0 libfwupd3 libgcc-s1 libgirepository-1.0-1 libglib2.0-0t64 67s libglib2.0-data libgnutls30t64 libgprofng0 libibverbs1 libjemalloc2 67s libjson-glib-1.0-0 libjson-glib-1.0-common libldap-common libldap2 liblz4-1 67s liblzma5 libmm-glib0 libncurses6 libncursesw6 libnl-3-200 libnl-genl-3-200 67s libnl-route-3-200 libnss-systemd libpam-systemd libpci3 libpng16-16t64 67s libpython3-stdlib libpython3.13 libpython3.13-minimal libpython3.13-stdlib 67s libselinux1 libsframe1 libsqlite3-0 libssl3t64 libstdc++6 libsystemd-shared 67s libsystemd0 libtinfo6 libudev1 libxml2 libxmlb2 linux-firmware linux-generic 67s linux-headers-generic linux-headers-virtual linux-image-generic 67s linux-image-virtual linux-libc-dev linux-tools-common linux-virtual locales 67s media-types ncurses-base ncurses-bin ncurses-term openssl 67s openssl-provider-legacy pci.ids pciutils pinentry-curses python-apt-common 67s python3 python3-apt python3-cffi-backend python3-dbus python3-gdbm 67s python3-gi python3-jaraco.context python3-jinja2 python3-lazr.uri 67s python3-markupsafe python3-minimal python3-passlib python3-systemd 67s python3-urllib3 python3-yaml python3.13 python3.13-gdbm python3.13-minimal 67s rsync rsyslog strace systemd systemd-cryptsetup systemd-resolved 67s systemd-sysv systemd-timesyncd ubuntu-pro-client ubuntu-pro-client-l10n udev 67s xz-utils 67s 148 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 67s Need to get 841 MB of archives. 67s After this operation, 300 MB of additional disk space will be used. 67s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 diffutils amd64 1:3.10-3 [192 kB] 67s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 67s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 67s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-11.11 [1724 kB] 67s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250315-1ubuntu1 [10.4 kB] 67s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250315-1ubuntu1 [53.5 kB] 67s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250315-1ubuntu1 [77.7 kB] 67s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250315-1ubuntu1 [804 kB] 67s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 68s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 68s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 68s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 openssl-provider-legacy amd64 3.4.1-1ubuntu2 [39.0 kB] 68s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libssl3t64 amd64 3.4.1-1ubuntu2 [2334 kB] 68s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.4-1ubuntu1 [596 kB] 68s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.4-1ubuntu1 [199 kB] 68s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.4-1ubuntu1 [11.9 kB] 68s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.4-1ubuntu1 [345 kB] 68s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.4-1ubuntu1 [302 kB] 68s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.4-1ubuntu1 [2372 kB] 69s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.4-1ubuntu1 [3052 kB] 69s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.4-1ubuntu1 [42.1 kB] 69s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.4-1ubuntu1 [124 kB] 69s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.4-1ubuntu1 [1404 kB] 69s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.4-1ubuntu1 [216 kB] 69s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 dbus-session-bus-common all 1.16.2-2ubuntu1 [54.2 kB] 69s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 dbus-user-session amd64 1.16.2-2ubuntu1 [9692 B] 69s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu11 [55.2 kB] 69s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 69s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 69s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 69s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 69s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 dbus-system-bus-common all 1.16.2-2ubuntu1 [55.7 kB] 69s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 dbus-bin amd64 1.16.2-2ubuntu1 [46.5 kB] 69s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 dbus amd64 1.16.2-2ubuntu1 [24.8 kB] 69s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 dbus-daemon amd64 1.16.2-2ubuntu1 [123 kB] 69s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libdbus-1-3 amd64 1.16.2-2ubuntu1 [195 kB] 69s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.34 [1143 kB] 69s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 dpkg amd64 1.22.18ubuntu2 [1359 kB] 70s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 70s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 70s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 70s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 70s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.34 [1440 kB] 70s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.34 [222 kB] 70s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 70s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 70s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 70s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 70s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 70s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 70s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 70s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 70s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 71s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 71s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 71s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 71s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 71s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 cron amd64 3.0pl1-194ubuntu1 [93.9 kB] 71s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 71s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-base amd64 14.2.0-19ubuntu1 [53.9 kB] 71s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 dhcpcd-base amd64 1:10.1.0-8 [250 kB] 71s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.84.0-1 [25.3 kB] 71s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 71s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 72s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.84.0-1 [89.5 kB] 72s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libdw1t64 amd64 0.192-4ubuntu1 [277 kB] 72s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libelf1t64 amd64 0.192-4ubuntu1 [58.6 kB] 72s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 72s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 72s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libgnutls30t64 amd64 3.8.9-2ubuntu3 [1093 kB] 72s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 72s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 73s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 openssl amd64 3.4.1-1ubuntu2 [1189 kB] 73s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 73s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 73s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 73s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 73s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 73s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 73s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 73s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-pro-client-l10n amd64 35 [19.7 kB] 73s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-pro-client amd64 35 [257 kB] 73s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu11 [702 kB] 73s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 cron-daemon-common all 3.0pl1-194ubuntu1 [14.6 kB] 73s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 73s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-2 [12.2 kB] 73s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-2 [192 kB] 73s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-2 [64.9 kB] 73s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libibverbs1 amd64 56.0-3ubuntu1 [68.6 kB] 73s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 ibverbs-providers amd64 56.0-3ubuntu1 [388 kB] 73s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 73s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 73s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 73s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 libpng16-16t64 amd64 1.6.47-1.1 [217 kB] 73s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 73s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gdbm amd64 3.13.2-1 [8708 B] 73s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 73s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 73s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 73s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 73s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 73s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 74s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 74s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 74s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 74s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 74s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 74s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 74s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 74s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 74s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 libldap-common all 2.6.9+dfsg-2ubuntu1 [35.5 kB] 74s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 libldap2 amd64 2.6.9+dfsg-2ubuntu1 [212 kB] 74s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 74s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 74s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 dpkg-dev all 1.22.18ubuntu2 [1089 kB] 74s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libdpkg-perl all 1.22.18ubuntu2 [281 kB] 74s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 74s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 libjson-glib-1.0-common all 1.10.6+ds-2 [5698 B] 74s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 libjson-glib-1.0-0 amd64 1.10.6+ds-2 [73.4 kB] 74s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-7 [5408 kB] 75s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-7 [137 kB] 75s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 75s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 libxmlb2 amd64 0.3.22-1 [74.8 kB] 75s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc amd64 2.12-5ubuntu9 [137 kB] 75s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 grub2-common amd64 2.12-5ubuntu9 [674 kB] 75s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc-bin amd64 2.12-5ubuntu9 [1131 kB] 75s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-common amd64 2.12-5ubuntu9 [2115 kB] 76s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-efi-amd64-unsigned amd64 2.12-5ubuntu9 [1393 kB] 76s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-efi-amd64-signed amd64 1.211+2.12-5ubuntu9 [1395 kB] 76s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-efi-amd64-bin amd64 2.12-5ubuntu9 [783 kB] 76s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 76s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 76s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 76s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 76s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250317.git1d4c88ee-0ubuntu1 [573 MB] 135s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-11-generic amd64 6.14.0-11.11 [41.2 MB] 137s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-11-generic amd64 6.14.0-11.11 [15.3 MB] 138s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-11-generic amd64 6.14.0-11.11 [120 MB] 146s Get:139 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-11.11 [1730 B] 146s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-11.11 [11.2 kB] 146s Get:141 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-11.11 [1724 B] 146s Get:142 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-11.11 [11.1 kB] 146s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-11.11 [1646 B] 146s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-11 all 6.14.0-11.11 [14.2 MB] 150s Get:145 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-11-generic amd64 6.14.0-11.11 [3915 kB] 151s Get:146 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-11.11 [11.0 kB] 151s Get:147 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-11.11 [296 kB] 151s Get:148 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 151s Get:149 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jaraco.context all 6.0.1-1 [8272 B] 151s Get:150 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 151s Get:151 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 151s Get:152 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-urllib3 all 2.3.0-2 [94.1 kB] 151s Get:153 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-passlib all 1.7.4-6ubuntu1 [375 kB] 151s Get:154 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 151s Preconfiguring packages ... 152s Fetched 841 MB in 1min 24s (9970 kB/s) 152s (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 ... 109138 files and directories currently installed.) 152s Preparing to unpack .../diffutils_1%3a3.10-3_amd64.deb ... 152s Unpacking diffutils (1:3.10-3) over (1:3.10-2) ... 152s Setting up diffutils (1:3.10-3) ... 152s (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 ... 109138 files and directories currently installed.) 152s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 152s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 152s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 152s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 152s Preparing to unpack .../linux-libc-dev_6.14.0-11.11_amd64.deb ... 152s Unpacking linux-libc-dev:amd64 (6.14.0-11.11) over (6.12.0-16.16) ... 152s Preparing to unpack .../libatomic1_15-20250315-1ubuntu1_amd64.deb ... 152s Unpacking libatomic1:amd64 (15-20250315-1ubuntu1) over (15-20250222-0ubuntu1) ... 152s Preparing to unpack .../gcc-15-base_15-20250315-1ubuntu1_amd64.deb ... 152s Unpacking gcc-15-base:amd64 (15-20250315-1ubuntu1) over (15-20250222-0ubuntu1) ... 153s Setting up gcc-15-base:amd64 (15-20250315-1ubuntu1) ... 153s (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 ... 109143 files and directories currently installed.) 153s Preparing to unpack .../libgcc-s1_15-20250315-1ubuntu1_amd64.deb ... 153s Unpacking libgcc-s1:amd64 (15-20250315-1ubuntu1) over (15-20250222-0ubuntu1) ... 153s Setting up libgcc-s1:amd64 (15-20250315-1ubuntu1) ... 153s (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 ... 109143 files and directories currently installed.) 153s Preparing to unpack .../libstdc++6_15-20250315-1ubuntu1_amd64.deb ... 153s Unpacking libstdc++6:amd64 (15-20250315-1ubuntu1) over (15-20250222-0ubuntu1) ... 153s Setting up libstdc++6:amd64 (15-20250315-1ubuntu1) ... 153s (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 ... 109143 files and directories currently installed.) 153s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 153s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 153s Setting up libc6:amd64 (2.41-1ubuntu2) ... 153s (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 ... 109143 files and directories currently installed.) 153s Preparing to unpack .../liblz4-1_1.10.0-4_amd64.deb ... 153s Unpacking liblz4-1:amd64 (1.10.0-4) over (1.10.0-3) ... 153s Setting up liblz4-1:amd64 (1.10.0-4) ... 153s (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 ... 109143 files and directories currently installed.) 153s Preparing to unpack .../liblzma5_5.6.4-1_amd64.deb ... 153s Unpacking liblzma5:amd64 (5.6.4-1) over (5.6.3-1) ... 153s Setting up liblzma5:amd64 (5.6.4-1) ... 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 ... 109143 files and directories currently installed.) 154s Preparing to unpack .../openssl-provider-legacy_3.4.1-1ubuntu2_amd64.deb ... 154s Unpacking openssl-provider-legacy (3.4.1-1ubuntu2) over (3.4.1-1ubuntu1) ... 154s Setting up openssl-provider-legacy (3.4.1-1ubuntu2) ... 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 ... 109143 files and directories currently installed.) 154s Preparing to unpack .../libssl3t64_3.4.1-1ubuntu2_amd64.deb ... 154s Unpacking libssl3t64:amd64 (3.4.1-1ubuntu2) over (3.4.1-1ubuntu1) ... 154s Setting up libssl3t64:amd64 (3.4.1-1ubuntu2) ... 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 ... 109143 files and directories currently installed.) 154s Preparing to unpack .../libsystemd0_257.4-1ubuntu1_amd64.deb ... 154s Unpacking libsystemd0:amd64 (257.4-1ubuntu1) over (257.3-1ubuntu3) ... 154s Setting up libsystemd0:amd64 (257.4-1ubuntu1) ... 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 ... 109143 files and directories currently installed.) 154s Preparing to unpack .../libnss-systemd_257.4-1ubuntu1_amd64.deb ... 154s Unpacking libnss-systemd:amd64 (257.4-1ubuntu1) over (257.3-1ubuntu3) ... 154s Preparing to unpack .../systemd-sysv_257.4-1ubuntu1_amd64.deb ... 154s Unpacking systemd-sysv (257.4-1ubuntu1) over (257.3-1ubuntu3) ... 154s Preparing to unpack .../systemd-resolved_257.4-1ubuntu1_amd64.deb ... 154s Unpacking systemd-resolved (257.4-1ubuntu1) over (257.3-1ubuntu3) ... 154s Preparing to unpack .../libpam-systemd_257.4-1ubuntu1_amd64.deb ... 154s Unpacking libpam-systemd:amd64 (257.4-1ubuntu1) over (257.3-1ubuntu3) ... 154s Preparing to unpack .../libsystemd-shared_257.4-1ubuntu1_amd64.deb ... 154s Unpacking libsystemd-shared:amd64 (257.4-1ubuntu1) over (257.3-1ubuntu3) ... 154s Setting up libsystemd-shared:amd64 (257.4-1ubuntu1) ... 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 ... 109143 files and directories currently installed.) 154s Preparing to unpack .../systemd_257.4-1ubuntu1_amd64.deb ... 154s Unpacking systemd (257.4-1ubuntu1) over (257.3-1ubuntu3) ... 155s Preparing to unpack .../systemd-timesyncd_257.4-1ubuntu1_amd64.deb ... 155s Unpacking systemd-timesyncd (257.4-1ubuntu1) over (257.3-1ubuntu3) ... 155s Preparing to unpack .../systemd-cryptsetup_257.4-1ubuntu1_amd64.deb ... 155s Unpacking systemd-cryptsetup (257.4-1ubuntu1) over (257.3-1ubuntu3) ... 155s Preparing to unpack .../udev_257.4-1ubuntu1_amd64.deb ... 155s Unpacking udev (257.4-1ubuntu1) over (257.3-1ubuntu3) ... 155s Preparing to unpack .../libudev1_257.4-1ubuntu1_amd64.deb ... 155s Unpacking libudev1:amd64 (257.4-1ubuntu1) over (257.3-1ubuntu3) ... 155s Setting up libudev1:amd64 (257.4-1ubuntu1) ... 155s (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 ... 109143 files and directories currently installed.) 155s Preparing to unpack .../dbus-session-bus-common_1.16.2-2ubuntu1_all.deb ... 155s Unpacking dbus-session-bus-common (1.16.2-2ubuntu1) over (1.16.2-1ubuntu1) ... 155s Preparing to unpack .../dbus-user-session_1.16.2-2ubuntu1_amd64.deb ... 155s Unpacking dbus-user-session (1.16.2-2ubuntu1) over (1.16.2-1ubuntu1) ... 155s Preparing to unpack .../libapparmor1_4.1.0~beta5-0ubuntu11_amd64.deb ... 155s Unpacking libapparmor1:amd64 (4.1.0~beta5-0ubuntu11) over (4.1.0~beta5-0ubuntu6) ... 155s Preparing to unpack .../libaudit-common_1%3a4.0.2-2ubuntu2_all.deb ... 155s Unpacking libaudit-common (1:4.0.2-2ubuntu2) over (1:4.0.2-2ubuntu1) ... 155s Setting up libaudit-common (1:4.0.2-2ubuntu2) ... 155s (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 ... 109143 files and directories currently installed.) 155s Preparing to unpack .../libcap-ng0_0.8.5-4build1_amd64.deb ... 155s Unpacking libcap-ng0:amd64 (0.8.5-4build1) over (0.8.5-4) ... 155s Setting up libcap-ng0:amd64 (0.8.5-4build1) ... 155s (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 ... 109143 files and directories currently installed.) 155s Preparing to unpack .../libaudit1_1%3a4.0.2-2ubuntu2_amd64.deb ... 155s Unpacking libaudit1:amd64 (1:4.0.2-2ubuntu2) over (1:4.0.2-2ubuntu1) ... 155s Setting up libaudit1:amd64 (1:4.0.2-2ubuntu2) ... 155s (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 ... 109143 files and directories currently installed.) 155s Preparing to unpack .../libselinux1_3.7-3ubuntu3_amd64.deb ... 155s Unpacking libselinux1:amd64 (3.7-3ubuntu3) over (3.7-3ubuntu2) ... 155s Setting up libselinux1:amd64 (3.7-3ubuntu3) ... 155s (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 ... 109143 files and directories currently installed.) 155s Preparing to unpack .../0-dbus-system-bus-common_1.16.2-2ubuntu1_all.deb ... 155s Unpacking dbus-system-bus-common (1.16.2-2ubuntu1) over (1.16.2-1ubuntu1) ... 155s Preparing to unpack .../1-dbus-bin_1.16.2-2ubuntu1_amd64.deb ... 155s Unpacking dbus-bin (1.16.2-2ubuntu1) over (1.16.2-1ubuntu1) ... 155s Preparing to unpack .../2-dbus_1.16.2-2ubuntu1_amd64.deb ... 156s Unpacking dbus (1.16.2-2ubuntu1) over (1.16.2-1ubuntu1) ... 156s Preparing to unpack .../3-dbus-daemon_1.16.2-2ubuntu1_amd64.deb ... 156s Unpacking dbus-daemon (1.16.2-2ubuntu1) over (1.16.2-1ubuntu1) ... 156s Preparing to unpack .../4-libdbus-1-3_1.16.2-2ubuntu1_amd64.deb ... 156s Unpacking libdbus-1-3:amd64 (1.16.2-2ubuntu1) over (1.16.2-1ubuntu1) ... 156s Preparing to unpack .../5-libapt-pkg7.0_2.9.34_amd64.deb ... 156s Unpacking libapt-pkg7.0:amd64 (2.9.34) over (2.9.31ubuntu1) ... 156s Setting up libapt-pkg7.0:amd64 (2.9.34) ... 156s (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 ... 109143 files and directories currently installed.) 156s Preparing to unpack .../dpkg_1.22.18ubuntu2_amd64.deb ... 156s Unpacking dpkg (1.22.18ubuntu2) over (1.22.15ubuntu1) ... 156s Setting up dpkg (1.22.18ubuntu2) ... 156s (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 ... 109142 files and directories currently installed.) 156s Preparing to unpack .../ncurses-bin_6.5+20250216-2_amd64.deb ... 156s Unpacking ncurses-bin (6.5+20250216-2) over (6.5+20250216-1) ... 156s Setting up ncurses-bin (6.5+20250216-2) ... 156s (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 ... 109142 files and directories currently installed.) 156s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ... 156s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 157s Setting up libc-bin (2.41-1ubuntu2) ... 157s (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 ... 109142 files and directories currently installed.) 157s Preparing to unpack .../ncurses-base_6.5+20250216-2_all.deb ... 157s Unpacking ncurses-base (6.5+20250216-2) over (6.5+20250216-1) ... 157s Setting up ncurses-base (6.5+20250216-2) ... 157s (Reading database ... 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previously unselected package linux-image-6.14.0-11-generic. 169s Preparing to unpack .../085-linux-image-6.14.0-11-generic_6.14.0-11.11_amd64.deb ... 169s Unpacking linux-image-6.14.0-11-generic (6.14.0-11.11) ... 169s Selecting previously unselected package linux-modules-extra-6.14.0-11-generic. 169s Preparing to unpack .../086-linux-modules-extra-6.14.0-11-generic_6.14.0-11.11_amd64.deb ... 169s Unpacking linux-modules-extra-6.14.0-11-generic (6.14.0-11.11) ... 170s Preparing to unpack .../087-linux-generic_6.14.0-11.11_amd64.deb ... 170s Unpacking linux-generic (6.14.0-11.11) over (6.12.0-16.16+2) ... 170s Preparing to unpack .../088-linux-image-generic_6.14.0-11.11_amd64.deb ... 170s Unpacking linux-image-generic (6.14.0-11.11) over (6.12.0-16.16+2) ... 170s Preparing to unpack .../089-linux-virtual_6.14.0-11.11_amd64.deb ... 170s Unpacking linux-virtual (6.14.0-11.11) over (6.12.0-16.16+2) ... 170s Preparing to unpack .../090-linux-image-virtual_6.14.0-11.11_amd64.deb ... 170s 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Preparing to unpack .../096-pinentry-curses_1.3.1-2ubuntu3_amd64.deb ... 174s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 174s Preparing to unpack .../097-python3-jaraco.context_6.0.1-1_all.deb ... 174s Unpacking python3-jaraco.context (6.0.1-1) over (6.0.0-1) ... 174s Preparing to unpack .../098-python3-lazr.uri_1.0.6-6_all.deb ... 174s Unpacking python3-lazr.uri (1.0.6-6) over (1.0.6-5) ... 174s Preparing to unpack .../099-python3-systemd_235-1build6_amd64.deb ... 174s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 174s Preparing to unpack .../100-python3-urllib3_2.3.0-2_all.deb ... 174s Unpacking python3-urllib3 (2.3.0-2) over (2.3.0-1) ... 174s Preparing to unpack .../101-python3-passlib_1.7.4-6ubuntu1_all.deb ... 174s Unpacking python3-passlib (1.7.4-6ubuntu1) over (1.7.4-4) ... 174s Preparing to unpack .../102-cloud-init_25.1-0ubuntu3_all.deb ... 174s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 174s Setting up libgnutls30t64:amd64 (3.8.9-2ubuntu3) ... 174s Setting up media-types (13.0.0) ... 174s Installing new version of config file /etc/mime.types ... 174s Setting up linux-headers-6.14.0-11 (6.14.0-11.11) ... 174s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu11) ... 174s Setting up pci.ids (0.0~2025.03.09-1) ... 174s Setting up apt-utils (2.9.34) ... 174s Setting up gcc-14-base:amd64 (14.2.0-19ubuntu1) ... 174s Setting up linux-firmware (20250317.git1d4c88ee-0ubuntu1) ... 174s Setting up libestr0:amd64 (0.1.11-2) ... 174s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 174s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 174s Setting up dosfstools (4.2-1.2) ... 174s Setting up rsyslog (8.2412.0-2ubuntu2) ... 174s info: The user `syslog' is already a member of `adm'. 175s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 175s Setting up linux-libc-dev:amd64 (6.14.0-11.11) ... 175s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 175s Setting up systemd (257.4-1ubuntu1) ... 175s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 175s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 176s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 176s Setting up libjemalloc2:amd64 (5.3.0-3) ... 176s Setting up locales (2.41-1ubuntu2) ... 177s Generating locales (this might take a while)... 178s en_US.UTF-8... done 178s Generation complete. 178s Setting up libldap-common (2.6.9+dfsg-2ubuntu1) ... 178s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 178s Setting up libelf1t64:amd64 (0.192-4ubuntu1) ... 178s Setting up libdw1t64:amd64 (0.192-4ubuntu1) ... 178s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 178s Setting up apparmor (4.1.0~beta5-0ubuntu11) ... 178s Installing new version of config file /etc/apparmor.d/openvpn ... 179s Removing obsolete conffile /etc/apparmor.d/unshare-userns-restrict ... 179s Reloading AppArmor profiles 181s Setting up libglib2.0-data (2.84.0-1) ... 181s Setting up systemd-cryptsetup (257.4-1ubuntu1) ... 181s Setting up libncurses6:amd64 (6.5+20250216-2) ... 181s Setting up strace (6.13+ds-1ubuntu1) ... 181s Setting up libdbus-1-3:amd64 (1.16.2-2ubuntu1) ... 181s Setting up xz-utils (5.6.4-1) ... 181s Setting up libpng16-16t64:amd64 (1.6.47-1.1) ... 181s Setting up systemd-timesyncd (257.4-1ubuntu1) ... 181s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 181s Setting up libatomic1:amd64 (15-20250315-1ubuntu1) ... 181s Setting up udev (257.4-1ubuntu1) ... 182s Setting up dhcpcd-base (1:10.1.0-8) ... 182s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 182s Setting up libdpkg-perl (1.22.18ubuntu2) ... 182s Setting up linux-headers-6.14.0-11-generic (6.14.0-11.11) ... 182s Setting up libpci3:amd64 (1:3.13.0-2) ... 182s Setting up python-apt-common (2.9.9build1) ... 182s Setting up pnp.ids (0.393-3) ... 182s Setting up dbus-session-bus-common (1.16.2-2ubuntu1) ... 182s Setting up libnl-3-200:amd64 (3.7.0-2) ... 182s Setting up python3.13-minimal (3.13.2-2) ... 183s Setting up libjson-glib-1.0-common (1.10.6+ds-2) ... 183s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 183s Setting up dbus-system-bus-common (1.16.2-2ubuntu1) ... 183s Setting up libc-dev-bin (2.41-1ubuntu2) ... 183s Setting up openssl (3.4.1-1ubuntu2) ... 183s Installing new version of config file /etc/ssl/openssl.cnf ... 183s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 183s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 183s Setting up libldap2:amd64 (2.6.9+dfsg-2ubuntu1) ... 183s Setting up dbus-bin (1.16.2-2ubuntu1) ... 183s Setting up linux-modules-6.14.0-11-generic (6.14.0-11.11) ... 185s Setting up rsync (3.4.1+ds1-3) ... 186s rsync.service is a disabled or a static unit not running, not starting it. 186s Setting up python3.13-gdbm (3.13.2-2) ... 186s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 186s Setting up ncurses-term (6.5+20250216-2) ... 186s Setting up cron-daemon-common (3.0pl1-194ubuntu1) ... 186s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 186s Setting up libpython3.13:amd64 (3.13.2-2) ... 186s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 186s Setting up systemd-sysv (257.4-1ubuntu1) ... 186s Setting up linux-modules-extra-6.14.0-11-generic (6.14.0-11.11) ... 188s Setting up linux-image-6.14.0-11-generic (6.14.0-11.11) ... 190s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 190s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 190s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-11-generic 190s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-11-generic 190s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 190s Setting up python3.13 (3.13.2-2) ... 191s Setting up htop (3.4.0-2) ... 191s Setting up cron (3.0pl1-194ubuntu1) ... 191s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 191s Setting up libnss-systemd:amd64 (257.4-1ubuntu1) ... 191s Setting up python3 (3.13.2-2) ... 192s Setting up linux-headers-generic (6.14.0-11.11) ... 192s Setting up dbus-daemon (1.16.2-2ubuntu1) ... 192s Setting up python3-markupsafe (2.1.5-1build4) ... 192s Setting up libnl-route-3-200:amd64 (3.7.0-2) ... 192s Setting up hwdata (0.393-3) ... 192s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 192s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 192s No schema files found: doing nothing. 192s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 192s Setting up dbus (1.16.2-2ubuntu1) ... 192s A reboot is required to replace the running dbus-daemon. 192s Please reboot the system when convenient. 192s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 192s Setting up pciutils (1:3.13.0-2) ... 192s Setting up python3-urllib3 (2.3.0-2) ... 192s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 192s Setting up libnl-genl-3-200:amd64 (3.7.0-2) ... 192s Setting up libpam-systemd:amd64 (257.4-1ubuntu1) ... 192s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 192s Setting up libgirepository-1.0-1:amd64 (1.84.0-1) ... 192s Setting up curl (8.12.1-3ubuntu1) ... 192s Setting up linux-image-virtual (6.14.0-11.11) ... 192s Setting up linux-tools-common (6.14.0-11.11) ... 192s Setting up python3-systemd (235-1build6) ... 193s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 193s Setting up systemd-resolved (257.4-1ubuntu1) ... 193s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 193s Setting up linux-image-generic (6.14.0-11.11) ... 193s Setting up libibverbs1:amd64 (56.0-3ubuntu1) ... 193s Setting up python3-dbus (1.3.2-5build5) ... 193s Setting up linux-headers-virtual (6.14.0-11.11) ... 193s Setting up linux-generic (6.14.0-11.11) ... 193s Setting up python3-jaraco.context (6.0.1-1) ... 193s Setting up python3-passlib (1.7.4-6ubuntu1) ... 194s Setting up ibverbs-providers:amd64 (56.0-3ubuntu1) ... 194s Setting up python3-gdbm:amd64 (3.13.2-1) ... 194s Setting up python3-apt (2.9.9build1) ... 194s Setting up libxmlb2:amd64 (0.3.22-1) ... 194s Setting up python3-yaml (6.0.2-1build2) ... 194s Setting up python3-lazr.uri (1.0.6-6) ... 194s Setting up binutils (2.44-3ubuntu1) ... 194s Setting up cloud-init-base (25.1-0ubuntu3) ... 195s Setting up dpkg-dev (1.22.18ubuntu2) ... 195s Setting up libjson-glib-1.0-0:amd64 (1.10.6+ds-2) ... 195s Setting up linux-virtual (6.14.0-11.11) ... 195s Setting up grub-common (2.12-5ubuntu9) ... 195s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 196s Setting up dbus-user-session (1.16.2-2ubuntu1) ... 196s Setting up gir1.2-girepository-2.0:amd64 (1.84.0-1) ... 196s Setting up python3-gi (3.50.0-4build1) ... 196s Setting up ubuntu-pro-client (35) ... 196s Installing new version of config file /etc/apparmor.d/ubuntu_pro_apt_news ... 196s Installing new version of config file /etc/apt/apt.conf.d/20apt-esm-hook.conf ... 198s Setting up ubuntu-pro-client-l10n (35) ... 198s Setting up cloud-init (25.1-0ubuntu3) ... 198s Setting up grub-efi-amd64-unsigned (2.12-5ubuntu9) ... 198s Setting up grub2-common (2.12-5ubuntu9) ... 198s Setting up libfwupd3:amd64 (2.0.6-7) ... 198s Setting up grub-pc-bin (2.12-5ubuntu9) ... 198s Setting up grub-pc (2.12-5ubuntu9) ... 198s Installing for i386-pc platform. 199s Installation finished. No error reported. 199s Sourcing file `/etc/default/grub' 199s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 199s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 199s Generating grub configuration file ... 199s Found linux image: /boot/vmlinuz-6.14.0-11-generic 199s Found linux image: /boot/vmlinuz-6.12.0-16-generic 199s Found initrd image: /boot/initrd.img-6.12.0-16-generic 199s Found linux image: /boot/vmlinuz-6.11.0-8-generic 199s Found initrd image: /boot/initrd.img-6.11.0-8-generic 200s Warning: os-prober will not be executed to detect other bootable partitions. 200s Systems on them will not be added to the GRUB boot configuration. 200s Check GRUB_DISABLE_OS_PROBER documentation entry. 200s Adding boot menu entry for UEFI Firmware Settings ... 200s done 200s Setting up grub-efi-amd64-bin (2.12-5ubuntu9) ... 200s Setting up fwupd (2.0.6-7) ... 200s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 200s fwupd.service is a disabled or a static unit not running, not starting it. 200s Setting up grub-efi-amd64-signed (1.211+2.12-5ubuntu9) ... 200s Installing for x86_64-efi platform. 201s grub-install: warning: EFI variables cannot be set on this system. 201s grub-install: warning: You will have to complete the GRUB setup manually. 201s Installation finished. No error reported. 201s Processing triggers for man-db (2.13.0-1) ... 202s Processing triggers for shared-mime-info (2.4-5) ... 202s Warning: program compiled against libxml 212 using older 209 203s Processing triggers for install-info (7.1.1-1) ... 203s Processing triggers for initramfs-tools (0.146ubuntu1) ... 203s update-initramfs: Generating /boot/initrd.img-6.12.0-16-generic 203s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 213s Processing triggers for libc-bin (2.41-1ubuntu2) ... 213s Processing triggers for linux-image-6.14.0-11-generic (6.14.0-11.11) ... 213s /etc/kernel/postinst.d/initramfs-tools: 213s update-initramfs: Generating /boot/initrd.img-6.14.0-11-generic 213s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 223s /etc/kernel/postinst.d/zz-update-grub: 223s Sourcing file `/etc/default/grub' 223s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 223s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 223s Generating grub configuration file ... 223s Found linux image: /boot/vmlinuz-6.14.0-11-generic 223s Found initrd image: /boot/initrd.img-6.14.0-11-generic 224s Found linux image: /boot/vmlinuz-6.12.0-16-generic 224s Found initrd image: /boot/initrd.img-6.12.0-16-generic 224s Found linux image: /boot/vmlinuz-6.11.0-8-generic 224s Found initrd image: /boot/initrd.img-6.11.0-8-generic 224s Warning: os-prober will not be executed to detect other bootable partitions. 224s Systems on them will not be added to the GRUB boot configuration. 224s Check GRUB_DISABLE_OS_PROBER documentation entry. 224s Adding boot menu entry for UEFI Firmware Settings ... 224s done 225s Reading package lists... 226s Building dependency tree... 226s Reading state information... 226s Starting pkgProblemResolver with broken count: 0 226s Starting 2 pkgProblemResolver with broken count: 0 226s Done 226s Solving dependencies... 226s The following packages will be REMOVED: 226s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 226s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 226s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 226s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* python3.12-gdbm* 227s 0 upgraded, 0 newly installed, 12 to remove and 0 not upgraded. 227s After this operation, 225 MB disk space will be freed. 227s (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 ... 148584 files and directories currently installed.) 227s Removing libnl-genl-3-200:amd64 (3.7.0-2) ... 227s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 227s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 227s Removing libpython3.12t64:amd64 (3.12.9-1) ... 227s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 227s Removing libnsl2:amd64 (1.3.0-3build3) ... 227s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 227s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 228s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 229s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 230s /etc/kernel/postrm.d/initramfs-tools: 230s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 230s /etc/kernel/postrm.d/zz-update-grub: 230s Sourcing file `/etc/default/grub' 230s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 230s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 230s Generating grub configuration file ... 230s Found linux image: /boot/vmlinuz-6.14.0-11-generic 230s Found initrd image: /boot/initrd.img-6.14.0-11-generic 230s Found linux image: /boot/vmlinuz-6.12.0-16-generic 230s Found initrd image: /boot/initrd.img-6.12.0-16-generic 230s Warning: os-prober will not be executed to detect other bootable partitions. 230s Systems on them will not be added to the GRUB boot configuration. 230s Check GRUB_DISABLE_OS_PROBER documentation entry. 230s Adding boot menu entry for UEFI Firmware Settings ... 230s done 230s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 230s Removing python3.12-gdbm (3.12.9-1) ... 231s Processing triggers for libc-bin (2.41-1ubuntu2) ... 231s (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 ... 115746 files and directories currently installed.) 231s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 231s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 231s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 231s autopkgtest [13:09:53]: rebooting testbed after setup commands that affected boot 235s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 246s autopkgtest [13:10:08]: testbed running kernel: Linux 6.14.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Mon Mar 17 12:39:41 UTC 2025 247s autopkgtest [13:10:09]: @@@@@@@@@@@@@@@@@@@@ apt-source cctbx 250s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe cctbx 2024.10+ds2+~3.22.1+ds1-4build2 (dsc) [4106 B] 250s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe cctbx 2024.10+ds2+~3.22.1+ds1-4build2 (tar) [378 kB] 250s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe cctbx 2024.10+ds2+~3.22.1+ds1-4build2 (tar) [23.9 MB] 250s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe cctbx 2024.10+ds2+~3.22.1+ds1-4build2 (diff) [418 kB] 250s gpgv: Signature made Tue Mar 4 14:45:06 2025 UTC 250s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 250s gpgv: Can't check signature: No public key 250s dpkg-source: warning: cannot verify inline signature for ./cctbx_2024.10+ds2+~3.22.1+ds1-4build2.dsc: no acceptable signature found 252s autopkgtest [13:10:14]: testing package cctbx version 2024.10+ds2+~3.22.1+ds1-4build2 253s autopkgtest [13:10:15]: build not needed 255s autopkgtest [13:10:17]: test cctbx: preparing testbed 255s Reading package lists... 255s Building dependency tree... 255s Reading state information... 255s Starting pkgProblemResolver with broken count: 0 255s Starting 2 pkgProblemResolver with broken count: 0 255s Done 256s The following NEW packages will be installed: 256s adwaita-icon-theme at-spi2-common blt cpp cpp-14 cpp-14-x86-64-linux-gnu 256s cpp-x86-64-linux-gnu dconf-gsettings-backend dconf-service fontconfig 256s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 256s fonts-lato fonts-lyx g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu 256s gcc gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu 256s gtk-update-icon-cache hicolor-icon-theme libaec0 libann-cctbx-dev 256s libann-cctbx0 libantlr3c-3.4-0 libasan8 libatk-bridge2.0-0t64 libatk1.0-0t64 256s libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 256s libblas3 libboost-numpy1.83.0 libboost-python-dev libboost-python1.83-dev 256s libboost-python1.83.0 libboost-thread1.83.0 libboost-timer1.83.0 256s libboost1.83-dev libcairo-gobject2 libcairo2 libcbf1t64 libcc1-0 256s libccp4-data libccp4-dev libccp4c0t64 libccp4f0t64 libcctbx-dev libcctbx0 256s libcolord2 libcups2t64 libdatrie1 libdconf1 libdeflate0 256s libdouble-conversion3 libdrm-intel1 libegl-mesa0 libegl1 libepoxy0 256s libexpat1-dev libfontconfig1 libgbm1 libgcc-14-dev libgdk-pixbuf-2.0-0 256s libgdk-pixbuf2.0-common libgfortran5 libgl1 libgl1-mesa-dri libglew2.2 256s libglu1-mesa libglut3.12 libglvnd0 libglx-mesa0 libglx0 libgomp1 256s libgraphite2-3 libgtk-3-0t64 libgtk-3-common libharfbuzz0b libhdf5-310 256s libhdf5-hl-310 libhwasan0 libice6 libimagequant0 libinput-bin libinput10 256s libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 256s libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 256s liblcms2-2 liblerc4 liblsan0 liblzf1 libmd4c0 libmmdb2-0 libmpc3 256s libmtdev1t64 libnetcdf22 libnotify4 libopengl0 libopenjp2-7 libpango-1.0-0 256s libpangocairo-1.0-0 libpangoft2-1.0-0 libpciaccess0 libpcre2-16-0 256s libpcre2-32-0 libpixman-1-0 libpython3-dev libpython3.13-dev libqhull-r8.0 256s libqt5core5t64 libqt5dbus5t64 libqt5designer5 libqt5gui5t64 libqt5help5 256s libqt5network5t64 libqt5opengl5t64 libqt5printsupport5t64 libqt5sql5t64 256s libqt5test5t64 libqt5widgets5t64 libqt5xml5t64 libquadmath0 libraqm0 256s libsharpyuv0 libsm6 libssm2 libstdc++-14-dev libsz2 libtcl8.6 libthai-data 256s libthai0 libtiff6 libtk8.6 libtsan2 libubsan1 libvulkan1 libwacom-common 256s libwacom9 libwayland-client0 libwayland-cursor0 libwayland-egl1 256s libwayland-server0 libwebp7 libwebpdemux2 libwebpmux3 libwxbase3.2-1t64 256s libwxgtk-gl3.2-1t64 libwxgtk3.2-1t64 libx11-xcb1 libxcb-dri3-0 libxcb-glx0 256s libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present0 libxcb-randr0 256s libxcb-render-util0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 256s libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 256s libxcomposite1 libxcursor1 libxdamage1 libxfixes3 libxft2 libxi6 256s libxinerama1 libxkbcommon-x11-0 libxrandr2 libxrender1 libxshmfence1 256s libxslt1.1 libxss1 libxtst6 libxxf86vm1 mesa-libgallium pymol-data 256s python-matplotlib-data python3-all python3-brotli python3-cctbx 256s python3-contourpy python3-cycler python3-dateutil python3-decorator 256s python3-dev python3-flexcache python3-flexparser python3-fonttools 256s python3-fs python3-h5py python3-h5py-serial python3-hdf5plugin 256s python3-iniconfig python3-kiwisolver python3-legacy-cgi python3-lxml 256s python3-lz4 python3-matplotlib python3-mpmath python3-mrcfile 256s python3-natsort python3-numpy python3-numpy-dev python3-nxmx python3-opengl 256s python3-ordered-set python3-packaging python3-pil python3-pil.imagetk 256s python3-pint python3-platformdirs python3-pluggy python3-procrunner 256s python3-pycbf python3-pymol python3-pyqt5 python3-pyqt5.qtopengl 256s python3-pyqt5.sip python3-pytest python3-scipy python3-six python3-sympy 256s python3-tk python3-tqdm python3-ufolib2 python3-wxgtk4.0 python3.13-dev 256s python3.13-tk sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data x11-common 256s zlib1g-dev 256s 0 upgraded, 256 newly installed, 0 to remove and 0 not upgraded. 256s Need to get 262 MB of archives. 256s After this operation, 1199 MB of additional disk space will be used. 256s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-lato all 2.015-1 [2781 kB] 256s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-5 [148 kB] 256s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 256s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250315-1ubuntu1 [925 kB] 256s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 257s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:2.2.3+ds-5 [5702 kB] 257s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [8004 B] 257s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 257s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 257s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 257s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 257s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 257s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 257s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 257s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 257s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [161 kB] 257s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 gtk-update-icon-cache amd64 4.18.2+ds-1 [53.9 kB] 257s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 hicolor-icon-theme all 0.18-2 [13.3 kB] 257s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 adwaita-icon-theme all 48.0-1 [578 kB] 257s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 at-spi2-common all 2.56.0-2 [9108 B] 257s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 257s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 257s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 257s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2.1ubuntu1 [37.6 kB] 257s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2.1ubuntu1 [164 kB] 257s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 257s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 257s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 257s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 257s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 257s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [694 kB] 257s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-8 [4824 B] 257s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 257s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 257s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu1 [11.9 MB] 258s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-19ubuntu1 [1032 B] 258s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B] 258s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB] 258s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libdconf1 amd64 0.40.0-5 [39.8 kB] 258s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 dconf-service amd64 0.40.0-5 [28.4 kB] 258s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [22.7 kB] 258s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2.1ubuntu1 [180 kB] 258s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 258s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.3-1 [171 kB] 258s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 15-20250315-1ubuntu1 [46.9 kB] 258s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250315-1ubuntu1 [150 kB] 258s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 15-20250315-1ubuntu1 [29.3 kB] 258s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 15-20250315-1ubuntu1 [3075 kB] 258s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 15-20250315-1ubuntu1 [1362 kB] 258s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 15-20250315-1ubuntu1 [2760 kB] 258s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 15-20250315-1ubuntu1 [1211 kB] 258s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 15-20250315-1ubuntu1 [1687 kB] 258s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 15-20250315-1ubuntu1 [153 kB] 258s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-19ubuntu1 [2815 kB] 258s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu1 [23.3 MB] 259s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-19ubuntu1 [539 kB] 259s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B] 259s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B] 259s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-19ubuntu1 [2488 kB] 259s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu1 [13.3 MB] 259s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-19ubuntu1 [22.2 kB] 259s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B] 259s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B] 259s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 259s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 libann-cctbx0 amd64 1.1.2+doc-9build1 [32.7 kB] 259s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 libann-cctbx-dev amd64 1.1.2+doc-9build1 [45.1 kB] 259s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 libantlr3c-3.4-0 amd64 3.4+dfsg-4build2 [44.9 kB] 259s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libatk1.0-0t64 amd64 2.56.0-2 [55.4 kB] 259s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libxi6 amd64 2:1.8.2-1 [32.4 kB] 259s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libatspi2.0-0t64 amd64 2.56.0-2 [91.1 kB] 259s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libatk-bridge2.0-0t64 amd64 2.56.0-2 [69.0 kB] 259s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common-data amd64 0.8-16ubuntu2 [31.0 kB] 259s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common3 amd64 0.8-16ubuntu2 [23.6 kB] 259s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-client3 amd64 0.8-16ubuntu2 [27.5 kB] 259s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-python1.83.0 amd64 1.83.0-4.1ubuntu2 [314 kB] 259s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 libboost-numpy1.83.0 amd64 1.83.0-4.1ubuntu2 [243 kB] 259s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost1.83-dev amd64 1.83.0-4.1ubuntu2 [10.7 MB] 259s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1-dev amd64 2.6.4-1 [148 kB] 259s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 259s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-dev amd64 3.13.2-2 [5503 kB] 259s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-dev amd64 3.13.2-2 [10.7 kB] 259s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-dev amd64 3.13.2-2 [509 kB] 259s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 259s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 259s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 259s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dev amd64 3.13.2-2 [26.7 kB] 259s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 libboost-python1.83-dev amd64 1.83.0-4.1ubuntu2 [338 kB] 259s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 libboost-python-dev amd64 1.83.0.2ubuntu1 [4516 B] 259s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-thread1.83.0 amd64 1.83.0-4.1ubuntu2 [278 kB] 259s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 libboost-timer1.83.0 amd64 1.83.0-4.1ubuntu2 [241 kB] 259s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 259s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 259s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 259s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.4-1 [662 kB] 259s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo-gobject2 amd64 1.18.4-1 [127 kB] 259s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 259s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-310 amd64 1.14.5+repack-3 [1519 kB] 259s Get:98 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcbf1t64 amd64 0.9.7+dfsg1-5build1 [361 kB] 259s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccp4-data all 8.0.0-4 [65.2 kB] 259s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccp4c0t64 amd64 8.0.0-4 [104 kB] 259s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmmdb2-0 amd64 2.0.22-1 [363 kB] 259s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccp4f0t64 amd64 8.0.0-4 [228 kB] 260s Get:103 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccp4-dev amd64 8.0.0-4 [42.4 kB] 260s Get:104 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libcctbx0 amd64 2024.10+ds2+~3.22.1+ds1-4build2 [2077 kB] 260s Get:105 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libcctbx-dev amd64 2024.10+ds2+~3.22.1+ds1-4build2 [1192 kB] 260s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 260s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libcolord2 amd64 1.4.7-3 [155 kB] 260s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 libcups2t64 amd64 2.4.11-0ubuntu2 [292 kB] 260s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 260s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 libdouble-conversion3 amd64 3.3.1-1 [41.7 kB] 260s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 260s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 libdrm-intel1 amd64 2.4.123-1 [68.8 kB] 260s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-server0 amd64 1.23.1-3 [37.2 kB] 260s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [7944 B] 260s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-dri3-0 amd64 1.17.0-2 [7508 B] 260s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-present0 amd64 1.17.0-2 [6064 B] 260s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-randr0 amd64 1.17.0-2 [17.9 kB] 260s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-sync1 amd64 1.17.0-2 [9312 B] 260s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xfixes0 amd64 1.17.0-2 [10.2 kB] 260s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 libxshmfence1 amd64 1.3-1build5 [4764 B] 260s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 mesa-libgallium amd64 25.0.1-2ubuntu2 [12.1 MB] 260s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 libgbm1 amd64 25.0.1-2ubuntu2 [33.3 kB] 260s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-client0 amd64 1.23.1-3 [29.7 kB] 260s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 libegl-mesa0 amd64 25.0.1-2ubuntu2 [136 kB] 260s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 libepoxy0 amd64 1.5.10-2 [218 kB] 260s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 libvulkan1 amd64 1.4.304.0-1 [147 kB] 260s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 libgl1-mesa-dri amd64 25.0.1-2ubuntu2 [35.7 kB] 260s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 libglvnd0 amd64 1.7.0-1build1 [69.6 kB] 260s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-glx0 amd64 1.17.0-2 [24.8 kB] 260s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 libxxf86vm1 amd64 1:1.1.4-1build4 [9282 B] 260s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 libglx-mesa0 amd64 25.0.1-2ubuntu2 [146 kB] 260s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 libglx0 amd64 1.7.0-1build1 [38.6 kB] 260s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 libgl1 amd64 1.7.0-1build1 [102 kB] 260s Get:134 http://ftpmaster.internal/ubuntu plucky/universe amd64 libglew2.2 amd64 2.2.0-4build1 [187 kB] 260s Get:135 http://ftpmaster.internal/ubuntu plucky/universe amd64 libglut3.12 amd64 3.4.0-4 [111 kB] 260s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 260s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 260s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 260s Get:139 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 260s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.3-1 [256 kB] 260s Get:141 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.3-1 [52.9 kB] 260s Get:142 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.3-1 [29.1 kB] 260s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-cursor0 amd64 1.23.1-3 [10.9 kB] 260s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-egl1 amd64 1.23.1-3 [6168 B] 260s Get:145 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcomposite1 amd64 1:0.4.6-1 [6642 B] 260s Get:146 http://ftpmaster.internal/ubuntu plucky/main amd64 libxfixes3 amd64 1:6.0.0-2build1 [10.8 kB] 260s Get:147 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcursor1 amd64 1:1.2.3-1 [23.1 kB] 260s Get:148 http://ftpmaster.internal/ubuntu plucky/main amd64 libxdamage1 amd64 1:1.1.6-1build1 [6150 B] 260s Get:149 http://ftpmaster.internal/ubuntu plucky/main amd64 libxinerama1 amd64 2:1.1.4-3build1 [6396 B] 260s Get:150 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrandr2 amd64 2:1.5.4-1 [19.6 kB] 260s Get:151 http://ftpmaster.internal/ubuntu plucky/main amd64 libgtk-3-common all 3.24.49-2ubuntu1 [1424 kB] 260s Get:152 http://ftpmaster.internal/ubuntu plucky/main amd64 libgtk-3-0t64 amd64 3.24.49-2ubuntu1 [3172 kB] 260s Get:153 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [62.6 kB] 260s Get:154 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 260s Get:155 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 260s Get:156 http://ftpmaster.internal/ubuntu plucky/main amd64 libwacom-common all 2.14.0-1 [103 kB] 260s Get:157 http://ftpmaster.internal/ubuntu plucky/main amd64 libwacom9 amd64 2.14.0-1 [27.3 kB] 260s Get:158 http://ftpmaster.internal/ubuntu plucky/main amd64 libinput-bin amd64 1.27.1-1 [23.4 kB] 260s Get:159 http://ftpmaster.internal/ubuntu plucky/main amd64 libmtdev1t64 amd64 1.1.7-1 [16.3 kB] 260s Get:160 http://ftpmaster.internal/ubuntu plucky/main amd64 libinput10 amd64 1.27.1-1 [155 kB] 260s Get:161 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 260s Get:162 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 260s Get:163 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 260s Get:164 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmd4c0 amd64 0.5.2-2 [50.1 kB] 260s Get:165 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnetcdf22 amd64 1:4.9.3-1 [574 kB] 261s Get:166 http://ftpmaster.internal/ubuntu plucky/main amd64 libnotify4 amd64 0.8.4-1 [26.9 kB] 261s Get:167 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-16-0 amd64 10.45-1 [268 kB] 261s Get:168 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-32-0 amd64 10.45-1 [251 kB] 261s Get:169 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 261s Get:170 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5core5t64 amd64 5.15.15+dfsg-4ubuntu1 [2038 kB] 261s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5dbus5t64 amd64 5.15.15+dfsg-4ubuntu1 [221 kB] 261s Get:172 http://ftpmaster.internal/ubuntu plucky/main amd64 libegl1 amd64 1.7.0-1build1 [28.7 kB] 261s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5network5t64 amd64 5.15.15+dfsg-4ubuntu1 [725 kB] 261s Get:174 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 261s Get:175 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-icccm4 amd64 0.4.2-1 [11.1 kB] 261s Get:176 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-util1 amd64 0.4.1-1 [11.2 kB] 261s Get:177 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-image0 amd64 0.4.0-2build1 [10.8 kB] 261s Get:178 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-keysyms1 amd64 0.4.1-1 [8738 B] 261s Get:179 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render-util0 amd64 0.3.10-1 [10.8 kB] 261s Get:180 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shape0 amd64 1.17.0-2 [6092 B] 261s Get:181 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xinerama0 amd64 1.17.0-2 [5412 B] 261s Get:182 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xinput0 amd64 1.17.0-2 [33.2 kB] 261s Get:183 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xkb1 amd64 1.17.0-2 [32.3 kB] 261s Get:184 http://ftpmaster.internal/ubuntu plucky/main amd64 libxkbcommon-x11-0 amd64 1.7.0-2 [15.2 kB] 261s Get:185 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5gui5t64 amd64 5.15.15+dfsg-4ubuntu1 [3791 kB] 261s Get:186 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5widgets5t64 amd64 5.15.15+dfsg-4ubuntu1 [2560 kB] 261s Get:187 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5xml5t64 amd64 5.15.15+dfsg-4ubuntu1 [124 kB] 261s Get:188 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5designer5 amd64 5.15.15-6build1 [2827 kB] 261s Get:189 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5sql5t64 amd64 5.15.15+dfsg-4ubuntu1 [122 kB] 261s Get:190 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5help5 amd64 5.15.15-6build1 [162 kB] 261s Get:191 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5opengl5t64 amd64 5.15.15+dfsg-4ubuntu1 [150 kB] 261s Get:192 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5printsupport5t64 amd64 5.15.15+dfsg-4ubuntu1 [208 kB] 261s Get:193 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5test5t64 amd64 5.15.15+dfsg-4ubuntu1 [149 kB] 261s Get:194 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 261s Get:195 http://ftpmaster.internal/ubuntu plucky/universe amd64 libssm2 amd64 1.4.0-2build1 [87.7 kB] 261s Get:196 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 261s Get:197 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 261s Get:198 http://ftpmaster.internal/ubuntu plucky/universe amd64 libwxbase3.2-1t64 amd64 3.2.6+dfsg-2ubuntu1 [980 kB] 261s Get:199 http://ftpmaster.internal/ubuntu plucky/main amd64 libxtst6 amd64 2:1.2.5-1 [13.0 kB] 261s Get:200 http://ftpmaster.internal/ubuntu plucky/universe amd64 libwxgtk3.2-1t64 amd64 3.2.6+dfsg-2ubuntu1 [4967 kB] 261s Get:201 http://ftpmaster.internal/ubuntu plucky/universe amd64 libwxgtk-gl3.2-1t64 amd64 3.2.6+dfsg-2ubuntu1 [53.9 kB] 261s Get:202 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu4 [176 kB] 261s Get:203 http://ftpmaster.internal/ubuntu plucky/universe amd64 pymol-data all 3.1.0+dfsg-1 [1394 kB] 262s Get:204 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-7build1 [2934 kB] 262s Get:205 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.13.2-2 [884 B] 262s Get:206 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build4 [367 kB] 262s Get:207 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-legacy-cgi all 2.6.2-1 [16.6 kB] 262s Get:208 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pycbf amd64 0.9.7+dfsg1-5build1 [166 kB] 262s Get:209 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py-serial amd64 3.13.0-1 [1230 kB] 262s Get:210 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py all 3.13.0-1 [7978 B] 262s Get:211 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-hdf5plugin all 5.0.0-1 [23.1 kB] 262s Get:212 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-4 [80.3 kB] 262s Get:213 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.3-2 [218 kB] 262s Get:214 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 11.1.0-5build1 [583 kB] 262s Get:215 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.2-2 [107 kB] 262s Get:216 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.13.2-1 [9818 B] 262s Get:217 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 11.1.0-5build1 [9828 B] 262s Get:218 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.1-1build1 [218 kB] 262s Get:219 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 262s Get:220 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-platformdirs all 4.3.6-1 [16.8 kB] 262s Get:221 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-7 [90.8 kB] 262s Get:222 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.1-1build1 [1408 kB] 262s Get:223 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.4.0+dfsg-1build1 [27.0 kB] 262s Get:224 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 262s Get:225 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.14.1-4ubuntu2 [18.7 MB] 263s Get:226 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 263s Get:227 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-5 [4229 kB] 263s Get:228 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 263s Get:229 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 263s Get:230 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.55.3-2build1 [1536 kB] 263s Get:231 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-3build1 [55.6 kB] 263s Get:232 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 263s Get:233 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-7build1 [17.4 MB] 264s Get:234 http://ftpmaster.internal/ubuntu plucky/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 264s Get:235 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mrcfile all 1.5.4-2 [116 kB] 264s Get:236 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-natsort all 8.0.2-2 [33.8 kB] 264s Get:237 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-flexcache all 0.3-2 [13.4 kB] 264s Get:238 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-flexparser all 0.4-1 [43.8 kB] 264s Get:239 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pint all 0.24.4-1 [203 kB] 264s Get:240 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-nxmx all 0.0.4-1 [16.4 kB] 264s Get:241 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ordered-set all 4.1.0-1 [9778 B] 264s Get:242 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-procrunner all 2.3.3-2 [12.0 kB] 264s Get:243 http://ftpmaster.internal/ubuntu plucky/main amd64 libopengl0 amd64 1.7.0-1build1 [32.8 kB] 264s Get:244 http://ftpmaster.internal/ubuntu plucky/main amd64 libglu1-mesa amd64 9.0.2-1.1build1 [152 kB] 264s Get:245 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-opengl all 3.1.9+dfsg-1syncable1 [631 kB] 264s Get:246 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyqt5.sip amd64 12.17.0-1build1 [76.5 kB] 264s Get:247 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyqt5 amd64 5.15.11+dfsg-2 [2725 kB] 264s Get:248 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyqt5.qtopengl amd64 5.15.11+dfsg-2 [128 kB] 264s Get:249 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pymol amd64 3.1.0+dfsg-1 [4171 kB] 264s Get:250 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.17.0-1 [13.2 kB] 264s Get:251 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-tqdm all 4.67.1-2 [92.5 kB] 264s Get:252 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-wxgtk4.0 amd64 4.2.2+dfsg-3build1 [7838 kB] 264s Get:253 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-cctbx amd64 2024.10+ds2+~3.22.1+ds1-4build2 [29.0 MB] 265s Get:254 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 265s Get:255 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 265s Get:256 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.5-1 [252 kB] 266s Fetched 262 MB in 9s (28.2 MB/s) 266s Selecting previously unselected package fonts-lato. 266s (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 ... 115743 files and directories currently installed.) 266s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ... 266s Unpacking fonts-lato (2.015-1) ... 266s Selecting previously unselected package python3-numpy-dev:amd64. 266s Preparing to unpack .../001-python3-numpy-dev_1%3a2.2.3+ds-5_amd64.deb ... 266s Unpacking python3-numpy-dev:amd64 (1:2.2.3+ds-5) ... 266s Selecting previously unselected package libblas3:amd64. 266s Preparing to unpack .../002-libblas3_3.12.1-2_amd64.deb ... 266s Unpacking libblas3:amd64 (3.12.1-2) ... 266s Selecting previously unselected package libgfortran5:amd64. 266s Preparing to unpack .../003-libgfortran5_15-20250315-1ubuntu1_amd64.deb ... 266s Unpacking libgfortran5:amd64 (15-20250315-1ubuntu1) ... 266s Selecting previously unselected package liblapack3:amd64. 266s Preparing to unpack .../004-liblapack3_3.12.1-2_amd64.deb ... 266s Unpacking liblapack3:amd64 (3.12.1-2) ... 267s Selecting previously unselected package python3-numpy. 267s Preparing to unpack .../005-python3-numpy_1%3a2.2.3+ds-5_amd64.deb ... 267s Unpacking python3-numpy (1:2.2.3+ds-5) ... 267s Selecting previously unselected package libgdk-pixbuf2.0-common. 267s Preparing to unpack .../006-libgdk-pixbuf2.0-common_2.42.12+dfsg-2_all.deb ... 267s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... 267s Selecting previously unselected package libjpeg-turbo8:amd64. 267s Preparing to unpack .../007-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 267s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 267s Selecting previously unselected package libjpeg8:amd64. 267s Preparing to unpack .../008-libjpeg8_8c-2ubuntu11_amd64.deb ... 267s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 267s Selecting previously unselected package libdeflate0:amd64. 267s Preparing to unpack .../009-libdeflate0_1.23-1_amd64.deb ... 267s Unpacking libdeflate0:amd64 (1.23-1) ... 267s Selecting previously unselected package libjbig0:amd64. 267s Preparing to unpack .../010-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 267s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 267s Selecting previously unselected package liblerc4:amd64. 267s Preparing to unpack .../011-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 267s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 267s Selecting previously unselected package libsharpyuv0:amd64. 267s Preparing to unpack .../012-libsharpyuv0_1.5.0-0.1_amd64.deb ... 267s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 267s Selecting previously unselected package libwebp7:amd64. 267s Preparing to unpack .../013-libwebp7_1.5.0-0.1_amd64.deb ... 267s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 267s Selecting previously unselected package libtiff6:amd64. 267s Preparing to unpack .../014-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 267s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 267s Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. 267s Preparing to unpack .../015-libgdk-pixbuf-2.0-0_2.42.12+dfsg-2_amd64.deb ... 267s Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... 267s Selecting previously unselected package gtk-update-icon-cache. 267s Preparing to unpack .../016-gtk-update-icon-cache_4.18.2+ds-1_amd64.deb ... 267s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 267s 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. 267s Unpacking gtk-update-icon-cache (4.18.2+ds-1) ... 267s Selecting previously unselected package hicolor-icon-theme. 267s Preparing to unpack .../017-hicolor-icon-theme_0.18-2_all.deb ... 267s Unpacking hicolor-icon-theme (0.18-2) ... 267s Selecting previously unselected package adwaita-icon-theme. 267s Preparing to unpack .../018-adwaita-icon-theme_48.0-1_all.deb ... 267s Unpacking adwaita-icon-theme (48.0-1) ... 267s Selecting previously unselected package at-spi2-common. 267s Preparing to unpack .../019-at-spi2-common_2.56.0-2_all.deb ... 267s Unpacking at-spi2-common (2.56.0-2) ... 267s Selecting previously unselected package libtcl8.6:amd64. 267s Preparing to unpack .../020-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 267s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 267s Selecting previously unselected package fonts-dejavu-mono. 268s Preparing to unpack .../021-fonts-dejavu-mono_2.37-8_all.deb ... 268s 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(2.3.6-1build1) ... 268s Selecting previously unselected package x11-common. 268s Preparing to unpack .../027-x11-common_1%3a7.7+23ubuntu3_all.deb ... 268s Unpacking x11-common (1:7.7+23ubuntu3) ... 268s Selecting previously unselected package libxss1:amd64. 268s Preparing to unpack .../028-libxss1_1%3a1.2.3-1build3_amd64.deb ... 268s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 268s Selecting previously unselected package libtk8.6:amd64. 268s Preparing to unpack .../029-libtk8.6_8.6.16-1_amd64.deb ... 268s Unpacking libtk8.6:amd64 (8.6.16-1) ... 268s Selecting previously unselected package tk8.6-blt2.5. 268s Preparing to unpack .../030-tk8.6-blt2.5_2.5.3+dfsg-8_amd64.deb ... 268s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 268s Selecting previously unselected package blt. 268s Preparing to unpack .../031-blt_2.5.3+dfsg-8_amd64.deb ... 268s Unpacking blt (2.5.3+dfsg-8) ... 268s Selecting previously unselected package libisl23:amd64. 268s Preparing to unpack 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cpp (4:14.2.0-1ubuntu1) ... 269s Selecting previously unselected package libdconf1:amd64. 269s Preparing to unpack .../038-libdconf1_0.40.0-5_amd64.deb ... 269s Unpacking libdconf1:amd64 (0.40.0-5) ... 269s Selecting previously unselected package dconf-service. 269s Preparing to unpack .../039-dconf-service_0.40.0-5_amd64.deb ... 269s Unpacking dconf-service (0.40.0-5) ... 269s Selecting previously unselected package dconf-gsettings-backend:amd64. 269s Preparing to unpack .../040-dconf-gsettings-backend_0.40.0-5_amd64.deb ... 269s Unpacking dconf-gsettings-backend:amd64 (0.40.0-5) ... 269s Selecting previously unselected package fontconfig. 269s Preparing to unpack .../041-fontconfig_2.15.0-2.1ubuntu1_amd64.deb ... 269s Unpacking fontconfig (2.15.0-2.1ubuntu1) ... 269s Selecting previously unselected package fonts-font-awesome. 269s Preparing to unpack .../042-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 269s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 269s Selecting previously unselected package fonts-lyx. 269s Preparing to unpack .../043-fonts-lyx_2.4.3-1_all.deb ... 269s Unpacking fonts-lyx (2.4.3-1) ... 269s Selecting previously unselected package libcc1-0:amd64. 269s Preparing to unpack .../044-libcc1-0_15-20250315-1ubuntu1_amd64.deb ... 269s Unpacking libcc1-0:amd64 (15-20250315-1ubuntu1) ... 269s Selecting previously unselected package libgomp1:amd64. 269s Preparing to unpack .../045-libgomp1_15-20250315-1ubuntu1_amd64.deb ... 269s Unpacking libgomp1:amd64 (15-20250315-1ubuntu1) ... 269s Selecting previously unselected package libitm1:amd64. 269s Preparing to unpack .../046-libitm1_15-20250315-1ubuntu1_amd64.deb ... 269s Unpacking libitm1:amd64 (15-20250315-1ubuntu1) ... 269s Selecting previously unselected package libasan8:amd64. 269s Preparing to unpack .../047-libasan8_15-20250315-1ubuntu1_amd64.deb ... 269s Unpacking libasan8:amd64 (15-20250315-1ubuntu1) ... 269s Selecting previously unselected package liblsan0:amd64. 269s 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Preparing to unpack .../053-libgcc-14-dev_14.2.0-19ubuntu1_amd64.deb ... 269s Unpacking libgcc-14-dev:amd64 (14.2.0-19ubuntu1) ... 269s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 269s Preparing to unpack .../054-gcc-14-x86-64-linux-gnu_14.2.0-19ubuntu1_amd64.deb ... 269s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-19ubuntu1) ... 270s Selecting previously unselected package gcc-14. 270s Preparing to unpack .../055-gcc-14_14.2.0-19ubuntu1_amd64.deb ... 270s Unpacking gcc-14 (14.2.0-19ubuntu1) ... 270s Selecting previously unselected package gcc-x86-64-linux-gnu. 270s Preparing to unpack .../056-gcc-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 270s Unpacking gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 270s Selecting previously unselected package gcc. 270s Preparing to unpack .../057-gcc_4%3a14.2.0-1ubuntu1_amd64.deb ... 270s Unpacking gcc (4:14.2.0-1ubuntu1) ... 270s Selecting previously unselected package libstdc++-14-dev:amd64. 270s Preparing to unpack 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271s Unpacking libxi6:amd64 (2:1.8.2-1) ... 271s Selecting previously unselected package libatspi2.0-0t64:amd64. 271s Preparing to unpack .../069-libatspi2.0-0t64_2.56.0-2_amd64.deb ... 271s Unpacking libatspi2.0-0t64:amd64 (2.56.0-2) ... 271s Selecting previously unselected package libatk-bridge2.0-0t64:amd64. 271s Preparing to unpack .../070-libatk-bridge2.0-0t64_2.56.0-2_amd64.deb ... 271s Unpacking libatk-bridge2.0-0t64:amd64 (2.56.0-2) ... 271s Selecting previously unselected package libavahi-common-data:amd64. 271s Preparing to unpack .../071-libavahi-common-data_0.8-16ubuntu2_amd64.deb ... 271s Unpacking libavahi-common-data:amd64 (0.8-16ubuntu2) ... 271s Selecting previously unselected package libavahi-common3:amd64. 271s Preparing to unpack .../072-libavahi-common3_0.8-16ubuntu2_amd64.deb ... 271s Unpacking libavahi-common3:amd64 (0.8-16ubuntu2) ... 271s Selecting previously unselected package libavahi-client3:amd64. 271s Preparing to unpack .../073-libavahi-client3_0.8-16ubuntu2_amd64.deb ... 271s Unpacking libavahi-client3:amd64 (0.8-16ubuntu2) ... 271s Selecting previously unselected package libboost-python1.83.0. 271s Preparing to unpack .../074-libboost-python1.83.0_1.83.0-4.1ubuntu2_amd64.deb ... 271s Unpacking libboost-python1.83.0 (1.83.0-4.1ubuntu2) ... 271s Selecting previously unselected package libboost-numpy1.83.0. 271s Preparing to unpack .../075-libboost-numpy1.83.0_1.83.0-4.1ubuntu2_amd64.deb ... 271s Unpacking libboost-numpy1.83.0 (1.83.0-4.1ubuntu2) ... 271s Selecting previously unselected package libboost1.83-dev:amd64. 271s Preparing to unpack .../076-libboost1.83-dev_1.83.0-4.1ubuntu2_amd64.deb ... 271s Unpacking libboost1.83-dev:amd64 (1.83.0-4.1ubuntu2) ... 273s Selecting previously unselected package libexpat1-dev:amd64. 273s Preparing to unpack .../077-libexpat1-dev_2.6.4-1_amd64.deb ... 273s Unpacking libexpat1-dev:amd64 (2.6.4-1) ... 273s Selecting previously unselected package zlib1g-dev:amd64. 273s Preparing to unpack .../078-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ... 273s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 273s Selecting previously unselected package libpython3.13-dev:amd64. 273s Preparing to unpack .../079-libpython3.13-dev_3.13.2-2_amd64.deb ... 273s Unpacking libpython3.13-dev:amd64 (3.13.2-2) ... 273s Selecting previously unselected package libpython3-dev:amd64. 273s Preparing to unpack .../080-libpython3-dev_3.13.2-2_amd64.deb ... 273s Unpacking libpython3-dev:amd64 (3.13.2-2) ... 273s Selecting previously unselected package python3.13-dev. 273s Preparing to unpack .../081-python3.13-dev_3.13.2-2_amd64.deb ... 273s Unpacking python3.13-dev (3.13.2-2) ... 273s Selecting previously unselected package libjs-jquery. 273s Preparing to unpack .../082-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 273s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 273s Selecting previously unselected package libjs-underscore. 273s Preparing to unpack .../083-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 273s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 273s Selecting previously unselected package libjs-sphinxdoc. 273s Preparing to unpack .../084-libjs-sphinxdoc_8.1.3-5_all.deb ... 273s Unpacking libjs-sphinxdoc (8.1.3-5) ... 273s Selecting previously unselected package python3-dev. 273s Preparing to unpack .../085-python3-dev_3.13.2-2_amd64.deb ... 273s Unpacking python3-dev (3.13.2-2) ... 273s Selecting previously unselected package libboost-python1.83-dev. 273s Preparing to unpack .../086-libboost-python1.83-dev_1.83.0-4.1ubuntu2_amd64.deb ... 273s Unpacking libboost-python1.83-dev (1.83.0-4.1ubuntu2) ... 273s Selecting previously unselected package libboost-python-dev. 273s Preparing to unpack .../087-libboost-python-dev_1.83.0.2ubuntu1_amd64.deb ... 273s Unpacking libboost-python-dev (1.83.0.2ubuntu1) ... 273s Selecting previously unselected package libboost-thread1.83.0:amd64. 273s Preparing to unpack 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.../093-libcairo2_1.18.4-1_amd64.deb ... 274s Unpacking libcairo2:amd64 (1.18.4-1) ... 274s Selecting previously unselected package libcairo-gobject2:amd64. 274s Preparing to unpack .../094-libcairo-gobject2_1.18.4-1_amd64.deb ... 274s Unpacking libcairo-gobject2:amd64 (1.18.4-1) ... 274s Selecting previously unselected package libsz2:amd64. 274s Preparing to unpack .../095-libsz2_1.1.3-1_amd64.deb ... 274s Unpacking libsz2:amd64 (1.1.3-1) ... 274s Selecting previously unselected package libhdf5-310:amd64. 274s Preparing to unpack .../096-libhdf5-310_1.14.5+repack-3_amd64.deb ... 274s Unpacking libhdf5-310:amd64 (1.14.5+repack-3) ... 274s Selecting previously unselected package libcbf1t64:amd64. 274s Preparing to unpack .../097-libcbf1t64_0.9.7+dfsg1-5build1_amd64.deb ... 274s Unpacking libcbf1t64:amd64 (0.9.7+dfsg1-5build1) ... 274s Selecting previously unselected package libccp4-data. 274s Preparing to unpack .../098-libccp4-data_8.0.0-4_all.deb ... 274s Unpacking libccp4-data (8.0.0-4) ... 274s Selecting previously unselected package libccp4c0t64:amd64. 274s Preparing to unpack .../099-libccp4c0t64_8.0.0-4_amd64.deb ... 274s Unpacking libccp4c0t64:amd64 (8.0.0-4) ... 274s Selecting previously unselected package libmmdb2-0:amd64. 274s Preparing to unpack .../100-libmmdb2-0_2.0.22-1_amd64.deb ... 274s Unpacking libmmdb2-0:amd64 (2.0.22-1) ... 274s Selecting previously unselected package libccp4f0t64:amd64. 274s Preparing to unpack .../101-libccp4f0t64_8.0.0-4_amd64.deb ... 274s Unpacking libccp4f0t64:amd64 (8.0.0-4) ... 274s Selecting previously unselected package libccp4-dev:amd64. 274s Preparing to unpack .../102-libccp4-dev_8.0.0-4_amd64.deb ... 274s Unpacking libccp4-dev:amd64 (8.0.0-4) ... 274s Selecting previously unselected package libcctbx0. 274s Preparing to unpack .../103-libcctbx0_2024.10+ds2+~3.22.1+ds1-4build2_amd64.deb ... 274s Unpacking libcctbx0 (2024.10+ds2+~3.22.1+ds1-4build2) ... 274s Selecting previously unselected package libcctbx-dev. 274s Preparing to unpack .../104-libcctbx-dev_2024.10+ds2+~3.22.1+ds1-4build2_amd64.deb ... 274s Unpacking libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4build2) ... 274s Selecting previously unselected package liblcms2-2:amd64. 274s Preparing to unpack .../105-liblcms2-2_2.16-2_amd64.deb ... 274s Unpacking liblcms2-2:amd64 (2.16-2) ... 274s Selecting previously unselected package libcolord2:amd64. 274s Preparing to unpack .../106-libcolord2_1.4.7-3_amd64.deb ... 274s Unpacking libcolord2:amd64 (1.4.7-3) ... 274s Selecting previously unselected package libcups2t64:amd64. 274s Preparing to unpack .../107-libcups2t64_2.4.11-0ubuntu2_amd64.deb ... 274s Unpacking libcups2t64:amd64 (2.4.11-0ubuntu2) ... 274s Selecting previously unselected package libdatrie1:amd64. 274s Preparing to unpack .../108-libdatrie1_0.2.13-3build1_amd64.deb ... 274s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 274s Selecting previously unselected package libdouble-conversion3:amd64. 274s Preparing to unpack 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libxshmfence1:amd64 (1.3-1build5) ... 275s Selecting previously unselected package mesa-libgallium:amd64. 275s Preparing to unpack .../120-mesa-libgallium_25.0.1-2ubuntu2_amd64.deb ... 275s Unpacking mesa-libgallium:amd64 (25.0.1-2ubuntu2) ... 275s Selecting previously unselected package libgbm1:amd64. 275s Preparing to unpack .../121-libgbm1_25.0.1-2ubuntu2_amd64.deb ... 275s Unpacking libgbm1:amd64 (25.0.1-2ubuntu2) ... 275s Selecting previously unselected package libwayland-client0:amd64. 275s Preparing to unpack .../122-libwayland-client0_1.23.1-3_amd64.deb ... 275s Unpacking libwayland-client0:amd64 (1.23.1-3) ... 275s Selecting previously unselected package libegl-mesa0:amd64. 275s Preparing to unpack .../123-libegl-mesa0_25.0.1-2ubuntu2_amd64.deb ... 275s Unpacking libegl-mesa0:amd64 (25.0.1-2ubuntu2) ... 275s Selecting previously unselected package libepoxy0:amd64. 275s Preparing to unpack .../124-libepoxy0_1.5.10-2_amd64.deb ... 275s Unpacking libepoxy0:amd64 (1.5.10-2) ... 275s Selecting previously unselected package libvulkan1:amd64. 275s Preparing to unpack .../125-libvulkan1_1.4.304.0-1_amd64.deb ... 275s Unpacking libvulkan1:amd64 (1.4.304.0-1) ... 275s Selecting previously unselected package libgl1-mesa-dri:amd64. 275s Preparing to unpack .../126-libgl1-mesa-dri_25.0.1-2ubuntu2_amd64.deb ... 275s Unpacking libgl1-mesa-dri:amd64 (25.0.1-2ubuntu2) ... 275s Selecting previously unselected package libglvnd0:amd64. 275s Preparing to unpack .../127-libglvnd0_1.7.0-1build1_amd64.deb ... 275s Unpacking libglvnd0:amd64 (1.7.0-1build1) ... 275s Selecting previously unselected package libxcb-glx0:amd64. 275s Preparing to unpack .../128-libxcb-glx0_1.17.0-2_amd64.deb ... 275s Unpacking libxcb-glx0:amd64 (1.17.0-2) ... 275s Selecting previously unselected package libxxf86vm1:amd64. 275s Preparing to unpack .../129-libxxf86vm1_1%3a1.1.4-1build4_amd64.deb ... 275s Unpacking libxxf86vm1:amd64 (1:1.1.4-1build4) ... 275s Selecting previously unselected package libglx-mesa0:amd64. 275s Preparing to unpack .../130-libglx-mesa0_25.0.1-2ubuntu2_amd64.deb ... 275s Unpacking libglx-mesa0:amd64 (25.0.1-2ubuntu2) ... 276s Selecting previously unselected package libglx0:amd64. 276s Preparing to unpack .../131-libglx0_1.7.0-1build1_amd64.deb ... 276s Unpacking libglx0:amd64 (1.7.0-1build1) ... 276s Selecting previously unselected package libgl1:amd64. 276s Preparing to unpack .../132-libgl1_1.7.0-1build1_amd64.deb ... 276s Unpacking libgl1:amd64 (1.7.0-1build1) ... 276s Selecting previously unselected package libglew2.2:amd64. 276s Preparing to unpack .../133-libglew2.2_2.2.0-4build1_amd64.deb ... 276s Unpacking libglew2.2:amd64 (2.2.0-4build1) ... 276s Selecting previously unselected package libglut3.12:amd64. 276s Preparing to unpack .../134-libglut3.12_3.4.0-4_amd64.deb ... 276s Unpacking libglut3.12:amd64 (3.4.0-4) ... 276s Selecting previously unselected package libgraphite2-3:amd64. 276s Preparing to unpack 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Selecting previously unselected package libgtk-3-0t64:amd64. 276s Preparing to unpack .../151-libgtk-3-0t64_3.24.49-2ubuntu1_amd64.deb ... 276s Unpacking libgtk-3-0t64:amd64 (3.24.49-2ubuntu1) ... 276s Selecting previously unselected package libhdf5-hl-310:amd64. 276s Preparing to unpack .../152-libhdf5-hl-310_1.14.5+repack-3_amd64.deb ... 276s Unpacking libhdf5-hl-310:amd64 (1.14.5+repack-3) ... 276s Selecting previously unselected package libice6:amd64. 276s Preparing to unpack .../153-libice6_2%3a1.1.1-1_amd64.deb ... 276s Unpacking libice6:amd64 (2:1.1.1-1) ... 277s Selecting previously unselected package libimagequant0:amd64. 277s Preparing to unpack .../154-libimagequant0_2.18.0-1build1_amd64.deb ... 277s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 277s Selecting previously unselected package libwacom-common. 277s Preparing to unpack .../155-libwacom-common_2.14.0-1_all.deb ... 277s Unpacking libwacom-common (2.14.0-1) ... 277s Selecting previously unselected package libwacom9:amd64. 277s Preparing to unpack .../156-libwacom9_2.14.0-1_amd64.deb ... 277s Unpacking libwacom9:amd64 (2.14.0-1) ... 277s Selecting previously unselected package libinput-bin. 277s Preparing to unpack .../157-libinput-bin_1.27.1-1_amd64.deb ... 277s Unpacking libinput-bin (1.27.1-1) ... 277s Selecting previously unselected package libmtdev1t64:amd64. 277s Preparing to unpack .../158-libmtdev1t64_1.1.7-1_amd64.deb ... 277s Unpacking libmtdev1t64:amd64 (1.1.7-1) ... 277s Selecting previously unselected package libinput10:amd64. 277s Preparing to unpack .../159-libinput10_1.27.1-1_amd64.deb ... 277s Unpacking libinput10:amd64 (1.27.1-1) ... 277s Selecting previously unselected package libjs-jquery-ui. 277s Preparing to unpack .../160-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 277s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 277s Selecting previously unselected package liblbfgsb0:amd64. 277s Preparing to unpack .../161-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 277s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 277s Selecting previously unselected package liblzf1:amd64. 277s Preparing to unpack .../162-liblzf1_3.6-4_amd64.deb ... 277s Unpacking liblzf1:amd64 (3.6-4) ... 277s Selecting previously unselected package libmd4c0:amd64. 277s Preparing to unpack .../163-libmd4c0_0.5.2-2_amd64.deb ... 277s Unpacking libmd4c0:amd64 (0.5.2-2) ... 277s Selecting previously unselected package libnetcdf22:amd64. 277s Preparing to unpack .../164-libnetcdf22_1%3a4.9.3-1_amd64.deb ... 277s Unpacking libnetcdf22:amd64 (1:4.9.3-1) ... 277s Selecting previously unselected package libnotify4:amd64. 277s Preparing to unpack .../165-libnotify4_0.8.4-1_amd64.deb ... 277s Unpacking libnotify4:amd64 (0.8.4-1) ... 277s Selecting previously unselected package libpcre2-16-0:amd64. 277s Preparing to unpack .../166-libpcre2-16-0_10.45-1_amd64.deb ... 277s Unpacking libpcre2-16-0:amd64 (10.45-1) ... 277s Selecting previously unselected package libpcre2-32-0:amd64. 277s Preparing to unpack .../167-libpcre2-32-0_10.45-1_amd64.deb ... 277s Unpacking libpcre2-32-0:amd64 (10.45-1) ... 277s Selecting previously unselected package libqhull-r8.0:amd64. 277s Preparing to unpack .../168-libqhull-r8.0_2020.2-6build1_amd64.deb ... 277s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 277s Selecting previously unselected package libqt5core5t64:amd64. 277s Preparing to unpack .../169-libqt5core5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 277s Unpacking libqt5core5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 277s Selecting previously unselected package libqt5dbus5t64:amd64. 277s Preparing to unpack .../170-libqt5dbus5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 277s Unpacking libqt5dbus5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 277s Selecting previously unselected package libegl1:amd64. 277s Preparing to unpack .../171-libegl1_1.7.0-1build1_amd64.deb ... 277s Unpacking libegl1:amd64 (1.7.0-1build1) ... 277s Selecting previously unselected package libqt5network5t64:amd64. 277s Preparing to unpack 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... 278s Selecting previously unselected package libxkbcommon-x11-0:amd64. 278s Preparing to unpack .../183-libxkbcommon-x11-0_1.7.0-2_amd64.deb ... 278s Unpacking libxkbcommon-x11-0:amd64 (1.7.0-2) ... 278s Selecting previously unselected package libqt5gui5t64:amd64. 278s Preparing to unpack .../184-libqt5gui5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 278s Unpacking libqt5gui5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 278s Selecting previously unselected package libqt5widgets5t64:amd64. 278s Preparing to unpack .../185-libqt5widgets5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 278s Unpacking libqt5widgets5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 278s Selecting previously unselected package libqt5xml5t64:amd64. 278s Preparing to unpack .../186-libqt5xml5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 278s Unpacking libqt5xml5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 278s Selecting previously unselected package libqt5designer5:amd64. 278s Preparing to unpack .../187-libqt5designer5_5.15.15-6build1_amd64.deb ... 278s Unpacking libqt5designer5:amd64 (5.15.15-6build1) ... 278s Selecting previously unselected package libqt5sql5t64:amd64. 278s Preparing to unpack .../188-libqt5sql5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 278s Unpacking libqt5sql5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 278s Selecting previously unselected package libqt5help5:amd64. 278s Preparing to unpack .../189-libqt5help5_5.15.15-6build1_amd64.deb ... 278s Unpacking libqt5help5:amd64 (5.15.15-6build1) ... 278s Selecting previously unselected package libqt5opengl5t64:amd64. 278s Preparing to unpack .../190-libqt5opengl5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 278s Unpacking libqt5opengl5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 278s Selecting previously unselected package libqt5printsupport5t64:amd64. 278s Preparing to unpack .../191-libqt5printsupport5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 278s Unpacking libqt5printsupport5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 278s Selecting previously unselected package libqt5test5t64:amd64. 278s 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.../197-libwxbase3.2-1t64_3.2.6+dfsg-2ubuntu1_amd64.deb ... 279s Unpacking libwxbase3.2-1t64:amd64 (3.2.6+dfsg-2ubuntu1) ... 279s Selecting previously unselected package libxtst6:amd64. 279s Preparing to unpack .../198-libxtst6_2%3a1.2.5-1_amd64.deb ... 279s Unpacking libxtst6:amd64 (2:1.2.5-1) ... 279s Selecting previously unselected package libwxgtk3.2-1t64:amd64. 279s Preparing to unpack .../199-libwxgtk3.2-1t64_3.2.6+dfsg-2ubuntu1_amd64.deb ... 279s Unpacking libwxgtk3.2-1t64:amd64 (3.2.6+dfsg-2ubuntu1) ... 279s Selecting previously unselected package libwxgtk-gl3.2-1t64:amd64. 279s Preparing to unpack .../200-libwxgtk-gl3.2-1t64_3.2.6+dfsg-2ubuntu1_amd64.deb ... 279s Unpacking libwxgtk-gl3.2-1t64:amd64 (3.2.6+dfsg-2ubuntu1) ... 279s Selecting previously unselected package libxslt1.1:amd64. 279s Preparing to unpack .../201-libxslt1.1_1.1.39-0exp1ubuntu4_amd64.deb ... 279s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu4) ... 279s Selecting previously unselected package pymol-data. 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unselected package python3-pil:amd64. 279s Preparing to unpack .../213-python3-pil_11.1.0-5build1_amd64.deb ... 279s Unpacking python3-pil:amd64 (11.1.0-5build1) ... 279s Selecting previously unselected package python3.13-tk. 279s Preparing to unpack .../214-python3.13-tk_3.13.2-2_amd64.deb ... 279s Unpacking python3.13-tk (3.13.2-2) ... 279s Selecting previously unselected package python3-tk:amd64. 280s Preparing to unpack .../215-python3-tk_3.13.2-1_amd64.deb ... 280s Unpacking python3-tk:amd64 (3.13.2-1) ... 280s Selecting previously unselected package python3-pil.imagetk:amd64. 280s Preparing to unpack .../216-python3-pil.imagetk_11.1.0-5build1_amd64.deb ... 280s Unpacking python3-pil.imagetk:amd64 (11.1.0-5build1) ... 280s Selecting previously unselected package python3-contourpy. 280s Preparing to unpack .../217-python3-contourpy_1.3.1-1build1_amd64.deb ... 280s Unpacking python3-contourpy (1.3.1-1build1) ... 280s Selecting previously unselected package python3-cycler. 280s 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285s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 285s Setting up libboost-python1.83.0 (1.83.0-4.1ubuntu2) ... 285s Setting up libxcb-dri3-0:amd64 (1.17.0-2) ... 285s Setting up liblcms2-2:amd64 (2.16-2) ... 285s Setting up python3-iniconfig (1.1.1-2) ... 285s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 285s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 285s Setting up libwayland-server0:amd64 (1.23.1-3) ... 285s Setting up libx11-xcb1:amd64 (2:1.8.10-2) ... 285s Setting up libpciaccess0:amd64 (0.17-3build1) ... 285s Setting up libdouble-conversion3:amd64 (3.3.1-1) ... 285s Setting up fonts-lato (2.015-1) ... 285s Setting up libxdamage1:amd64 (1:1.1.6-1build1) ... 285s Setting up libxcb-xfixes0:amd64 (1.17.0-2) ... 285s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 285s Setting up libantlr3c-3.4-0:amd64 (3.4+dfsg-4build2) ... 285s Setting up hicolor-icon-theme (0.18-2) ... 285s Setting up libxi6:amd64 (2:1.8.2-1) ... 285s Setting up libxcb-xinput0:amd64 (1.17.0-2) ... 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up libavahi-common-data:amd64 (0.8-16ubuntu2) ... 287s Setting up libatspi2.0-0t64:amd64 (2.56.0-2) ... 287s Setting up liblzf1:amd64 (3.6-4) ... 287s Setting up libquadmath0:amd64 (15-20250315-1ubuntu1) ... 287s Setting up python3-cycler (0.12.1-1) ... 287s Setting up libxinerama1:amd64 (2:1.1.4-3build1) ... 287s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 287s Setting up pymol-data (3.1.0+dfsg-1) ... 287s Setting up libxkbcommon-x11-0:amd64 (1.7.0-2) ... 287s Setting up fonts-dejavu-mono (2.37-8) ... 287s Setting up python3-kiwisolver (1.4.7-3build1) ... 287s Setting up libmpc3:amd64 (1.3.1-1build2) ... 287s Setting up python3-numpy-dev:amd64 (1:2.2.3+ds-5) ... 287s Setting up libxrandr2:amd64 (2:1.5.4-1) ... 287s Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... 287s Setting up fonts-dejavu-core (2.37-8) ... 287s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 287s Setting up libgfortran5:amd64 (15-20250315-1ubuntu1) ... 287s Setting up libvulkan1:amd64 (1.4.304.0-1) ... 287s Setting up python3-pluggy (1.5.0-1) ... 287s Setting up libwebp7:amd64 (1.5.0-0.1) ... 287s Setting up libubsan1:amd64 (15-20250315-1ubuntu1) ... 287s Setting up python3-legacy-cgi (2.6.2-1) ... 287s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 287s Setting up python3-pyqt5.sip (12.17.0-1build1) ... 287s Setting up libmtdev1t64:amd64 (1.1.7-1) ... 287s Setting up libxshmfence1:amd64 (1.3-1build5) ... 287s Setting up libhwasan0:amd64 (15-20250315-1ubuntu1) ... 287s Setting up at-spi2-common (2.56.0-2) ... 287s Setting up libccp4c0t64:amd64 (8.0.0-4) ... 287s Setting up libxcb-randr0:amd64 (1.17.0-2) ... 287s Setting up libasan8:amd64 (15-20250315-1ubuntu1) ... 287s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu4) ... 287s Setting up libqt5sql5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 287s Setting up libmd4c0:amd64 (0.5.2-2) ... 287s Setting up libopenjp2-7:amd64 (2.5.3-2) ... 287s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 287s Setting up libthai-data 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288s Setting up libsz2:amd64 (1.1.3-1) ... 288s Setting up libitm1:amd64 (15-20250315-1ubuntu1) ... 288s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 288s Setting up libann-cctbx-dev (1.1.2+doc-9build1) ... 288s Setting up libwacom-common (2.14.0-1) ... 288s Setting up libwayland-client0:amd64 (1.23.1-3) ... 288s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 288s Setting up python3-sympy (1.13.3-5) ... 293s Setting up libice6:amd64 (2:1.1.1-1) ... 293s Setting up mesa-libgallium:amd64 (25.0.1-2ubuntu2) ... 293s Setting up liblapack3:amd64 (3.12.1-2) ... 293s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 293s Setting up libqt5dbus5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 293s Setting up libssm2:amd64 (1.4.0-2build1) ... 293s Setting up libatk1.0-0t64:amd64 (2.56.0-2) ... 293s Setting up libgbm1:amd64 (25.0.1-2ubuntu2) ... 293s Setting up libwacom9:amd64 (2.14.0-1) ... 293s Setting up fontconfig-config (2.15.0-2.1ubuntu1) ... 293s Setting up python3-pytest (8.3.5-1) ... 294s Setting up libxtst6:amd64 (2:1.2.5-1) ... 294s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 294s Setting up libxcursor1:amd64 (1:1.2.3-1) ... 294s Setting up libgl1-mesa-dri:amd64 (25.0.1-2ubuntu2) ... 294s Setting up libqt5network5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 294s Setting up libavahi-common3:amd64 (0.8-16ubuntu2) ... 294s Setting up libqt5xml5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 294s Setting up dconf-service (0.40.0-5) ... 294s Setting up libqt5test5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 294s Setting up libccp4f0t64:amd64 (8.0.0-4) ... 294s Setting up libinput-bin (1.27.1-1) ... 294s Setting up python3-pint (0.24.4-1) ... 294s Setting up libthai0:amd64 (0.1.29-2build1) ... 294s Setting up libegl-mesa0:amd64 (25.0.1-2ubuntu2) ... 294s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 294s Setting up libraqm0:amd64 (0.10.2-1) ... 294s Setting up libpython3.13-dev:amd64 (3.13.2-2) ... 294s Setting up cpp-14-x86-64-linux-gnu (14.2.0-19ubuntu1) ... 294s Setting up python3-numpy (1:2.2.3+ds-5) ... 296s Setting up libjs-sphinxdoc (8.1.3-5) ... 296s Setting up cpp-14 (14.2.0-19ubuntu1) ... 296s Setting up libhdf5-310:amd64 (1.14.5+repack-3) ... 296s Setting up python3-lxml:amd64 (5.3.1-1build1) ... 296s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 296s Setting up libwayland-cursor0:amd64 (1.23.1-3) ... 296s Setting up libegl1:amd64 (1.7.0-1build1) ... 296s Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... 296s Setting up python3-contourpy (1.3.1-1build1) ... 296s Setting up libfontconfig1:amd64 (2.15.0-2.1ubuntu1) ... 296s Setting up libgcc-14-dev:amd64 (14.2.0-19ubuntu1) ... 296s Setting up libstdc++-14-dev:amd64 (14.2.0-19ubuntu1) ... 296s Setting up libsm6:amd64 (2:1.2.4-1) ... 296s Setting up libavahi-client3:amd64 (0.8-16ubuntu2) ... 296s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 296s Setting up python3-mrcfile (1.5.4-2) ... 296s Setting up cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 296s Setting up libatk-bridge2.0-0t64:amd64 (2.56.0-2) ... 296s Setting up libinput10:amd64 (1.27.1-1) ... 296s Setting up gtk-update-icon-cache (4.18.2+ds-1) ... 296s Setting up libhdf5-hl-310:amd64 (1.14.5+repack-3) ... 296s Setting up fontconfig (2.15.0-2.1ubuntu1) ... 298s Regenerating fonts cache... done. 298s Setting up libxft2:amd64 (2.3.6-1build1) ... 298s Setting up libboost1.83-dev:amd64 (1.83.0-4.1ubuntu2) ... 298s Setting up libglx-mesa0:amd64 (25.0.1-2ubuntu2) ... 298s Setting up python3-scipy (1.14.1-4ubuntu2) ... 301s Setting up libpython3-dev:amd64 (3.13.2-2) ... 301s Setting up libcbf1t64:amd64 (0.9.7+dfsg1-5build1) ... 301s Setting up libglx0:amd64 (1.7.0-1build1) ... 301s Setting up dconf-gsettings-backend:amd64 (0.40.0-5) ... 301s Setting up libccp4-dev:amd64 (8.0.0-4) ... 301s Setting up python3.13-dev (3.13.2-2) ... 301s Setting up libtk8.6:amd64 (8.6.16-1) ... 301s Setting up libpango-1.0-0:amd64 (1.56.3-1) ... 301s Setting up libnetcdf22:amd64 (1:4.9.3-1) ... 301s Setting up python3-h5py-serial (3.13.0-1) ... 301s Setting up libcairo2:amd64 (1.18.4-1) ... 301s Setting up python3.13-tk (3.13.2-2) ... 301s Setting up python3-pil:amd64 (11.1.0-5build1) ... 302s Setting up libgl1:amd64 (1.7.0-1build1) ... 302s Setting up adwaita-icon-theme (48.0-1) ... 302s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 302s Setting up libglut3.12:amd64 (3.4.0-4) ... 302s Setting up libnotify4:amd64 (0.8.4-1) ... 302s Setting up python3-dev (3.13.2-2) ... 302s Setting up libboost-python1.83-dev (1.83.0-4.1ubuntu2) ... 302s Setting up python3-pycbf (0.9.7+dfsg1-5build1) ... 302s Setting up python3-h5py (3.13.0-1) ... 302s Setting up libglew2.2:amd64 (2.2.0-4build1) ... 302s Setting up python3-hdf5plugin (5.0.0-1) ... 302s Setting up cpp (4:14.2.0-1ubuntu1) ... 302s Setting up libcairo-gobject2:amd64 (1.18.4-1) ... 302s Setting up gcc-14-x86-64-linux-gnu (14.2.0-19ubuntu1) ... 302s Setting up libpangoft2-1.0-0:amd64 (1.56.3-1) ... 302s Setting up python3-nxmx (0.0.4-1) ... 302s Setting up libcups2t64:amd64 (2.4.11-0ubuntu2) ... 302s Setting up libgtk-3-common (3.24.49-2ubuntu1) ... 302s Setting up libpangocairo-1.0-0:amd64 (1.56.3-1) ... 302s Setting up libcctbx0 (2024.10+ds2+~3.22.1+ds1-4build2) ... 302s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 302s Setting up gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 302s Setting up blt (2.5.3+dfsg-8) ... 302s Setting up python3-tk:amd64 (3.13.2-1) ... 302s Setting up python3-opengl (3.1.9+dfsg-1syncable1) ... 302s /usr/lib/python3/dist-packages/OpenGL/GL/AMD/vertex_shader_tessellator.py:30: SyntaxWarning: invalid escape sequence '\ ' 302s |\ |\ 304s Setting up gcc-14 (14.2.0-19ubuntu1) ... 304s Setting up libboost-python-dev (1.83.0.2ubuntu1) ... 304s Setting up libqt5gui5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 304s Setting up python3-pil.imagetk:amd64 (11.1.0-5build1) ... 304s Setting up g++-14-x86-64-linux-gnu (14.2.0-19ubuntu1) ... 304s Setting up g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 304s Setting up g++-14 (14.2.0-19ubuntu1) ... 304s Setting up libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4build2) ... 304s Setting up libqt5widgets5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 304s Setting up libqt5help5:amd64 (5.15.15-6build1) ... 304s Setting up gcc (4:14.2.0-1ubuntu1) ... 304s Setting up g++ (4:14.2.0-1ubuntu1) ... 304s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 304s Setting up libqt5opengl5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 304s Setting up libqt5printsupport5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 304s Setting up libqt5designer5:amd64 (5.15.15-6build1) ... 304s Setting up python3-pyqt5 (5.15.11+dfsg-2) ... 304s Setting up python3-pyqt5.qtopengl (5.15.11+dfsg-2) ... 304s Setting up python3-pymol (3.1.0+dfsg-1) ... 304s Setting up python3-fonttools (4.55.3-2build1) ... 305s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 305s Setting up python3-matplotlib (3.8.3-7build1) ... 307s Processing triggers for libc-bin (2.41-1ubuntu2) ... 307s Processing triggers for man-db (2.13.0-1) ... 308s Processing triggers for libglib2.0-0t64:amd64 (2.84.0-1) ... 308s Setting up libgtk-3-0t64:amd64 (3.24.49-2ubuntu1) ... 308s Processing triggers for udev (257.4-1ubuntu1) ... 309s Setting up libwxgtk3.2-1t64:amd64 (3.2.6+dfsg-2ubuntu1) ... 309s Setting up libwxgtk-gl3.2-1t64:amd64 (3.2.6+dfsg-2ubuntu1) ... 309s Setting up python3-wxgtk4.0 (4.2.2+dfsg-3build1) ... 310s Setting up python3-cctbx (2024.10+ds2+~3.22.1+ds1-4build2) ... 312s /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:18: SyntaxWarning: invalid escape sequence '\{' 312s []_,.;:"&<>()/\{}'`~!@#$%*|+- 312s /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:46: SyntaxWarning: invalid escape sequence '\/' 312s special_characters = """[]_,.;:"&<>()\/\{}'`~!@#$%*|+-""" 322s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:724: SyntaxWarning: invalid escape sequence '\o' 322s width=pairwise_differences_db, label='$\omega_{hkl}$' 322s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:739: SyntaxWarning: invalid escape sequence '\o' 322s axes[0].set_ylabel('Distribution of $\omega_{hbk}$') 322s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:740: SyntaxWarning: invalid escape sequence '\o' 322s axes[0].set_xlabel('Normalized PD ($\omega_{hbk}$)') 322s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:759: SyntaxWarning: invalid escape sequence '\o' 322s axes[1].set_xlabel('Sorted Normalized PD ($\omega_{hbk}$)') 322s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:778: SyntaxWarning: invalid escape sequence '\s' 322s axes[2].set_ylabel('Standard Deviation of $I_{hbk}/\sigma_{hbk}$') 322s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:807: SyntaxWarning: invalid escape sequence '\m' 322s axes_sadd.set_ylabel('$s_{\mathrm{fac}}^2 \\times s_{\mathrm{add}}^2$') 322s Processing triggers for libc-bin (2.41-1ubuntu2) ... 323s autopkgtest [13:11:25]: test cctbx: [----------------------- 323s Testing cctbx with python3.13: 323s Running 546 tests on 2 processors: 323s libtbx.python "/usr/lib/python3/dist-packages/annlib_adaptbx/annlib_adaptbx/sample.py" 323s libtbx.python "/usr/lib/python3/dist-packages/annlib_adaptbx/annlib_adaptbx/self_match.py" 323s "/usr/lib/cctbx/python3.13/boost_adaptbx/tests/tst_optional_copy" 323s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_libc_backtrace.py" 323s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_rational.py" 323s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_optional.py" 323s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_std_pair.py" 323s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_tuple.py" 323s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_stdout.py" 323s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_stderr_stdout.py" 323s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_deprecation_tools.py" 323s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_python_streambuf.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sf_low_res_accuracy.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_double_step_filtration.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_is_periodic.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_reindexing.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_map_to_asu_isym.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_data_manipulation.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_bfgs.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_dev.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry/tests/tst_geometry.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/covariance/tests/tst_covariance.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_goodness_of_symmetry.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_from_map.py" P312 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_aniso_restraints.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/math/boost_python/tst_math.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_targets_fd.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_xray.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray.py" I41/acd 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_r1.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_shelxl_wght_ls.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_f_model.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/array_family/boost_python/tst_flex.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_uctbx.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_crystal_orientation.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_sgtbx.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_N_fold_rot.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_ext.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_distance_based_connectivity.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_super_cell.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adptbx/boost_python/tst_adptbx.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/boost_python/tst_miller.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_chemical_elements.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_xray_scattering.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_henke.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_icsd_radii.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_covalent_radii.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_neutron.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_sasaki.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_tiny_pse.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_wavelengths.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_formula.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_attenuation_coefficient.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/boost_python/tst_maptbx.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_bcr.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_loft.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/dmtbx/boost_python/tst_dmtbx.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/translation_search/boost_python/tst_translation_search.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_ext.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_proxy_registry.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_nonbonded_overlaps.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_process_nonbonded_proxies.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_angle_derivs.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_motif.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adp_restraints/tst_ext.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_math_module.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_krivy_gruber.py" --Quick 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_itvb_2001_table_a1427_hall_symbols.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_space_group_type_tidy_cb_op_t.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_denominators.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_subgroups.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_lattice_symmetry.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints.py" P3 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints_cartesian.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_site_constraints.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reflection_statistics.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_harker.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_special_op_simplifier.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_twin_target.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/symbol_confidence.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/bravais_types.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_lookup_utils.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal.py" I41/acd 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_direct_space_asu.py" I41/acd 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pair_asu_table.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_asu_clusters.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_coordination_sequences.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_close_packing.py" R-3mr 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fourier_transform_real_part_at_x.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem_2.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reciprocal_space_asu.py" P312 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_triplet_generator.py" P41 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_emma.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_expand_to_p1.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_change_basis.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wilson_plot.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_derivatives.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_fast_gradients.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F_sq P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_structure_factors.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_weights_for_symmetry_summation.py" Pmmm 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_real_space_refinement_simple.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation_2.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_loc_res.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_target_and_gradients.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_merge_equivalents.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grouped_data.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_fft_map.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sampled_model_density.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fast_nv1995.py" F222 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_lbfgs.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_2.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grm_pickling.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_french_wilson.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/make_cns_input.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/tst_cns_epsilon.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/tst_cns_hl.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/run_shelx76.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pointgroup_tools.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/sub_lattice_tools.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/rational_matrices_point_groups.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/cosets.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_pg_tools.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_twin_laws.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_find_best_cell.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_amplitude_normalisation.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_statistics_graphs.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_web_change_basis.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/direct_space_asu/proto/tst_asu.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_tidy_pickling.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/masks/tests/tst_flood_fill.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_r_free_utils.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/observations/tst_observations.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_ccp.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_mask.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_map_peak_3d_as_2d.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_asymmetric_map.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_peak_volume_estimate.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_resolution_from_map_and_model.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_curves.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_radius_as_central_peak_width.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_get_percentile_cutoffs.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_box.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_create_models_or_maps.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sphericity.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_statistics.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/merging/brehm_diederichs.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/multipolar/regression/tst_multipolar.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity_allsym.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grm_modifications.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_prepare_map_for_docking.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wavelength_units.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fcalc_fft_stability.py" 323s libtbx.python "/usr/lib/python3/dist-packages/cma_es/tst_cma_es.py" 323s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_ext.py" 323s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_equivalence.py" 323s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_read.py" 323s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_cout.py" 323s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_show_calls.py" 323s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_command_line.py" 323s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_separate_files.py" 323s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_cout_compile.py" stop 323s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_io.py" 323s libtbx.python "/usr/lib/python3/dist-packages/gltbx/tst_ellipsoids.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mrc_io.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_wildcard.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/gui_tools/tst.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_parser.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phil.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_cif_inputs.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_manager.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager_wrapping.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_2.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_3.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_4.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_model_sharpening_5.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_model_sharpening_5_cif.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_call_consistency.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_external_sharpening_7.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_half_map_sharpening_6.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_tls_from_map_8.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_cif.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry_cif.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_local_resolution_10.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_tools.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_patterson.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_restraints_merge.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_atom_selections_10k.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/ranges.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_crystal_symmetry_from_any.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_poscar.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/kriber/tst_strudat.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_geometry.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_lex_parse_build.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_restraints.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_parser.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_citations.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model_builder.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_lex_parse_build.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_hklf.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_writer.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_fvar_encoding.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_pdb.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy_2.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_tls.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/hybrid_36.py" exercise 323s "/usr/lib/cctbx/python3.13/iotbx/pdb/hybrid_36_fem" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy_atom_sort.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy_flip_symmetric.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_selected_hierarchy_flip.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_ext.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_rna_dna_atom_names.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_name_interpretation.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_extract_rfactors_resolutions_sigma.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/modified_aa_names.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/modified_rna_dna_names.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_sheet.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation_long.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/secondary_structure.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection_string.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_secondary_structure.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_utils.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_secondary_structure_2.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/remediation/tst_remediator.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_to_map_simple.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_truncate_to_ala/tst.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_tardy_conf_sampling_simple.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_examples.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/space_group_symbols.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/tst_cns.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_merge.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/no_merge_original_index.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/ccp4_map/tst.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_ext.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_extract_from_symmetry_lib.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_dano.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_miller_dict.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_unmerged.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/tst_mtz_free_flipper.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_utils.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_adsc.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_detectors.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xplor/tst_xplormap.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phases.py" P31 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdbx_mmcif_tutorial.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_statistics.py" Fdd2 P31m 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_plots.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_csv_utils.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_file_reader.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_bioinformatics.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_segids.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_input.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_forward_compatible_pdb.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_multimodel.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_add_conformations.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_symmetry.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reindex.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_editor.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_as_fasta.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_link_records.py" 323s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_merging_statistics.py" 323s libtbx.python 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"/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_func_free_line_search.py" 323s "/usr/lib/cctbx/python3.13/scitbx/lbfgs/tst_lbfgs" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgsb/boost_python/tst_lbfgsb.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/fftpack/boost_python/tst_fftpack.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_grid.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_array_loops.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/principal_axes_of_inertia.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_recipe.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_linear_least_squares_fit.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/chebyshev_lsq_example.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/immoptibox_ports.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/rigid_body_refinement_core.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/integrating_a_weighted_sinc_function.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/minimizer_comparisons.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_utils.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/rigidity.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_rigidity.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/rigidity_matrix_symbolic.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree_find_paths.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/test_cases_tardy_pdb.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_basic.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_tardy.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_energy_plots.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/tst.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/free_motion_reference_impl.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_featherstone.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion_hard.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_joint_lib.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_singular.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_spherical_refinement.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_molecules.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_sparse.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_lu_factorization.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/iso_surface/tst_iso_surface.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/simplex.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/differential_evolution.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/golden_section_search.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/direct_search_simulated_annealing.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/random/tests/tst_random.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/tst_normal_equations.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/test_problems.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/glmtbx/tests/tst.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_basic.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_booth.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_twisted.py" 323s libtbx.python "/usr/lib/python3/dist-packages/scitbx/suffixtree/test/tst_single.py" 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/absolute_structure/tests/tst_absolute_structure.py" --fix_random_seeds 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/ab_initio/tests/tst_ab_initio_ext.py" 323s 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" 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/masks/tests/tst_masks.py" 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/structure_factors/direct/tests/tst_standard_xray.py" 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_weighting_schemes.py" --fix_random_seeds 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_lbfgs.py" 323s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_reparametrisation" 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_occupancies.py" 323s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens" 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_same_group.py" 323s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_special_position" 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_reparametrisation.py" 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=naive 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_disorder.py" 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=levenberg-marquardt 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_rigid.py" 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_direction.py" 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_adp_restraints.py" 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_manager.py" 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_restraints.py" --verbose --scatterers=5 --resolution=0.2 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_refine.py" 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py" 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/tests/tst_utils.py" 323s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_least_squares.py" 323s libtbx.python "/usr/lib/python3/dist-packages/rstbx/dps_core/tst_iotbx_converter.py" 323s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_predict.py" 323s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_ewald_sphere.py" 323s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_partial_derivatives.py" 323s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/fastbragg/tst_bragg_minimal.py" 323s libtbx.python "/usr/lib/python3/dist-packages/rstbx/sublattice_support/tst_sublattice.py" 323s libtbx.python -c "from rstbx.run_tests import run; run()" 323s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/core_toolbox/boost_python/tst_small_image.py" 323s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/diffraction/geometry.py" 323s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/math_support/sphere_formulae.py" 323s 323s libtbx.python "/usr/lib/python3/dist-packages/annlib_adaptbx/annlib_adaptbx/self_match.py" [OK] 0.2s 323s Time: 0.18 323s Return code: 0 323s OKs: 1 323s Standard out: 323s OK 323s "/usr/lib/cctbx/python3.13/boost_adaptbx/tests/tst_optional_copy" [OK] 0.0s 323s Time: 0.01 323s Return code: 0 323s OKs: 1 323s Standard out: 323s OK 323s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_libc_backtrace.py" [OK] 0.1s 323s Time: 0.06 323s Return code: 0 323s OKs: 1 323s Standard out: 323s OK 323s Standard error: 323s show_stack(1): /usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_libc_backtrace.py(9) run 323s show_stack(2): /usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_libc_backtrace.py(15) 323s libc backtrace (20 frames, most recent call last): 323s /usr/bin/python3.13(_start+0x25) [0x648645] 323s /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b) [0x78288142a3fb] 323s /lib/x86_64-linux-gnu/libc.so.6(+0x2a338) [0x78288142a338] 323s /usr/bin/python3.13(Py_BytesMain+0x2d) [0x6492cd] 323s /usr/bin/python3.13(Py_RunMain+0x3ea) [0x68e86a] 323s /usr/bin/python3.13() [0x68faa5] 323s /usr/bin/python3.13() [0x68fc65] 323s /usr/bin/python3.13() [0x690384] 323s /usr/bin/python3.13() [0x67685e] 323s /usr/bin/python3.13() [0x67b092] 323s /usr/bin/python3.13(PyEval_EvalCode+0xcd) [0x659ced] 323s /usr/bin/python3.13(_PyEval_EvalFrameDefault+0x33ee) [0x56580e] 323s /usr/bin/python3.13(_PyObject_MakeTpCall+0x283) [0x548e33] 323s /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0(+0x23a0e) [0x782880ae5a0e] 323s /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0(boost::python::handle_exception_impl(boost::function0)+0x7b) [0x782880ae590b] 323s /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0(+0x276c4) [0x782880ae96c4] 323s /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0(boost::python::objects::function::call(_object*, _object*) const+0x94) [0x782880ae9244] 323s /usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-313-x86_64-linux-gnu.so(+0x19972) [0x782881333972] 323s /usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-313-x86_64-linux-gnu.so(+0x219ec) [0x78288133b9ec] 323s /usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-313-x86_64-linux-gnu.so(+0x2157a) [0x78288133b57a] 323s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_rational.py" [OK] 0.1s 323s Time: 0.11 323s Return code: 0 323s OKs: 1 323s Standard out: 323s OK 324s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_optional.py" [OK] 0.1s 324s Time: 0.09 324s Return code: 0 324s OKs: 1 324s Standard out: 324s exercise_wstring: 324s OK 324s libtbx.python "/usr/lib/python3/dist-packages/annlib_adaptbx/annlib_adaptbx/sample.py" [OK] 0.5s 324s Time: 0.48 324s Return code: 0 324s OKs: 1 324s Standard out: 324s OK 324s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_tuple.py" [OK] 0.1s 324s Time: 0.06 324s Return code: 0 324s OKs: 1 324s Standard out: 324s OK 324s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_std_pair.py" [OK] 0.1s 324s Time: 0.09 324s Return code: 0 324s OKs: 1 324s Standard out: 324s OK 324s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_stderr_stdout.py" [OK] 0.1s 324s Time: 0.06 324s Return code: 0 324s OKs: 1 324s Standard out: 324s OK 324s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_stdout.py" [OK] 0.1s 324s Time: 0.11 324s Return code: 0 324s OKs: 1 324s Standard out: 324s OK 324s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_deprecation_tools.py" [OK] 0.1s 324s Time: 0.06 324s Return code: 0 324s OKs: 1 324s Standard out: 324s OK 327s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 327s 1 327s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 327s libtbx.python "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_python_streambuf.py" [EXPECTED FAIL] 3.3s 327s Time: 3.32 327s Return code: 1 327s OKs: 0 327s Standard error: 327s Traceback (most recent call last): 327s File "/usr/lib/python3/dist-packages/boost_adaptbx/tests/tst_python_streambuf.py", line 7, in 327s import StringIO 327s ModuleNotFoundError: No module named 'StringIO' 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/regression/tst_sf_low_res_accuracy.py" [FAIL] 4.3s 328s Time: 4.34 328s Return code: 139 328s OKs: 0 328s Standard error: 328s Segmentation fault (core dumped) 332s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 332s 139 332s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 332s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_double_step_filtration.py" [FAIL] 4.4s 332s Time: 4.43 332s Return code: 139 332s OKs: 0 332s Standard error: 332s Segmentation fault (core dumped) 335s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 335s 139 335s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 335s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_is_periodic.py" [FAIL] 6.8s 335s Time: 6.76 335s Return code: 139 335s OKs: 0 335s Standard error: 335s Segmentation fault (core dumped) 335s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_map_to_asu_isym.py" [OK] 0.5s 335s Time: 0.48 335s Return code: 0 335s OKs: 1 335s Standard out: 335s OK 338s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 338s 139 338s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 338s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_reindexing.py" [FAIL] 6.8s 338s Time: 6.77 338s Return code: 139 338s OKs: 0 338s Standard error: 338s Segmentation fault (core dumped) 342s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 342s 139 342s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 342s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_data_manipulation.py" [FAIL] 6.2s 342s Time: 6.23 342s Return code: 139 342s OKs: 0 342s Standard error: 342s Segmentation fault (core dumped) 345s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 345s 139 345s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 345s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_bfgs.py" [FAIL] 6.5s 345s Time: 6.54 345s Return code: 139 345s OKs: 0 345s Standard error: 345s Segmentation fault (core dumped) 348s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 348s 139 348s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 348s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_dev.py" P31 [FAIL] 6.6s 348s Time: 6.61 348s Return code: 139 348s OKs: 0 348s Standard error: 348s Segmentation fault (core dumped) 352s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 352s 139 352s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 352s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry/tests/tst_geometry.py" [FAIL] 6.8s 352s Time: 6.79 352s Return code: 139 352s OKs: 0 352s Standard error: 352s Segmentation fault (core dumped) 355s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 355s 139 355s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 355s libtbx.python "/usr/lib/python3/dist-packages/cctbx/covariance/tests/tst_covariance.py" [FAIL] 6.8s 355s Time: 6.84 355s Return code: 139 355s OKs: 0 355s Standard error: 355s Segmentation fault (core dumped) 358s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 358s 139 358s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 358s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_goodness_of_symmetry.py" [FAIL] 6.7s 358s Time: 6.70 358s Return code: 139 358s OKs: 0 358s Standard error: 358s Segmentation fault (core dumped) 359s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_aniso_restraints.py" [OK] 0.2s 359s Time: 0.24 359s Return code: 0 359s OKs: 1 359s Standard out: 359s Skipping exercise(): chem_data directory not available 359s OK 359s libtbx.python "/usr/lib/python3/dist-packages/cctbx/math/boost_python/tst_math.py" [OK] 0.1s 359s Time: 0.10 359s Return code: 0 359s OKs: 1 359s Standard out: 359s OK 359s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_targets_fd.py" [OK] 0.4s 359s Time: 0.37 359s Return code: 0 359s OKs: 1 359s Standard out: 359s OK 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/symmetry_search/tests/tst_from_map.py" P312 [FAIL] 6.8s 362s Time: 6.84 362s Return code: 139 362s OKs: 0 362s Standard error: 362s Segmentation fault (core dumped) 365s Standard error: 365s 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_xray.py" [FAIL] 6.4s 365s Time: 6.38 365s Return code: 139 365s OKs: 0 369s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 369s 139 369s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 369s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray.py" I41/acd [FAIL] 7.0s 369s Time: 6.98 369s Return code: 139 369s OKs: 0 369s Standard error: 369s Segmentation fault (core dumped) 372s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 372s 139 372s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 372s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_r1.py" [FAIL] 6.9s 372s Time: 6.90 372s Return code: 139 372s OKs: 0 372s Standard error: 372s Segmentation fault (core dumped) 376s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 376s 139 376s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 376s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_shelxl_wght_ls.py" [FAIL] 6.8s 376s Time: 6.77 376s Return code: 139 376s OKs: 0 376s Standard error: 376s Segmentation fault (core dumped) 379s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 379s 139 379s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 379s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_f_model.py" [FAIL] 6.5s 379s Time: 6.50 379s Return code: 139 379s OKs: 0 379s Standard error: 379s Segmentation fault (core dumped) 382s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 382s 139 382s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 382s libtbx.python "/usr/lib/python3/dist-packages/cctbx/array_family/boost_python/tst_flex.py" [FAIL] 6.4s 382s Time: 6.45 382s Return code: 139 382s OKs: 0 382s Standard error: 382s Segmentation fault (core dumped) 385s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 385s 139 385s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 385s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_uctbx.py" [FAIL] 6.5s 385s Standard error: 385s Segmentation fault (core dumped) 385s Time: 6.48 385s Return code: 139 385s OKs: 0 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/uctbx/boost_python/tst_crystal_orientation.py" [FAIL] 6.3s 388s Time: 6.32 388s Return code: 139 388s OKs: 0 388s Standard error: 388s Segmentation fault (core dumped) 389s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_N_fold_rot.py" [OK] 0.2s 389s Time: 0.21 389s Return code: 0 389s OKs: 1 389s Standard out: 389s OK 392s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 392s 139 392s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 392s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_sgtbx.py" [FAIL] 6.4s 392s Time: 6.43 392s Return code: 139 392s OKs: 0 392s Standard error: 392s Segmentation fault (core dumped) 395s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 395s 139 395s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 395s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_ext.py" [FAIL] 6.4s 395s Time: 6.44 395s Return code: 139 395s OKs: 0 395s Standard error: 395s Segmentation fault (core dumped) 398s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 398s 139 398s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 398s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_distance_based_connectivity.py" [FAIL] 6.5s 398s Time: 6.49 398s Return code: 139 398s OKs: 0 398s Standard error: 398s Segmentation fault (core dumped) 402s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 402s 139 402s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 402s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_super_cell.py" [FAIL] 7.2s 402s Time: 7.25 402s Return code: 139 402s OKs: 0 402s Standard error: 402s Segmentation fault (core dumped) 406s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 406s 139 406s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 406s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adptbx/boost_python/tst_adptbx.py" [FAIL] 7.4s 406s Time: 7.42 406s Return code: 139 406s OKs: 0 406s Standard error: 406s Segmentation fault (core dumped) 406s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_chemical_elements.py" [OK] 0.1s 406s Time: 0.09 406s Return code: 0 406s OKs: 1 406s Standard out: 406s OK 409s Standard error: 409s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 409s 139 409s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 409s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/boost_python/tst_miller.py" [FAIL] 6.6s 409s Time: 6.65 409s Return code: 139 409s OKs: 0 409s Segmentation fault (core dumped) 409s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_henke.py" [OK] 0.1s 409s Time: 0.12 409s Return code: 0 409s OKs: 1 409s Standard out: 409s OK 409s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_icsd_radii.py" [OK] 0.1s 409s Time: 0.09 409s Return code: 0 409s OKs: 1 409s Standard out: 409s OK 409s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_covalent_radii.py" [OK] 0.1s 409s Time: 0.09 409s Return code: 0 409s OKs: 1 409s Standard out: 409s OK 409s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_neutron.py" [OK] 0.1s 409s Time: 0.09 409s Return code: 0 409s OKs: 1 409s Standard out: 409s OK 409s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_sasaki.py" [OK] 0.1s 409s Time: 0.09 409s Return code: 0 409s OKs: 1 409s Standard out: 409s OK 410s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_tiny_pse.py" [OK] 0.1s 410s Time: 0.09 410s Return code: 0 410s OKs: 1 410s Standard out: 410s OK 410s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_wavelengths.py" [OK] 0.1s 410s Time: 0.09 410s Return code: 0 410s OKs: 1 410s Standard out: 410s OK 412s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 412s 139 412s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 412s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_xray_scattering.py" [FAIL] 6.4s 412s Time: 6.37 412s Return code: 139 412s OKs: 0 412s Standard error: 412s Segmentation fault (core dumped) 415s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 415s 139 415s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 415s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_formula.py" [FAIL] 5.5s 415s Time: 5.50 415s Return code: 139 415s OKs: 0 415s Standard error: 415s Segmentation fault (core dumped) 418s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 418s 139 418s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 418s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_attenuation_coefficient.py" [FAIL] 6.0s 418s Time: 5.95 418s Return code: 139 418s OKs: 0 418s Standard error: 418s Segmentation fault (core dumped) 421s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 421s 139 421s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 421s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/boost_python/tst_maptbx.py" [FAIL] 6.3s 421s Time: 6.32 421s Return code: 139 421s OKs: 0 421s Standard error: 421s Segmentation fault (core dumped) 425s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 425s 139 425s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 425s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_bcr.py" [FAIL] 7.4s 425s Time: 7.36 425s Return code: 139 425s OKs: 0 425s Standard error: 425s Segmentation fault (core dumped) 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/maptbx/tst_loft.py" [FAIL] 7.4s 429s Time: 7.42 429s Return code: 139 429s OKs: 0 429s Standard error: 429s Segmentation fault (core dumped) 432s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 432s 139 432s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 432s libtbx.python "/usr/lib/python3/dist-packages/cctbx/dmtbx/boost_python/tst_dmtbx.py" [FAIL] 6.4s 432s Time: 6.42 432s Return code: 139 432s OKs: 0 432s Standard error: 432s Segmentation fault (core dumped) 435s Standard error: 435s Segmentation fault (core dumped) 435s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 435s 139 435s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 435s libtbx.python "/usr/lib/python3/dist-packages/cctbx/translation_search/boost_python/tst_translation_search.py" [FAIL] 6.1s 435s Time: 6.13 435s Return code: 139 435s OKs: 0 435s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_proxy_registry.py" [OK] 0.2s 435s Time: 0.24 435s Return code: 0 435s OKs: 1 435s Standard out: 435s OK 436s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_nonbonded_overlaps.py" [OK] 0.7s 436s Time: 0.69 436s Return code: 0 436s OKs: 0 436s Standard out: 436s chem_data not present, skipping 437s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_process_nonbonded_proxies.py" [OK] 0.7s 437s Time: 0.68 437s Return code: 0 437s OKs: 0 437s Standard out: 437s Test skipped, need monomer library 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/geometry_restraints/tst_ext.py" [FAIL] 6.5s 438s Time: 6.52 438s Return code: 139 438s OKs: 0 438s Standard error: 438s Segmentation fault (core dumped) 439s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_motif.py" [OK] 0.2s 439s Time: 0.22 439s Return code: 0 439s OKs: 0 439s Standard out: 439s u+s,u,s: 0.18 0.14 0.04 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/geometry_restraints/tst_angle_derivs.py" [FAIL] 4.9s 442s Time: 4.91 442s Return code: 139 442s OKs: 0 442s Standard error: 442s Segmentation fault (core dumped) 442s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_math_module.py" [OK] 0.1s 442s Time: 0.09 442s Return code: 0 442s OKs: 1 442s Standard out: 442s OK 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/adp_restraints/tst_ext.py" [FAIL] 6.2s 445s Time: 6.16 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_krivy_gruber.py" --Quick [FAIL] 6.2s 448s Time: 6.19 448s Return code: 139 448s OKs: 0 448s Standard error: 448s Segmentation fault (core dumped) 448s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_itvb_2001_table_a1427_hall_symbols.py" [OK] 0.2s 448s Time: 0.18 448s Return code: 0 448s OKs: 1 448s Standard out: 448s Skipping exercise(): input file not available 448s OK 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_sgtbx.py" [FAIL] 6.1s 451s Time: 6.10 451s Return code: 139 451s OKs: 0 451s Standard error: 451s Segmentation fault (core dumped) 454s Standard error: 454s Segmentation fault (core dumped) 454s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 454s 139 454s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 454s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_space_group_type_tidy_cb_op_t.py" [FAIL] 5.9s 454s Time: 5.94 454s Return code: 139 454s OKs: 0 457s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 457s 139 457s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 457s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_denominators.py" P31 [FAIL] 6.1s 457s Time: 6.11 457s Return code: 139 457s OKs: 0 457s Standard error: 457s Segmentation fault (core dumped) 460s Standard error: 460s Segmentation fault (core dumped) 460s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 460s 139 460s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 460s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_subgroups.py" [FAIL] 6.1s 460s Time: 6.05 460s Return code: 139 460s OKs: 0 463s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 463s 139 463s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 463s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_lattice_symmetry.py" [FAIL] 6.0s 463s Time: 5.97 463s Return code: 139 463s OKs: 0 463s Standard error: 463s Segmentation fault (core dumped) 466s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 466s 139 466s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 466s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints.py" P3 [FAIL] 6.1s 466s Time: 6.13 466s Return code: 139 466s OKs: 0 466s Standard error: 466s Segmentation fault (core dumped) 466s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_site_constraints.py" [OK] 0.3s 466s Time: 0.35 466s Return code: 0 466s OKs: 0 466s Standard out: 466s Skipping process_zeolite_atlas(): input file not available 466s u+s,u,s: 0.28 0.24 0.04 469s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 469s 139 469s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 469s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints_cartesian.py" [FAIL] 6.2s 469s Time: 6.19 469s Return code: 139 469s OKs: 0 469s Standard error: 469s Segmentation fault (core dumped) 472s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 472s 139 472s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 472s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reflection_statistics.py" [FAIL] 5.8s 472s Time: 5.83 472s Return code: 139 472s OKs: 0 472s Standard error: 472s 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/regression/tst_sgtbx_harker.py" [FAIL] 6.2s 475s Time: 6.18 475s Return code: 139 475s OKs: 0 475s Standard error: 475s Segmentation fault (core dumped) 479s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 479s 139 479s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 479s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_special_op_simplifier.py" [FAIL] 6.2s 479s Time: 6.24 479s Return code: 139 479s OKs: 0 479s Standard error: 479s 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_twin_target.py" [FAIL] 6.5s 482s Time: 6.46 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/sgtbx/symbol_confidence.py" [FAIL] 6.2s 485s Time: 6.21 485s Return code: 139 485s OKs: 0 485s Standard error: 485s Segmentation fault (core dumped) 488s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 488s 139 488s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 488s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/bravais_types.py" [FAIL] 6.0s 488s Time: 6.02 488s Return code: 139 488s OKs: 0 488s Standard error: 488s Segmentation fault (core dumped) 491s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 491s 139 491s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 491s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_lookup_utils.py" [FAIL] 6.2s 491s Time: 6.24 491s Return code: 139 491s OKs: 0 491s Standard error: 491s Segmentation fault (core dumped) 494s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 494s 139 494s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 494s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal.py" I41/acd [FAIL] 6.4s 494s Time: 6.40 494s Return code: 139 494s OKs: 0 494s Standard error: 494s Segmentation fault (core dumped) 497s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 497s 139 497s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 497s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_direct_space_asu.py" I41/acd [FAIL] 6.4s 497s Time: 6.40 497s Return code: 139 497s OKs: 0 497s Standard error: 497s Segmentation fault (core dumped) 501s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 501s 139 501s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 501s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pair_asu_table.py" [FAIL] 6.4s 501s Time: 6.43 501s Return code: 139 501s OKs: 0 501s Standard error: 501s Segmentation fault (core dumped) 501s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_coordination_sequences.py" [OK] 0.3s 501s Time: 0.34 501s Return code: 0 501s OKs: 1 501s Standard out: 501s Skipping exercise(): input file not available 501s OK 504s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 504s 139 504s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 504s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_asu_clusters.py" [FAIL] 6.3s 504s Time: 6.30 504s Return code: 139 504s OKs: 0 504s Standard error: 504s Segmentation fault (core dumped) 507s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 507s 139 507s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 507s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_close_packing.py" R-3mr [FAIL] 5.9s 507s Time: 5.92 507s Return code: 139 507s OKs: 0 507s Standard error: 507s 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_fourier_transform_real_part_at_x.py" P31 [FAIL] 6.2s 510s Time: 6.16 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_miller.py" P31 [FAIL] 6.4s 513s Time: 6.43 513s Return code: 139 513s OKs: 0 513s Standard error: 513s Segmentation fault (core dumped) 514s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem_2.py" [OK] 0.3s 514s Time: 0.26 514s Return code: 0 514s OKs: 0 514s Standard out: 514s Skipping test: phenix not available 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_mem.py" [FAIL] 6.8s 517s Standard error: 517s Segmentation fault (core dumped) 517s Time: 6.83 517s Return code: 139 517s OKs: 0 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_reciprocal_space_asu.py" P312 [FAIL] 6.2s 520s Time: 6.23 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_triplet_generator.py" P41 [FAIL] 6.3s 523s Time: 6.32 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_emma.py" P31 [FAIL] 6.7s 526s Time: 6.66 526s Return code: 139 526s OKs: 0 526s Standard error: 526s 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_expand_to_p1.py" P31 [FAIL] 6.8s 530s Time: 6.82 530s Return code: 139 530s OKs: 0 530s Standard error: 530s Segmentation fault (core dumped) 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_change_basis.py" P31 [FAIL] 6.5s 533s Standard error: 533s Segmentation fault (core dumped) 533s Time: 6.54 533s Return code: 139 533s OKs: 0 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_wilson_plot.py" P31 [FAIL] 6.3s 536s Time: 6.33 536s Return code: 139 536s OKs: 0 536s Standard error: 536s 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_xray_derivatives.py" P31 [FAIL] 6.3s 539s Time: 6.31 539s Return code: 139 539s OKs: 0 539s Standard error: 539s 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_xray_fast_gradients.py" P31 [FAIL] 6.5s 543s Time: 6.46 543s Return code: 139 543s OKs: 0 543s Standard error: 543s Segmentation fault (core dumped) 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/regression/tst_xray_minimization.py" --F P31 [FAIL] 6.4s 546s Time: 6.44 546s Return code: 139 546s OKs: 0 546s Standard error: 546s Segmentation fault (core dumped) 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/regression/tst_xray_minimization.py" --F_sq P31 [FAIL] 3.2s 546s Time: 3.17 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/regression/tst_maptbx_structure_factors.py" P31 [FAIL] 3.6s 549s Time: 3.60 549s Return code: 139 549s OKs: 0 549s Standard error: 549s Segmentation fault (core dumped) 553s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 553s 139 553s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 553s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_weights_for_symmetry_summation.py" Pmmm [FAIL] 6.9s 553s Time: 6.85 553s Return code: 139 553s OKs: 0 553s Standard error: 553s 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/maptbx/tst_real_space_refinement_simple.py" [FAIL] 6.6s 556s Time: 6.60 556s Return code: 139 556s OKs: 0 556s Standard error: 556s Segmentation fault (core dumped) 559s Standard error: 559s 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_interpolation.py" [FAIL] 6.4s 559s Time: 6.41 559s Return code: 139 559s OKs: 0 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/maptbx/tst_interpolation_2.py" [FAIL] 6.5s 563s Time: 6.54 563s Return code: 139 563s OKs: 0 563s Standard error: 563s Segmentation fault (core dumped) 567s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 567s 139 567s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 567s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_loc_res.py" [FAIL] 7.5s 567s Time: 7.50 567s Return code: 139 567s OKs: 0 567s Standard error: 567s 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/maptbx/tst_target_and_gradients.py" [FAIL] 7.2s 570s Time: 7.24 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_miller_merge_equivalents.py" P31 [FAIL] 6.4s 573s Time: 6.45 573s Return code: 139 573s OKs: 0 573s Standard error: 573s Segmentation fault (core dumped) 576s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 576s 139 576s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 576s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grouped_data.py" P31 [FAIL] 6.5s 576s Time: 6.49 576s Return code: 139 576s OKs: 0 576s Standard error: 576s Segmentation fault (core dumped) 580s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 580s 139 580s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 580s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_fft_map.py" P31 [FAIL] 6.5s 580s Time: 6.54 580s Return code: 139 580s OKs: 0 580s Standard error: 580s Segmentation fault (core dumped) 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_sampled_model_density.py" P31 [FAIL] 6.6s 583s Time: 6.64 583s Return code: 139 583s OKs: 0 583s Standard error: 583s Segmentation fault (core dumped) 583s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints.py" [OK] 0.6s 583s Time: 0.63 583s Return code: 0 583s OKs: 1 583s Standard out: 583s OK 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_fast_nv1995.py" F222 [FAIL] 6.6s 586s Time: 6.58 586s Return code: 139 586s OKs: 0 586s Standard error: 586s Segmentation fault (core dumped) 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/regression/tst_geometry_restraints_lbfgs.py" [FAIL] 6.0s 589s Time: 5.98 589s Return code: 139 589s OKs: 0 589s Standard error: 589s Segmentation fault (core dumped) 590s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grm_pickling.py" [OK] 0.4s 590s Time: 0.41 590s Return code: 0 590s OKs: 0 590s Standard out: 590s Can not initialize monomer_library, skipping test. 593s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 593s 139 593s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 593s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_2.py" [FAIL] 7.0s 593s Time: 7.04 593s Return code: 139 593s OKs: 0 593s Standard error: 593s Segmentation fault (core dumped) 596s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 596s 139 596s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 596s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_french_wilson.py" [FAIL] 6.5s 596s Time: 6.47 596s Return code: 139 596s OKs: 0 596s Standard error: 596s Segmentation fault (core dumped) 597s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/tst_cns_epsilon.py" P31 [OK] 0.2s 597s Time: 0.24 597s Return code: 0 597s OKs: 0 597s Standard out: 597s Skipping tests: cns not available. 597s u+s,u,s: 0.18 0.15 0.03 597s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/tst_cns_hl.py" P31 [OK] 0.2s 597s Time: 0.24 597s Return code: 0 597s OKs: 0 597s Standard out: 597s Skipping tests: cns not available. 597s u+s,u,s: 0.19 0.16 0.03 597s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/run_shelx76.py" P31 [OK] 0.3s 597s Time: 0.25 597s Return code: 0 597s OKs: 0 597s Standard out: 597s shelx76 not available. 600s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 600s 139 600s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 600s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/make_cns_input.py" P31 [FAIL] 6.5s 600s Time: 6.49 600s Return code: 139 600s OKs: 0 600s Standard error: 600s Segmentation fault (core dumped) 603s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 603s 139 603s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 603s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pointgroup_tools.py" [FAIL] 5.8s 603s Time: 5.75 603s Return code: 139 603s OKs: 0 603s Standard error: 603s Segmentation fault (core dumped) 606s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 606s 139 606s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 606s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/sub_lattice_tools.py" [FAIL] 6.3s 606s Time: 6.32 606s Return code: 139 606s OKs: 0 606s Standard error: 606s Segmentation fault (core dumped) 609s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 609s 139 609s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 609s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/rational_matrices_point_groups.py" [FAIL] 6.4s 609s Time: 6.37 609s Return code: 139 609s OKs: 0 609s Standard error: 609s Segmentation fault (core dumped) 612s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 612s 139 612s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 612s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/cosets.py" [FAIL] 6.4s 612s Time: 6.38 612s Return code: 139 612s OKs: 0 612s Standard error: 612s Segmentation fault (core dumped) 615s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 615s 139 615s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 615s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_pg_tools.py" [FAIL] 6.2s 615s Time: 6.22 615s Return code: 139 615s OKs: 0 615s Standard error: 615s Segmentation fault (core dumped) 619s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 619s 139 619s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 619s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_twin_laws.py" [FAIL] 6.3s 619s Time: 6.29 619s Return code: 139 619s OKs: 0 619s Standard error: 619s Segmentation fault (core dumped) 622s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 622s 139 622s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 622s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_find_best_cell.py" [FAIL] 6.4s 622s Time: 6.42 622s Return code: 139 622s OKs: 0 622s Standard error: 622s Segmentation fault (core dumped) 625s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 625s 139 625s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 625s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_amplitude_normalisation.py" [FAIL] 6.6s 625s Time: 6.60 625s Return code: 139 625s OKs: 0 625s Standard error: 625s Segmentation fault (core dumped) 628s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 628s 139 628s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 628s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_statistics_graphs.py" [FAIL] 6.6s 628s Time: 6.61 628s Return code: 139 628s OKs: 0 628s Standard error: 628s Segmentation fault (core dumped) 632s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 632s 139 632s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 632s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_web_change_basis.py" [FAIL] 6.3s 632s Time: 6.28 632s Return code: 139 632s OKs: 0 632s Standard error: 632s Segmentation fault (core dumped) 635s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 635s 139 635s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 635s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/direct_space_asu/proto/tst_asu.py" [FAIL] 6.1s 635s Time: 6.15 635s Return code: 139 635s OKs: 0 635s Standard error: 635s Segmentation fault (core dumped) 638s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 638s 139 638s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 638s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_tidy_pickling.py" [FAIL] 6.5s 638s Time: 6.51 638s Return code: 139 638s OKs: 0 638s Standard error: 638s Segmentation fault (core dumped) 641s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 641s 139 641s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 641s libtbx.python "/usr/lib/python3/dist-packages/cctbx/masks/tests/tst_flood_fill.py" [FAIL] 6.6s 641s Time: 6.59 641s Return code: 139 641s OKs: 0 641s Standard error: 641s Segmentation fault (core dumped) 641s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/observations/tst_observations.py" [OK] 0.3s 641s Time: 0.27 641s Return code: 0 641s OKs: 1 641s Standard out: 641s OK 645s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 645s 139 645s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 645s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_r_free_utils.py" [FAIL] 6.5s 645s Time: 6.51 645s Return code: 139 645s OKs: 0 645s Standard error: 645s Segmentation fault (core dumped) 648s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 648s 139 648s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 648s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_ccp.py" [FAIL] 6.4s 648s Time: 6.44 648s Return code: 139 648s OKs: 0 648s Standard error: 648s Segmentation fault (core dumped) 651s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 651s 139 651s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 651s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_mask.py" [FAIL] 6.7s 651s Time: 6.72 651s Return code: 139 651s OKs: 0 651s Standard error: 651s Segmentation fault (core dumped) 655s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 655s 139 655s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 655s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_map_peak_3d_as_2d.py" [FAIL] 6.7s 655s Standard error: 655s Segmentation fault (core dumped) 655s Time: 6.67 655s Return code: 139 655s OKs: 0 658s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 658s 139 658s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 658s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_asymmetric_map.py" [FAIL] 6.6s 658s Time: 6.60 658s Return code: 139 658s OKs: 0 658s Standard error: 658s Segmentation fault (core dumped) 661s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 661s 139 661s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 661s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_peak_volume_estimate.py" [FAIL] 6.6s 661s Time: 6.62 661s Return code: 139 661s OKs: 0 661s Standard error: 661s Segmentation fault (core dumped) 665s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 665s 139 665s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 665s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_resolution_from_map_and_model.py" [FAIL] 6.7s 665s Time: 6.67 665s Return code: 139 665s OKs: 0 665s Standard error: 665s Segmentation fault (core dumped) 668s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 668s 139 668s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 668s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_curves.py" [FAIL] 6.7s 668s Time: 6.68 668s Return code: 139 668s OKs: 0 668s Standard error: 668s Segmentation fault (core dumped) 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/maptbx/tst_atom_radius_as_central_peak_width.py" [FAIL] 6.6s 671s Time: 6.59 671s Return code: 139 671s OKs: 0 671s Standard error: 671s Segmentation fault (core dumped) 672s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_box.py" [OK] 0.7s 672s Time: 0.71 672s Return code: 0 672s OKs: 0 672s Standard out: 672s phenix is not available, skipping test 673s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_create_models_or_maps.py" [OK] 0.7s 673s Time: 0.68 673s Return code: 0 673s OKs: 1 673s Standard out: 673s Skipping exercise(): chem_data directory not available 673s OK 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/maptbx/tst_get_percentile_cutoffs.py" [FAIL] 6.6s 674s Time: 6.62 674s Return code: 139 674s OKs: 0 674s Standard error: 674s Segmentation fault (core dumped) 678s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 678s 139 678s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 678s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sphericity.py" [FAIL] 5.3s 678s Time: 5.32 678s Return code: 139 678s OKs: 0 678s Standard error: 678s Segmentation fault (core dumped) 678s libtbx.python "/usr/lib/python3/dist-packages/cctbx/merging/brehm_diederichs.py" [OK] 0.3s 678s Time: 0.26 678s Return code: 0 678s OKs: 1 678s Standard out: 678s OK 678s libtbx.python "/usr/lib/python3/dist-packages/cctbx/multipolar/regression/tst_multipolar.py" [OK] 0.2s 678s Time: 0.17 678s Return code: 0 678s OKs: 3 678s Standard out: 678s OK 678s 0 678s 1 678s 2 678s OK 678s Skipping exercise(): chem_data directory not available 678s OK 681s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 681s 139 681s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 681s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_statistics.py" [FAIL] 6.6s 681s Time: 6.58 681s Return code: 139 681s OKs: 0 681s Standard error: 681s Segmentation fault (core dumped) 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_connectivity.py" [FAIL] 6.3s 685s Time: 6.25 685s Return code: 139 685s OKs: 0 685s Standard error: 685s Segmentation fault (core dumped) 688s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 688s 139 688s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 688s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity_allsym.py" [FAIL] 6.7s 688s Time: 6.68 688s Return code: 139 688s OKs: 0 688s Standard error: 688s Segmentation fault (core dumped) 688s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grm_modifications.py" [OK] 0.7s 688s Time: 0.72 688s Return code: 0 688s OKs: 1 688s Standard out: 688s Can not initialize monomer_library, skipping test. 688s OK 694s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 694s 1 694s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 694s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py" [FAIL] 9.5s 694s Time: 9.49 694s Return code: 1 694s OKs: 0 694s Standard error: 694s Segmentation fault (core dumped) 694s Traceback (most recent call last): 694s File "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py", line 140, in 694s exercise() 694s ~~~~~~~~^^ 694s File "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py", line 126, in exercise 694s assert not easy_run.call(cmd) 694s ^^^^^^^^^^^^^^^^^^^^^^ 694s AssertionError 696s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 696s 139 696s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 696s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_prepare_map_for_docking.py" [FAIL] 7.2s 696s Time: 7.16 696s Return code: 139 696s OKs: 0 696s Standard error: 696s Segmentation fault (core dumped) 697s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wavelength_units.py" [OK] 2.7s 697s Time: 2.69 697s Return code: 0 697s OKs: 1 697s Standard out: 697s OK 699s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 699s 139 699s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 699s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fcalc_fft_stability.py" [EXPECTED UNSTABLE] 3.8s 699s Standard error: 699s Segmentation fault (core dumped) 699s Time: 3.76 699s Return code: 139 699s OKs: 0 699s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_ext.py" [OK] 0.1s 699s Time: 0.10 699s Return code: 0 699s OKs: 1 699s Standard out: 699s OK 700s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_equivalence.py" [OK] 0.1s 700s Time: 0.10 700s Return code: 0 700s OKs: 1 700s Standard out: 700s OK 700s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_read.py" [OK] 0.6s 700s Time: 0.59 700s Return code: 0 700s OKs: 1 700s Standard out: 700s OK 701s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_cout.py" [OK] 0.4s 701s Time: 0.42 701s Return code: 0 701s OKs: 1 701s Standard out: 701s OK 701s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_show_calls.py" [OK] 0.4s 701s Time: 0.38 701s Return code: 0 701s OKs: 1 701s Standard out: 701s OK 703s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 703s 139 703s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 703s libtbx.python "/usr/lib/python3/dist-packages/cma_es/tst_cma_es.py" [FAIL] 5.9s 703s Time: 5.86 703s Return code: 139 703s OKs: 0 703s Standard error: 703s Segmentation fault (core dumped) 707s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_command_line.py" [OK] 6.4s 707s Time: 6.42 707s Return code: 0 707s OKs: 1 707s Standard out: 707s fable.split "/usr/lib/python3/dist-packages/fable/test/valid/subroutine_1.f" 707s fable.read --each "/usr/lib/python3/dist-packages/fable/test/valid/write_star.f" 707s fable.read --warnings "/usr/lib/python3/dist-packages/fable/test/valid/equivalence_mixed.f" 707s fable.show_calls --write-graphviz-dot=tmp.dot --top-procedure=sub "/usr/lib/python3/dist-packages/fable/test/valid/external_arg_layers.f" 707s fable.show_calls "/usr/lib/python3/dist-packages/fable/test/valid/dependency_cycle.f" 707s fable.fem_include_search_paths --with-quotes 707s fable.cout --each "/usr/lib/python3/dist-packages/fable/test/valid/write_star.f" 707s fable.cout "/usr/lib/python3/dist-packages/fable/test/valid/common_variants.f" 707s fable.cout "/usr/lib/python3/dist-packages/fable/test/valid/subroutine_3.f" --top-procedure=sub3 --fortran-file-comments 707s fable.cout --compile "/usr/lib/python3/dist-packages/fable/test/valid/write_star.f" 707s fable.cout --namespace=test --run "/usr/lib/python3/dist-packages/fable/test/valid/write_star.f" 707s fable.cout --example 707s fable.cout /usr/lib/python3/dist-packages/fable/test/valid/sf.f --namespace example --run 707s fable.cout "/usr/lib/python3/dist-packages/fable/test/valid/dynamic_parameters_1.f" --dynamic-parameter="int root_size=1" 707s OK 711s libtbx.python "/usr/lib/python3/dist-packages/fable/tst_cout_compile.py" stop [OK] 3.7s 711s Time: 3.68 711s Return code: 0 711s OKs: 1 711s Standard out: 711s 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" 711s 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" 711s 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" 711s OK 711s usr+sys time: 0.11 seconds 711s wall clock time: 3.65 seconds 714s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_separate_files.py" [OK] 11.6s 714s Time: 11.55 714s Return code: 0 714s OKs: 1 714s Standard out: 714s 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" 714s 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" 714s 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" 714s 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" 714s 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" 714s 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" 714s 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" 714s 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" 714s 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" 714s 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" 714s 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" 714s 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" 714s 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" 714s 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" 714s 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" 714s 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" 714s 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" 714s OK 714s usr+sys time: 0.22 seconds 714s wall clock time: 11.52 seconds 714s libtbx.python "/usr/lib/python3/dist-packages/gltbx/tst_ellipsoids.py" [OK] 0.3s 714s Time: 0.30 714s Return code: 0 714s OKs: 1 714s Standard out: 714s OK 718s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 718s 139 718s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 718s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mrc_io.py" [FAIL] 3.5s 718s Time: 3.45 718s Return code: 139 718s OKs: 0 718s Standard error: 718s Segmentation fault (core dumped) 718s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_wildcard.py" [OK] 0.1s 718s Time: 0.09 718s Return code: 0 718s OKs: 1 718s Standard out: 718s OK 719s libtbx.python "/usr/lib/python3/dist-packages/fable/test/tst_io.py" [OK] 8.0s 719s Time: 8.01 719s Return code: 0 719s OKs: 1 719s Standard out: 719s OK 719s usr+sys time: 0.18 seconds 719s wall clock time: 7.97 seconds 719s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_parser.py" [OK] 0.1s 719s Time: 0.08 719s Return code: 0 719s OKs: 1 719s Standard out: 719s OK 722s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 722s 139 722s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 722s libtbx.python "/usr/lib/python3/dist-packages/iotbx/gui_tools/tst.py" [FAIL] 3.7s 722s Time: 3.71 722s Return code: 139 722s OKs: 0 722s Standard error: 722s Segmentation fault (core dumped) 722s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_cif_inputs.py" [OK] 0.2s 722s Time: 0.25 722s Return code: 0 722s OKs: 1 722s Standard out: 722s OK 725s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 725s 139 725s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 725s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phil.py" [FAIL] 5.4s 725s Time: 5.45 725s Return code: 139 725s OKs: 0 725s Standard error: 725s Segmentation fault (core dumped) 729s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 729s 139 729s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 729s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_manager.py" [FAIL] 7.0s 729s Time: 6.96 729s Return code: 139 729s OKs: 0 729s Standard error: 729s Segmentation fault (core dumped) 732s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 732s 139 732s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 732s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager_wrapping.py" [FAIL] 7.5s 732s Time: 7.47 732s Return code: 139 732s OKs: 0 732s Standard error: 732s Segmentation fault (core dumped) 733s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager.py" [OK] 0.7s 733s Time: 0.67 733s Return code: 0 733s OKs: 1 733s Standard out: 733s Skip test_01, chem_data not available 733s OK 733s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_2.py" [OK] 0.7s 733s Time: 0.69 733s Return code: 0 733s OKs: 0 733s Standard out: 733s chem_data is not available, skipping 734s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_3.py" [OK] 0.7s 734s Time: 0.69 734s Return code: 0 734s OKs: 1 734s Standard out: 734s Skipped: Requires phenix module 734s OK 734s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_4.py" [OK] 0.2s 734s Time: 0.17 734s Return code: 0 734s OKs: 1 734s Standard out: 734s Skipping tst_map_model_manager_4 tests becuase Phenix is not available. 734s OK 735s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_model_sharpening_5.py" [OK] 0.7s 735s Time: 0.66 735s Return code: 0 735s OKs: 1 735s Standard out: 735s Skip test_01, chem_data not available 735s OK 736s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 736s 139 736s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 736s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager.py" [FAIL] 6.8s 736s Time: 6.77 736s Return code: 139 736s OKs: 0 736s Standard error: 736s Segmentation fault (core dumped) 736s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_model_sharpening_5_cif.py" [OK] 0.7s 736s Time: 0.65 736s Return code: 0 736s OKs: 1 736s Standard out: 736s Skip test_01, chem_data not available 736s OK 736s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_call_consistency.py" [OK] 0.7s 736s Time: 0.67 736s Return code: 0 736s OKs: 1 736s Standard out: 736s 736s Expected and actual args in calls for with_bounds 736s 736s box.with_bounds.__init__ : 736s Expected :['log', 'lower_bounds', 'map_manager', 'model', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'upper_bounds', 'use_cubic_boxing', 'wrapping'] 736s Found : ['log', 'lower_bounds', 'map_manager', 'model', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'upper_bounds', 'use_cubic_boxing', 'wrapping'] 736s 736s box_all_maps_with_bounds_and_shift_origin : 736s Expected :['extract_box', 'lower_bounds', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'upper_bounds', 'use_cubic_boxing'] 736s Found : ['boundary_to_smoothing_ratio', 'extract_box', 'lower_bounds', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'soft_mask_around_edges', 'soft_mask_radius', 'stay_inside_current_map', 'upper_bounds', 'use_cubic_boxing'] 736s 736s extract_all_maps_with_bounds : 736s Expected :['lower_bounds', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'upper_bounds', 'use_cubic_boxing'] 736s Found : ['boundary_to_smoothing_ratio', 'lower_bounds', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'soft_mask_around_edges', 'soft_mask_radius', 'stay_inside_current_map', 'upper_bounds', 'use_cubic_boxing'] 736s 736s Expected and actual args in calls for around_model 736s 736s box.around_model.__init__ : 736s Expected :['box_cushion', 'log', 'map_manager', 'model', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'use_cubic_boxing', 'wrapping'] 736s Found : ['box_cushion', 'log', 'map_manager', 'model', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'use_cubic_boxing', 'wrapping'] 736s 736s box_all_maps_around_model_and_shift_origin : 736s Expected :['box_cushion', 'extract_box', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'select_unique_by_ncs', 'selection', 'selection_string', 'self', 'stay_inside_current_map', 'use_cubic_boxing'] 736s Found : ['boundary_to_smoothing_ratio', 'box_cushion', 'extract_box', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'select_unique_by_ncs', 'selection', 'selection_string', 'self', 'soft_mask_around_edges', 'soft_mask_radius', 'stay_inside_current_map', 'use_cubic_boxing'] 736s 736s extract_all_maps_around_model : 736s Expected :['box_cushion', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'select_unique_by_ncs', 'selection', 'selection_string', 'self', 'stay_inside_current_map', 'use_cubic_boxing'] 736s Found : ['boundary_to_smoothing_ratio', 'box_cushion', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'select_unique_by_ncs', 'selection', 'selection_string', 'self', 'soft_mask_around_edges', 'soft_mask_radius', 'stay_inside_current_map', 'use_cubic_boxing'] 736s 736s Expected and actual args in calls for around_density 736s 736s box.around_density.__init__ : 736s Expected :['box_cushion', 'get_half_height_width', 'log', 'map_manager', 'model', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'threshold', 'use_cubic_boxing', 'wrapping'] 736s Found : ['box_cushion', 'get_half_height_width', 'log', 'map_manager', 'model', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'threshold', 'use_cubic_boxing', 'wrapping'] 736s 736s box_all_maps_around_density_and_shift_origin : 736s Expected :['box_cushion', 'extract_box', 'get_half_height_width', 'map_id', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'threshold', 'use_cubic_boxing'] 736s Found : ['boundary_to_smoothing_ratio', 'box_cushion', 'extract_box', 'get_half_height_width', 'map_id', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'soft_mask_around_edges', 'soft_mask_radius', 'stay_inside_current_map', 'threshold', 'use_cubic_boxing'] 736s 736s extract_all_maps_around_density : 736s Expected :['box_cushion', 'get_half_height_width', 'map_id', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'threshold', 'use_cubic_boxing'] 736s Found : ['boundary_to_smoothing_ratio', 'box_cushion', 'get_half_height_width', 'map_id', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'soft_mask_around_edges', 'soft_mask_radius', 'stay_inside_current_map', 'threshold', 'use_cubic_boxing'] 736s 736s Expected and actual args in calls for around_mask 736s 736s box.around_mask.__init__ : 736s Expected :['box_cushion', 'log', 'map_manager', 'mask_as_map_manager', 'model', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'use_cubic_boxing', 'wrapping'] 736s Found : ['box_cushion', 'log', 'map_manager', 'mask_as_map_manager', 'model', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'use_cubic_boxing', 'wrapping'] 736s 736s box_all_maps_around_mask_and_shift_origin : 736s Expected :['box_cushion', 'extract_box', 'mask_id', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'use_cubic_boxing'] 736s Found : ['boundary_to_smoothing_ratio', 'box_cushion', 'extract_box', 'mask_id', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'soft_mask_around_edges', 'soft_mask_radius', 'stay_inside_current_map', 'use_cubic_boxing'] 736s 736s extract_all_maps_around_mask : 736s Expected :['box_cushion', 'mask_id', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'stay_inside_current_map', 'use_cubic_boxing'] 736s Found : ['boundary_to_smoothing_ratio', 'box_cushion', 'mask_id', 'model_can_be_outside_bounds', 'require_match_unit_cell_crystal_symmetry', 'self', 'soft_mask_around_edges', 'soft_mask_radius', 'stay_inside_current_map', 'use_cubic_boxing'] 736s 736s Expected and actual args in calls for around_unique 736s 736s box.around_unique.__init__ : 736s Expected :['box_cushion', 'chain_type', 'keep_low_density', 'keep_this_region_only', 'log', 'map_manager', 'mask_expand_ratio', 'model', 'molecular_mass', 'regions_to_keep', 'require_match_unit_cell_crystal_symmetry', 'residues_per_region', 'resolution', 'self', 'sequence', 'soft_mask', 'solvent_content', 'stay_inside_current_map', 'symmetry', 'target_ncs_au_model', 'use_cubic_boxing', 'use_symmetry_in_extract_unique', 'wrapping'] 736s Found : ['box_cushion', 'chain_type', 'keep_low_density', 'keep_this_region_only', 'log', 'map_manager', 'mask_expand_ratio', 'model', 'molecular_mass', 'regions_to_keep', 'require_match_unit_cell_crystal_symmetry', 'residues_per_region', 'resolution', 'self', 'sequence', 'soft_mask', 'solvent_content', 'stay_inside_current_map', 'symmetry', 'target_ncs_au_model', 'use_cubic_boxing', 'use_symmetry_in_extract_unique', 'wrapping'] 736s 736s box_all_maps_around_unique_and_shift_origin : 736s Expected :['box_cushion', 'chain_type', 'extract_box', 'keep_low_density', 'keep_this_region_only', 'mask_expand_ratio', 'molecular_mass', 'regions_to_keep', 'require_match_unit_cell_crystal_symmetry', 'residues_per_region', 'resolution', 'self', 'sequence', 'soft_mask', 'solvent_content', 'stay_inside_current_map', 'symmetry', 'target_ncs_au_model', 'use_cubic_boxing', 'use_symmetry_in_extract_unique'] 736s Found : ['boundary_to_smoothing_ratio', 'box_cushion', 'chain_type', 'extract_box', 'keep_low_density', 'keep_this_region_only', 'mask_expand_ratio', 'molecular_mass', 'regions_to_keep', 'require_match_unit_cell_crystal_symmetry', 'residues_per_region', 'resolution', 'self', 'sequence', 'soft_mask', 'soft_mask_around_edges', 'soft_mask_radius', 'solvent_content', 'stay_inside_current_map', 'symmetry', 'target_ncs_au_model', 'use_cubic_boxing', 'use_symmetry_in_extract_unique'] 736s 736s extract_all_maps_around_unique : 736s Expected :['box_cushion', 'chain_type', 'keep_low_density', 'keep_this_region_only', 'mask_expand_ratio', 'molecular_mass', 'regions_to_keep', 'require_match_unit_cell_crystal_symmetry', 'residues_per_region', 'resolution', 'self', 'sequence', 'soft_mask', 'solvent_content', 'stay_inside_current_map', 'symmetry', 'target_ncs_au_model', 'use_cubic_boxing', 'use_symmetry_in_extract_unique'] 736s Found : ['boundary_to_smoothing_ratio', 'box_cushion', 'chain_type', 'keep_low_density', 'keep_this_region_only', 'mask_expand_ratio', 'molecular_mass', 'regions_to_keep', 'require_match_unit_cell_crystal_symmetry', 'residues_per_region', 'resolution', 'self', 'sequence', 'soft_mask', 'soft_mask_around_edges', 'soft_mask_radius', 'solvent_content', 'stay_inside_current_map', 'symmetry', 'target_ncs_au_model', 'use_cubic_boxing', 'use_symmetry_in_extract_unique'] 736s 736s Expected and actual args in calls for around_atoms 736s 736s cctbx.maptbx.mask.create_mask_around_atoms.__init__ : 736s Expected :['invert_mask', 'map_manager', 'mask_atoms_atom_radius', 'model', 'n_real', 'self', 'wrapping', 'xray_structure'] 736s Found : ['invert_mask', 'map_manager', 'mask_atoms_atom_radius', 'model', 'n_real', 'self', 'wrapping', 'xray_structure'] 736s 736s map_model_manager.create_mask_around_atoms : 736s Expected :['invert_mask', 'mask_atoms_atom_radius', 'mask_id', 'model', 'self', 'soft_mask', 'soft_mask_radius'] 736s Found : ['invert_mask', 'mask_atoms_atom_radius', 'mask_id', 'model', 'self', 'soft_mask', 'soft_mask_radius'] 736s 736s Expected and actual args in calls for around_edges 736s 736s cctbx.maptbx.mask.create_mask_around_edges.__init__ : 736s Expected :['boundary_radius', 'map_manager', 'self'] 736s Found : ['boundary_radius', 'map_manager', 'self'] 736s 736s map_model_manager.create_mask_around_edges : 736s Expected :['boundary_radius', 'mask_id', 'self'] 736s Found : ['boundary_radius', 'boundary_to_smoothing_ratio', 'mask_id', 'self', 'soft_mask_radius'] 736s 736s Expected and actual args in calls for around_density 736s 736s cctbx.maptbx.mask.create_mask_around_density.__init__ : 736s Expected :['map_manager', 'molecular_mass', 'resolution', 'self', 'sequence', 'solvent_content'] 736s Found : ['map_manager', 'molecular_mass', 'resolution', 'self', 'sequence', 'solvent_content'] 736s 736s map_model_manager.create_mask_around_density : 736s Expected :['map_id', 'mask_id', 'resolution', 'self', 'soft_mask', 'soft_mask_radius', 'solvent_content'] 736s Found : ['map_id', 'mask_id', 'resolution', 'self', 'soft_mask', 'soft_mask_radius', 'solvent_content'] 736s OK 736s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_external_sharpening_7.py" [OK] 0.7s 736s Time: 0.66 736s Return code: 0 736s OKs: 1 736s Standard out: 736s Skip test_01, chem_data not available 736s OK 737s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_tls_from_map_8.py" [OK] 0.7s 737s Time: 0.65 737s Return code: 0 737s OKs: 1 737s Standard out: 737s Skip test_01, chem_data not available 737s OK 737s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_half_map_sharpening_6.py" [OK] 0.7s 737s Time: 0.67 737s Return code: 0 737s OKs: 1 737s Standard out: 737s Skip test_01, chem_data not available 737s OK 738s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_cif.py" [OK] 0.7s 738s Time: 0.67 738s Return code: 0 738s OKs: 1 738s Standard out: 738s Skip test_01, chem_data not available 738s OK 742s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 742s 139 742s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 742s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry.py" [FAIL] 4.8s 742s Time: 4.84 742s Return code: 139 742s OKs: 0 742s Standard error: 742s Segmentation fault (core dumped) 742s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_local_resolution_10.py" [OK] 0.6s 742s Time: 0.64 742s Return code: 0 742s OKs: 1 742s Standard out: 742s Skip test_01, chem_data not available 742s OK 746s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 746s 139 746s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 746s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_model_manager_9_remove_origin_shift_and_unit_cell_crystal_symmetry_cif.py" [FAIL] 8.2s 746s Time: 8.22 746s Return code: 139 746s OKs: 0 746s Standard error: 746s Segmentation fault (core dumped) 746s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_patterson.py" [OK] 0.1s 746s Time: 0.07 746s Return code: 0 746s OKs: 1 746s Standard out: 746s phenix_regression not available, skipping 746s OK 746s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_restraints_merge.py" [OK] 0.3s 746s Time: 0.26 746s Return code: 0 746s OKs: 0 749s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 749s 139 749s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 749s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_tools.py" [FAIL] 6.7s 749s Time: 6.70 749s Return code: 139 749s OKs: 0 749s Standard error: 749s Segmentation fault (core dumped) 749s libtbx.python "/usr/lib/python3/dist-packages/iotbx/ranges.py" [OK] 0.0s 749s Time: 0.03 749s Return code: 0 749s OKs: 1 749s Standard out: 749s OK 752s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 752s 139 752s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 752s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_atom_selections_10k.py" [FAIL] 6.2s 752s Time: 6.23 752s Return code: 139 752s OKs: 0 752s Standard error: 752s Segmentation fault (core dumped) 753s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_poscar.py" [OK] 0.1s 753s Time: 0.08 753s Return code: 0 753s OKs: 1 753s Standard out: 753s Skipping POSCAR tests: input files not available 753s OK 756s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 756s 139 756s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 756s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_crystal_symmetry_from_any.py" [FAIL] 6.6s 756s Time: 6.62 756s Return code: 139 756s OKs: 0 756s Standard error: 756s Segmentation fault (core dumped) 759s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 759s 139 759s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 759s libtbx.python "/usr/lib/python3/dist-packages/iotbx/kriber/tst_strudat.py" [FAIL] 6.6s 759s Time: 6.63 759s Return code: 139 759s OKs: 0 759s Standard error: 759s Segmentation fault (core dumped) 762s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 762s 139 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_geometry.py" [FAIL] 6.6s 762s Time: 6.61 762s Return code: 139 762s OKs: 0 762s Standard error: 762s Segmentation fault (core dumped) 766s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 766s 139 766s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 766s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_lex_parse_build.py" [FAIL] 6.8s 766s Time: 6.81 766s Return code: 139 766s OKs: 0 766s Standard error: 766s Segmentation fault (core dumped) 769s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 769s 139 769s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 769s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model.py" [FAIL] 6.8s 769s Time: 6.82 769s Return code: 139 769s OKs: 0 769s Standard error: 769s 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/cif/tests/tst_restraints.py" [FAIL] 6.6s 773s Time: 6.61 773s Return code: 139 773s OKs: 0 773s Standard error: 773s Segmentation fault (core dumped) 773s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_parser.py" [OK] 0.2s 773s Time: 0.23 773s Return code: 0 773s OKs: 0 773s Standard out: 773s 1 0 0 773s 1 0 0 773s 1 0 0 773s 1 0 0 773s 1 0 0 773s 1 0 0 773s 1 0 0 773s 1 0 0 773s 1 0 0 773s 0 0 0 773s 0 0 0 773s 1 0 0 773s 0 0 0 773s 0 0 0 773s 1 0 0 773s 1 0 0 773s 1 0 0 773s 1 0 0 773s 1 0 0 773s 1 0 0 773s 1 0 0 773s 1 0 0 773s 1 0 0 773s 1 0 0 773s 1 0 0 773s 1 0 0 773s 0 0 0 773s 1 0 0 773s 1 0 0 773s 1 0 0 773s 1 0 0 773s 1 0 0 773s 0 0 0 773s 0 1 0 773s 0 1 0 773s 0 0 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 0 1 0 773s 1 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s 2 0 0 773s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_citations.py" [OK] 0.3s 773s Time: 0.32 773s Return code: 0 773s OKs: 1 773s Standard out: 773s OK 773s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model_builder.py" [OK] 0.2s 773s Time: 0.23 773s Return code: 0 773s OKs: 0 777s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 777s 139 777s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 777s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_lex_parse_build.py" [FAIL] 3.8s 777s Time: 3.81 777s Return code: 139 777s OKs: 0 777s Standard error: 777s Segmentation fault (core dumped) 781s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 781s 139 781s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 781s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_hklf.py" [FAIL] 3.5s 781s Time: 3.52 781s Return code: 139 781s OKs: 0 781s Standard error: 781s Segmentation fault (core dumped) 782s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 782s 1 782s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 782s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py" [FAIL] 13.0s 782s Time: 12.99 782s Return code: 1 782s OKs: 0 782s Standard out: 782s Skipping tst_validation.exercise_smart_load() because of URLError. 782s Standard error: 782s Traceback (most recent call last): 782s File "/usr/lib/python3.13/urllib/request.py", line 1541, in ftp_open 782s fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout) 782s File "/usr/lib/python3.13/urllib/request.py", line 1561, in connect_ftp 782s return ftpwrapper(user, passwd, host, port, dirs, timeout, 782s persistent=False) 782s File "/usr/lib/python3.13/urllib/request.py", line 2409, in __init__ 782s self.init() 782s ~~~~~~~~~^^ 782s File "/usr/lib/python3.13/urllib/request.py", line 2418, in init 782s self.ftp.connect(self.host, self.port, self.timeout) 782s ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 782s File "/usr/lib/python3.13/ftplib.py", line 158, in connect 782s self.sock = socket.create_connection((self.host, self.port), self.timeout, 782s ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 782s source_address=self.source_address) 782s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 782s File "/usr/lib/python3.13/socket.py", line 864, in create_connection 782s raise exceptions[0] 782s File "/usr/lib/python3.13/socket.py", line 849, in create_connection 782s sock.connect(sa) 782s ~~~~~~~~~~~~^^^^ 782s TimeoutError: timed out 782s 782s The above exception was the direct cause of the following exception: 782s 782s Traceback (most recent call last): 782s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 327, in 782s exercise(sys.argv[1:]) 782s ~~~~~~~~^^^^^^^^^^^^^^ 782s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 26, in exercise 782s exercise_validation() 782s ~~~~~~~~~~~~~~~~~~~^^ 782s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 29, in exercise_validation 782s cd = validation.smart_load_dictionary(name="cif_core.dic") 782s File "/usr/lib/python3/dist-packages/iotbx/cif/validation.py", line 111, in smart_load_dictionary 782s url = locate_dictionary(name, registry_location=registry_location) 782s File "/usr/lib/python3/dist-packages/iotbx/cif/validation.py", line 129, in locate_dictionary 782s cm = cif.reader(file_object=urlopen(registry_location)).model() 782s ~~~~~~~^^^^^^^^^^^^^^^^^^^ 782s File "/usr/lib/python3.13/urllib/request.py", line 189, in urlopen 782s return opener.open(url, data, timeout) 782s ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 782s File "/usr/lib/python3.13/urllib/request.py", line 489, in open 782s response = self._open(req, data) 782s File "/usr/lib/python3.13/urllib/request.py", line 506, in _open 782s result = self._call_chain(self.handle_open, protocol, protocol + 782s '_open', req) 782s File "/usr/lib/python3.13/urllib/request.py", line 466, in _call_chain 782s result = func(*args) 782s File "/usr/lib/python3.13/urllib/request.py", line 1558, in ftp_open 782s raise URLError(exp) from exp 782s urllib.error.URLError: 784s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 784s 139 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/shelx/tst_writer.py" [FAIL] 3.7s 784s Time: 3.66 784s Return code: 139 784s OKs: 0 784s Standard error: 784s Segmentation fault (core dumped) 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/shelx/tst_fvar_encoding.py" [FAIL] 5.3s 788s Time: 5.26 788s Return code: 139 788s OKs: 0 788s Standard error: 788s Segmentation fault (core dumped) 788s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif.py" [OK] 0.3s 788s Time: 0.26 788s Return code: 0 788s OKs: 1 788s Standard out: 788s OK 791s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 791s 134 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_pdb.py" [FAIL] 6.8s 791s Time: 6.81 791s Return code: 134 791s OKs: 0 791s Standard error: 791s *** buffer overflow detected ***: terminated 791s Aborted (core dumped) 793s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy_2.py" [OK] 2.2s 793s Time: 2.23 793s Return code: 0 793s OKs: 1 793s Standard out: 793s OK 794s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_tls.py" [OK] 0.6s 794s Time: 0.64 794s Return code: 0 794s OKs: 1 794s Standard out: 794s Skipping exercise_mmcif_tls(): missing phenix_regression directory. 794s OK 794s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/hybrid_36.py" exercise [OK] 0.1s 794s Time: 0.10 794s Return code: 0 794s OKs: 1 794s Standard out: 794s OK 795s "/usr/lib/cctbx/python3.13/iotbx/pdb/hybrid_36_fem" [OK] 1.0s 795s Time: 0.96 795s Return code: 0 795s OKs: 0 795s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 795s 134 795s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 795s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy.py" [FAIL] 7.5s 795s Time: 7.51 795s Return code: 134 795s OKs: 0 795s Standard error: 795s *** buffer overflow detected ***: terminated 795s Aborted (core dumped) 796s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy_atom_sort.py" [OK] 0.3s 796s Time: 0.30 796s Return code: 0 796s OKs: 1 796s Standard out: 796s OK 796s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy_flip_symmetric.py" [OK] 0.2s 796s Time: 0.24 796s Return code: 0 796s OKs: 0 796s Standard out: 796s chem_data is missing, skipping test 796s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_selected_hierarchy_flip.py" [OK] 0.3s 796s Time: 0.27 796s Return code: 0 796s OKs: 0 799s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 799s 139 799s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 799s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy.py" [FAIL] 4.2s 799s Time: 4.15 799s Return code: 139 799s OKs: 0 799s Standard error: 799s Segmentation fault (core dumped) 803s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 803s 139 803s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 803s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_ext.py" [FAIL] 6.8s 803s Time: 6.81 803s Return code: 139 803s OKs: 0 803s Standard error: 803s Segmentation fault (core dumped) 803s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_rna_dna_atom_names.py" [OK] 0.3s 803s Time: 0.29 803s Return code: 0 803s OKs: 1 803s Standard out: 803s OK 803s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_name_interpretation.py" [OK] 0.3s 803s Time: 0.25 803s Return code: 0 803s OKs: 1 803s Standard out: 803s OK 804s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_extract_rfactors_resolutions_sigma.py" [OK] 0.2s 804s Time: 0.24 804s Return code: 0 804s OKs: 1 804s Standard out: 804s OK 804s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/modified_aa_names.py" [OK] 0.0s 804s Time: 0.03 804s Return code: 0 804s OKs: 0 804s Standard out: 804s 2141 804s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/modified_rna_dna_names.py" [OK] 0.0s 804s Time: 0.03 804s Return code: 0 804s OKs: 0 804s Standard out: 804s 792 804s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_sheet.py" [OK] 0.2s 804s Time: 0.24 804s Return code: 0 804s OKs: 1 804s Standard out: 804s OK 804s u+s,u,s: 0.19 0.15 0.04 806s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 806s 139 806s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 806s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection.py" [FAIL] 6.9s 806s Time: 6.93 806s Return code: 139 806s OKs: 0 806s Standard error: 806s Segmentation fault (core dumped) 806s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation_long.py" [OK] 0.3s 806s Time: 0.26 806s Return code: 0 806s OKs: 1 806s Standard out: 806s OK time = 0.014 807s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/secondary_structure.py" [OK] 0.3s 807s Time: 0.26 807s Return code: 0 807s OKs: 0 810s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 810s 139 810s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 810s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation.py" [FAIL] 5.9s 810s Time: 5.86 810s Return code: 139 810s OKs: 0 810s Standard error: 810s Segmentation fault (core dumped) 811s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_secondary_structure.py" [OK] 0.8s 811s Time: 0.76 811s Return code: 0 811s OKs: 5 811s Standard out: 811s OK 811s OK 811s OK 811s OK 811s OK 813s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 813s 139 813s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 813s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection_string.py" [FAIL] 6.6s 813s Time: 6.63 813s Return code: 139 813s OKs: 0 813s Standard error: 813s Segmentation fault (core dumped) 815s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_secondary_structure_2.py" [OK] 1.6s 815s Time: 1.61 815s Return code: 0 815s OKs: 2 815s Standard out: 815s OK 815s OK 816s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/remediation/tst_remediator.py" [OK] 0.7s 816s Time: 0.67 816s Return code: 0 816s OKs: 0 816s Standard out: 816s chem_data is not available for remediator tests, skipping 816s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_to_map_simple.py" [OK] 0.2s 816s Time: 0.24 816s Return code: 0 816s OKs: 0 816s Standard out: 816s Usage: iotbx.python pdb_to_map_simple.py [options] pdb_file... 816s 816s Options: 816s -h, --help show this help message and exit 816s --d_min=FLOAT high-resolution limit for structure-factor calculation 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/pdb/tst_utils.py" [FAIL] 6.0s 817s Time: 6.02 817s Return code: 139 817s OKs: 0 817s Standard error: 817s Segmentation fault (core dumped) 817s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_tardy_conf_sampling_simple.py" [OK] 0.3s 817s Time: 0.26 817s Return code: 0 817s OKs: 0 817s Standard out: 817s Time importing extensions: 0.20 817s skipping test: phenix_regression not available. 820s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 820s 134 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/examples/pdb_truncate_to_ala/tst.py" [FAIL] 4.3s 820s Time: 4.27 820s Return code: 134 820s OKs: 0 820s Standard error: 820s *** buffer overflow detected ***: terminated 820s Aborted (core dumped) 824s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 824s 139 824s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 824s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_examples.py" [FAIL] 7.3s 824s Time: 7.29 824s Return code: 139 824s OKs: 0 824s Standard error: 824s Segmentation fault (core dumped) 827s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 827s 139 827s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 827s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/space_group_symbols.py" [FAIL] 7.1s 827s Time: 7.11 827s Return code: 139 827s OKs: 0 827s Standard error: 827s Segmentation fault (core dumped) 830s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 830s 139 830s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 830s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/tst_cns.py" [FAIL] 6.2s 830s Time: 6.21 830s Return code: 139 830s OKs: 0 830s Standard error: 830s Segmentation fault (core dumped) 834s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 834s 139 834s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 834s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_merge.py" P31 [FAIL] 6.5s 834s Time: 6.45 834s Return code: 139 834s OKs: 0 834s Standard error: 834s Segmentation fault (core dumped) 837s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 837s 139 837s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 837s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/no_merge_original_index.py" [FAIL] 6.4s 837s Time: 6.39 837s Return code: 139 837s OKs: 0 837s Standard error: 837s Segmentation fault (core dumped) 840s Standard error: 840s Segmentation fault (core dumped) 840s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 840s 139 840s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 840s libtbx.python "/usr/lib/python3/dist-packages/iotbx/ccp4_map/tst.py" [FAIL] 6.4s 840s Time: 6.37 840s Return code: 139 840s OKs: 0 844s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 844s 139 844s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 844s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_ext.py" [FAIL] 6.9s 844s Time: 6.89 844s Return code: 139 844s OKs: 0 844s Standard error: 844s Segmentation fault (core dumped) 847s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 847s 139 847s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 847s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_extract_from_symmetry_lib.py" [FAIL] 7.2s 847s Time: 7.24 847s Return code: 139 847s OKs: 0 847s Standard error: 847s /usr/lib/python3/dist-packages/ccp4io_adaptbx/__init__.py:25: UserWarning: ccp4io_adaptbx: cannot locate syminfo.lib 847s warnings.warn("ccp4io_adaptbx: cannot locate syminfo.lib") 847s Segmentation fault (core dumped) 848s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_miller_dict.py" [OK] 0.2s 848s Time: 0.23 848s Return code: 0 848s OKs: 0 848s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_unmerged.py" [OK] 0.2s 848s Time: 0.23 848s Return code: 0 848s OKs: 0 848s Standard out: 848s Title: . 848s Space group symbol from file: I23 848s Space group number from file: 197 848s Space group from matrices: I 2 3 (No. 197) 848s Point group symbol from file: PG23 848s Number of batches: 45 848s Number of crystals: 2 848s Number of Miller indices: 13 848s Resolution range: 39.0022 31.8451 848s History: 848s From MTZUTILS 21/11/2017 16:26:11 after history: 848s From MOSFLM run on 1/ 7/08 848s From MOSFLM run on 1/ 7/08 848s Crystal 1: 848s Name: HKL_base 848s Project: HKL_base 848s Id: 1 848s Unit cell: (78.0043, 78.0043, 78.0043, 90, 90, 90) 848s Number of datasets: 1 848s Dataset 1: 848s Name: HKL_base 848s Id: 0 848s Wavelength: 0 848s Number of columns: 18 848s label #valid %valid min max type 848s H 13 100.00% 0.00 1.00 H: index h,k,l 848s K 13 100.00% 2.00 2.00 H: index h,k,l 848s L 13 100.00% 0.00 1.00 H: index h,k,l 848s M_ISYM 13 100.00% 6.00 272.00 Y: M/ISYM, packed partial/reject flag and symmetry number 848s BATCH 13 100.00% 16.00 43.00 B: BATCH number 848s I 13 100.00% -19.71 7.39 J: intensity 848s SIGI 13 100.00% 0.41 3.05 Q: standard deviation 848s IPR 13 100.00% -10.84 4.99 J: intensity 848s SIGIPR 13 100.00% 0.41 3.05 Q: standard deviation 848s FRACTIONCALC 13 100.00% 0.07 1.15 R: real 848s XDET 13 100.00% 1099.43 1215.80 R: real 848s YDET 13 100.00% 1110.92 1201.06 R: real 848s ROT 13 100.00% 15.33 41.55 R: real 848s WIDTH 13 100.00% 0.37 2.19 R: real 848s LP 13 100.00% 0.00 0.03 R: real 848s MPART 13 100.00% 0.00 303.00 I: integer 848s FLAG 13 100.00% 0.00 40.00 I: integer 848s BGPKRATIOS 13 100.00% 8.04 10610.05 R: real 848s Crystal 2: 848s Name: DEFAULT 848s Project: AUTOMATIC 848s Id: 2 848s Unit cell: (78.0043, 78.0043, 78.0043, 90, 90, 90) 848s Number of datasets: 1 848s Dataset 1: 848s Name: NATIVE_SWEEP1 848s Id: 1 848s Wavelength: 0.979 848s Number of columns: 0 848s asu: (1, 2, 1) orig: (-1, 1, -2) M/ISYM: 15 848s asu: (1, 2, 1) orig: (1, -1, 2) M/ISYM: 272 848s asu: (1, 2, 1) orig: (1, -1, 2) M/ISYM: 272 848s asu: (1, 2, 1) orig: (-1, 2, 1) M/ISYM: 6 848s asu: (1, 2, 1) orig: (1, -2, -1) M/ISYM: 261 848s asu: (1, 2, 1) orig: (-1, 2, -1) M/ISYM: 263 848s asu: (1, 2, 1) orig: (1, -2, -1) M/ISYM: 261 848s asu: (1, 2, 1) orig: (-1, 2, -1) M/ISYM: 263 848s asu: (1, 2, 1) orig: (1, -2, 1) M/ISYM: 264 848s asu: (1, 2, 1) orig: (1, -2, 1) M/ISYM: 264 848s asu: (0, 2, 0) orig: (0, 0, -2) M/ISYM: 266 848s asu: (0, 2, 0) orig: (0, 0, -2) M/ISYM: 266 848s asu: (0, 2, 0) orig: (0, 0, -2) M/ISYM: 266 851s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 851s 139 851s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 851s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_dano.py" [FAIL] 6.9s 851s Time: 6.92 851s Return code: 139 851s OKs: 0 851s Standard error: 851s Segmentation fault (core dumped) 851s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/tst_mtz_free_flipper.py" [OK] 0.3s 851s Time: 0.29 851s Return code: 0 851s OKs: 0 851s Standard out: 851s Skipping exercise(): input file not available 851s u+s,u,s: 0.23 0.16 0.07 854s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 854s 139 854s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 854s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst.py" P31 [FAIL] 6.2s 854s Time: 6.16 854s Return code: 139 854s OKs: 0 854s Standard error: 854s Segmentation fault (core dumped) 854s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_adsc.py" [OK] 0.2s 854s Time: 0.21 854s Return code: 0 854s OKs: 1 854s Standard out: 854s Skipping exercise_adscread(): input file not available 854s OK 854s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_detectors.py" [OK] 0.1s 854s Time: 0.07 854s Return code: 0 854s OKs: 0 854s Standard out: 854s bpcx_regression not configured, skipping test 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_reflection_file_utils.py" [FAIL] 6.6s 858s Time: 6.62 858s Return code: 139 858s OKs: 0 858s Standard error: 858s Segmentation fault (core dumped) 861s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 861s 139 861s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 861s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xplor/tst_xplormap.py" [FAIL] 6.6s 861s Time: 6.59 861s Return code: 139 861s OKs: 0 861s Standard error: 861s Segmentation fault (core dumped) 861s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdbx_mmcif_tutorial.py" [OK] 0.1s 861s Time: 0.08 861s Return code: 0 861s OKs: 1 861s Standard out: 861s phenix_regression not configured, skipping tst_pdbx_mmcif_tutorial.py 861s OK 864s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 864s 139 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_phases.py" P31 [FAIL] 6.6s 864s Time: 6.63 864s Return code: 139 864s OKs: 0 864s Standard error: 864s Segmentation fault (core dumped) 870s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 870s 1 870s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 870s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py" [FAIL] 9.4s 870s Time: 9.36 870s Return code: 1 870s OKs: 0 870s Standard error: 870s Traceback (most recent call last): 870s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 477, in 870s exercise(sys.argv[1:]) 870s ~~~~~~~~^^^^^^^^^^^^^^ 870s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 22, in exercise 870s run_and_compare( 870s ~~~~~~~~~~~~~~~^ 870s ['iotbx.lattice_symmetry' 870s ^^^^^^^^^^^^^^^^^^^^^^^^^ 870s ...<31 lines>... 870s 870s 870s """) 870s ^^^^ 870s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 17, in run_and_compare 870s command=command).raise_if_errors().stdout_lines 870s ~~~~~~~~~~~~~~~^^ 870s File "/usr/lib/python3/dist-packages/libtbx/easy_run.py", line 46, in raise_if_errors 870s raise Error(msg) 870s RuntimeError: child process stderr output: 870s command: 'iotbx.lattice_symmetry --unit_cell="12.7923,12.8923,29.4356,102.846,103.846,22.7475"' 870s Segmentation fault (core dumped) 870s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_plots.py" [OK] 0.1s 870s Time: 0.09 870s Return code: 0 870s OKs: 1 870s Standard out: 870s OK 870s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_csv_utils.py" [OK] 0.2s 870s Time: 0.17 870s Return code: 0 870s OKs: 1 870s Standard out: 870s 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_reflection_statistics.py" Fdd2 P31m [FAIL] 7.1s 871s Time: 7.08 871s Return code: 139 871s OKs: 0 871s Standard error: 871s Segmentation fault (core dumped) 871s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_bioinformatics.py" [OK] 0.1s 871s Time: 0.12 871s Return code: 0 871s OKs: 3 871s Standard out: 871s Testing guess_chain_types ... OK 871s Testing merge_sequences ... OK 871s testEquality (__main__.test_sequence.testEquality) ... ok 871s testNonEquality (__main__.test_sequence.testNonEquality) ... ok 871s testFormat (__main__.test_fasta_sequence.testFormat) ... ok 871s testStr (__main__.test_fasta_sequence.testStr) ... ok 871s testFormat (__main__.test_pir_sequence.testFormat) ... ok 871s testStr (__main__.test_pir_sequence.testStr) ... ok 871s testConservationCode (__main__.test_midline.testConservationCode) ... ok 871s testMidline (__main__.test_midline.testMidline) ... ok 871s test__str__ (__main__.test_alignment.test__str__) ... ok 871s test_copy (__main__.test_alignment.test_copy) ... ok 871s test_error (__main__.test_alignment.test_error) ... ok 871s test_extend (__main__.test_alignment.test_extend) ... ok 871s test_identity_count (__main__.test_alignment.test_identity_count) ... ok 871s test_identity_fraction (__main__.test_alignment.test_identity_fraction) ... ok 871s test_length (__main__.test_alignment.test_length) ... ok 871s test_multiplicity (__main__.test_alignment.test_multiplicity) ... ok 871s test__str__ (__main__.test_fasta_alignment.test__str__) ... ok 871s test_copy (__main__.test_fasta_alignment.test_copy) ... ok 871s test_error (__main__.test_fasta_alignment.test_error) ... ok 871s test_format (__main__.test_fasta_alignment.test_format) ... ok 871s test__str__ (__main__.test_pir_alignment.test__str__) ... ok 871s test_copy (__main__.test_pir_alignment.test_copy) ... ok 871s test_error (__main__.test_pir_alignment.test_error) ... ok 871s test_format (__main__.test_pir_alignment.test_format) ... ok 871s test__str__ (__main__.test_clustal_alignment.test__str__) ... ok 871s test_copy (__main__.test_clustal_alignment.test_copy) ... ok 871s test_format (__main__.test_clustal_alignment.test_format) ... ok 871s testFasta (__main__.test_sequence_parse.testFasta) ... ok 871s testPir (__main__.test_sequence_parse.testPir) ... ok 871s testSequence (__main__.test_sequence_parse.testSequence) ... ok 871s testTolerantPir (__main__.test_sequence_parse.testTolerantPir) ... ok 871s test_dbfetch_parse (__main__.test_sequence_parse.test_dbfetch_parse) ... ok 871s test_filename_selection (__main__.test_sequence_parse.test_filename_selection) ... ok 871s test_known_formats (__main__.test_sequence_parse.test_known_formats) ... ok 871s test_ls_parse (__main__.test_sequence_parse.test_ls_parse) ... ok 871s test_tf_parse (__main__.test_sequence_parse.test_tf_parse) ... ok 871s testAli (__main__.test_alignment_parse.testAli) ... ok 871s testClustal (__main__.test_alignment_parse.testClustal) ... ok 871s testFasta (__main__.test_alignment_parse.testFasta) ... ok 871s testPir (__main__.test_alignment_parse.testPir) ... ok 871s test_filename_selection (__main__.test_alignment_parse.test_filename_selection) ... ok 871s test_known_formats (__main__.test_alignment_parse.test_known_formats) ... ok 871s test_process_header (__main__.test_hhsearch_parser.test_process_header) ... ok 871s test_process_hits (__main__.test_hhsearch_parser.test_process_hits) ... ok 871s test_process_header (__main__.test_hhalign_parser.test_process_header) ... ok 871s test_process_hits (__main__.test_hhalign_parser.test_process_hits) ... ok 871s 871s ---------------------------------------------------------------------- 871s Ran 46 tests in 0.008s 871s 871s OK 875s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 875s 139 875s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 875s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_file_reader.py" [FAIL] 4.2s 875s Time: 4.25 875s Return code: 139 875s OKs: 0 875s Standard error: 875s Segmentation fault (core dumped) 881s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 881s 1 881s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 881s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py" [FAIL] 10.1s 881s Time: 10.08 881s Return code: 1 881s OKs: 0 881s Standard out: 881s Starting iotbx.pdb.box_around_molecule 881s on Sat Mar 22 13:20:34 2025 by ubuntu 881s =============================================================================== 881s 881s Standard error: 881s *** buffer overflow detected ***: terminated 881s Aborted (core dumped) 881s Traceback (most recent call last): 881s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py", line 138, in 881s exercise() 881s ~~~~~~~~^^ 881s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py", line 48, in exercise 881s assert not easy_run.call("iotbx.pdb.box_around_molecule %s.pdb" % ( 881s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 881s prefix)) 881s ^^^^^^^^ 881s AssertionError 882s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_input.py" [OK] 0.2s 882s Time: 0.24 882s Return code: 0 882s OKs: 0 882s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 882s 134 882s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 882s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_segids.py" [FAIL] 7.7s 882s Time: 7.70 882s Return code: 134 882s OKs: 0 882s Standard error: 882s *** buffer overflow detected ***: terminated 882s Aborted (core dumped) 883s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_multimodel.py" [OK] 0.6s 883s Time: 0.64 883s Return code: 0 883s OKs: 0 883s Standard out: 883s ['_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'] 883s ['_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'] 883s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_add_conformations.py" [OK] 0.3s 883s Time: 0.25 883s Return code: 0 883s OKs: 0 883s Standard out: 883s phenix_regression not available, skipping test. 886s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 886s 134 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_hierarchy_forward_compatible_pdb.py" [FAIL] 4.1s 886s Time: 4.09 886s Return code: 134 886s OKs: 0 886s Standard error: 886s *** buffer overflow detected ***: terminated 886s Aborted (core dumped) 886s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reindex.py" [OK] 0.1s 886s Time: 0.08 886s Return code: 0 886s OKs: 1 886s Standard out: 886s Skipping 886s OK 889s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 889s 139 889s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 889s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_symmetry.py" [FAIL] 5.5s 889s Time: 5.49 889s Return code: 139 889s OKs: 0 889s Standard error: 889s Segmentation fault (core dumped) 892s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 892s 139 892s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 892s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_editor.py" [FAIL] 6.3s 892s Time: 6.33 892s Return code: 139 892s OKs: 0 892s Standard error: 892s Segmentation fault (core dumped) 892s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_as_fasta.py" [OK] 0.3s 892s Time: 0.28 892s Return code: 0 892s OKs: 1 892s Standard out: 892s OK 893s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_link_records.py" [OK] 0.3s 893s Time: 0.30 893s Return code: 0 893s OKs: 0 893s Standard out: 893s Can not initialize monomer_library, skipping test. 893s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_merging_statistics.py" [OK] 0.2s 893s Time: 0.20 893s Return code: 0 893s OKs: 1 893s Standard out: 893s phenix_regression not configured, skipping. 893s OK 898s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 898s 1 898s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 898s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py" [FAIL] 9.2s 898s Time: 9.24 898s Return code: 1 898s OKs: 0 898s Standard error: 898s Traceback (most recent call last): 898s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py", line 60, in 898s exercise() 898s ~~~~~~~~^^ 898s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py", line 48, in exercise 898s assert (len(out.stdout_lines) == 2) and (len(out.stderr_lines) == 0) 898s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 898s AssertionError 899s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 899s 139 899s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 899s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_map_coefficients.py" [FAIL] 5.8s 899s Time: 5.76 899s Return code: 139 899s OKs: 0 899s Standard error: 899s Segmentation fault (core dumped) 899s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_xparm.py" [OK] 0.1s 899s Time: 0.09 899s Return code: 0 899s OKs: 3 899s Standard out: 899s OK 899s OK 899s OK 899s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_xds_inp.py" [OK] 0.1s 899s Time: 0.09 899s Return code: 0 899s OKs: 1 899s Standard out: 899s OK 905s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 905s 1 905s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 905s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py" [FAIL] 7.3s 905s Time: 7.34 905s Return code: 1 905s OKs: 0 905s Standard out: 905s iotbx.pdb.sort_atoms tst_sort_atoms_1.pdb 905s Standard error: 905s Segmentation fault (core dumped) 905s Traceback (most recent call last): 905s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py", line 815, in 905s exercise_1() 905s ~~~~~~~~~~^^ 905s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py", line 806, in exercise_1 905s assert not easy_run.call(cmd) 905s ^^^^^^^^^^^^^^^^^^^^^^ 905s AssertionError 905s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_spots_xds.py" [OK] 0.1s 905s Time: 0.08 905s Return code: 0 905s OKs: 1 905s Standard out: 905s OK 906s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_pdb_as_cif.py" [OK] 0.4s 906s Time: 0.40 906s Return code: 0 906s OKs: 1 906s Standard out: 906s Can not initialize monomer_library, skipping tst_pdb_as_cif. 906s OK 907s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 907s 139 907s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 907s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_integrate_hkl.py" [FAIL] 7.6s 907s Time: 7.60 907s Return code: 139 907s OKs: 0 907s Standard error: 907s 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/scalepack/tst_no_merge_original_index.py" [FAIL] 4.1s 910s Time: 4.07 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/tst_export_scalepack_unmerged.py" [FAIL] 7.0s 914s Time: 7.04 914s Return code: 139 914s OKs: 0 914s Standard error: 914s Segmentation fault (core dumped) 914s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_mtrix_biomt_cmdl.py" [OK] 0.3s 914s Time: 0.26 914s Return code: 0 914s OKs: 0 914s Standard out: 914s Skipping tests: phenix not found 914s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_mmcif_biomt_reduction_output.py" [OK] 0.7s 914s Time: 0.68 914s Return code: 0 914s OKs: 0 914s Standard out: 914s chem_data is not available, skipping 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/dsn6/tst.py" P31 [FAIL] 6.9s 917s Time: 6.88 917s Return code: 139 917s OKs: 0 917s Standard error: 917s Segmentation fault (core dumped) 920s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 920s 139 920s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 920s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_ligs.py" [FAIL] 5.9s 920s Time: 5.90 920s Return code: 139 920s OKs: 0 920s Standard error: 920s 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_search_broken_chain.py" [FAIL] 7.1s 924s Time: 7.11 924s Return code: 139 924s OKs: 0 924s Standard error: 924s Segmentation fault (core dumped) 927s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 927s 139 927s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 927s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_shortcut_1.py" [FAIL] 7.0s 927s Time: 6.98 927s Return code: 139 927s OKs: 0 927s Standard error: 927s Segmentation fault (core dumped) 932s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 932s 139 932s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 932s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_groups_preprocessing.py" [FAIL] 7.6s 932s Time: 7.62 932s Return code: 139 932s OKs: 0 932s Standard error: 932s Segmentation fault (core dumped) 935s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 935s 139 935s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 935s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_input.py" [FAIL] 7.6s 935s Time: 7.60 935s Return code: 139 935s OKs: 0 935s Standard error: 935s Segmentation fault (core dumped) 939s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 939s 139 939s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 939s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_user_selections.py" [FAIL] 7.0s 939s Time: 7.01 939s Return code: 139 939s OKs: 0 939s Standard error: 939s Segmentation fault (core dumped) 943s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 943s 139 943s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 943s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs.py" [FAIL] 7.8s 943s Time: 7.79 943s Return code: 139 943s OKs: 0 943s Standard error: 943s Segmentation fault (core dumped) 946s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 946s 139 946s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 946s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_without_validation.py" [FAIL] 7.7s 946s Time: 7.66 946s Return code: 139 946s OKs: 0 946s Standard error: 946s Segmentation fault (core dumped) 950s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 950s 139 950s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 950s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_read_mtrix_records_from_cif.py" [FAIL] 7.5s 950s Time: 7.47 950s Return code: 139 950s OKs: 0 950s Standard error: 950s Segmentation fault (core dumped) 954s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 954s 139 954s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 954s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_show_systematic_absences.py" [FAIL] 7.6s 954s Time: 7.60 954s Return code: 139 954s OKs: 0 954s Standard error: 954s Segmentation fault (core dumped) 954s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_reader.py" [OK] 0.4s 954s Time: 0.36 954s Return code: 0 954s OKs: 1 954s Standard out: 954s OK 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_miller_sort_asu.py" [FAIL] 6.9s 957s Time: 6.95 957s Return code: 139 957s OKs: 0 957s Standard error: 957s Segmentation fault (core dumped) 957s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_alignment_as_hsearch.py" [OK] 0.1s 957s Time: 0.11 957s Return code: 0 957s OKs: 0 957s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_ebi_wu_blast_xml.py" [OK] 0.1s 957s Time: 0.12 957s Return code: 0 957s OKs: 0 958s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/tst_ncbi_blast_xml.py" [OK] 0.1s 958s Time: 0.11 958s Return code: 0 958s OKs: 0 958s libtbx.python "/usr/lib/python3/dist-packages/iotbx/bioinformatics/pdb_info.py" [OK] 0.5s 958s Time: 0.51 958s Return code: 0 958s OKs: 0 961s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 961s 134 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_xray_scale.py" [FAIL] 7.1s 961s Time: 7.10 961s Return code: 134 961s OKs: 0 961s Standard error: 961s *** buffer overflow detected ***: terminated 961s Aborted (core dumped) 965s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 965s 139 965s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 965s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_as_pdb_1atom.py" [FAIL] 7.4s 965s Time: 7.36 965s Return code: 139 965s OKs: 0 965s Standard error: 965s Segmentation fault (core dumped) 969s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 969s 139 969s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 969s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_1.py" [FAIL] 8.2s 969s Time: 8.17 969s Return code: 139 969s OKs: 0 969s Standard error: 969s Segmentation fault (core dumped) 976s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 976s 1 976s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 976s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py" [FAIL] 10.7s 976s Time: 10.66 976s Return code: 1 976s OKs: 0 976s Standard error: 976s Traceback (most recent call last): 976s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py", line 395, in 976s tst_1() 976s ~~~~~^^ 976s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py", line 370, in tst_1 976s assert os.path.isfile('%s.cif_%s_000.mtz' % (prefix, bn)) 976s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 976s AssertionError 978s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 978s 134 978s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 978s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_all_chain_ids.py" [FAIL] 8.3s 978s Time: 8.31 978s Return code: 134 978s OKs: 0 978s Standard error: 978s *** buffer overflow detected ***: terminated 978s Aborted (core dumped) 981s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 981s 139 981s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 981s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_extract_xtal_data.py" [FAIL] 5.3s 981s Time: 5.28 981s Return code: 139 981s OKs: 0 981s Standard error: 981s Segmentation fault (core dumped) 982s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mtz_as_cif.py" [OK] 0.4s 982s Time: 0.36 982s Return code: 0 982s OKs: 1 982s Standard out: 982s Skipping 1akg.mtz test: input file not available 982s Skipping 1zff.mtz test: input file not available 982s Skipping l.mtz test: input file not available 982s Skipping outside_4_exptl_fobs_phases_freeR_flags.mtz test: input file not available 982s Skipping r1wqzsf.mtz test: input file not available 982s Skipping ur0013.sf.mtz test: input file not available 982s Skipping 1aba_test.mtz test: input file not available 982s OK 982s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_group_rounding.py" [OK] 0.2s 982s Time: 0.24 982s Return code: 0 982s OKs: 0 985s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 985s 139 985s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 985s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cli_parser.py" [FAIL] 7.7s 985s Time: 7.71 985s Return code: 139 985s OKs: 0 985s Standard error: 985s Segmentation fault (core dumped) 986s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_merge_atoms_at_end_to_residues.py" [OK] 0.2s 986s Time: 0.25 986s Return code: 0 986s OKs: 1 986s Standard out: 986s [('1', 22), ('3', 17), ('1', 1), ('3', 1)] 986s [('1', 22), ('3', 18), ('1', 1)] 986s OK 987s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_chain_ids_1.py" [OK] 1.1s 987s Time: 1.10 987s Return code: 0 987s OKs: 1 987s Standard out: 987s 987s total number of: 987s models: 1 987s chains: 3 987s alt. conf.: 0 987s residues: 12 987s atoms: 174 987s anisou: 0 987s number of atom element+charge types: 4 987s histogram of atom element+charge frequency: 987s " H " 78 987s " C " 60 987s " O " 21 987s " N " 15 987s residue name classes: 987s "common_amino_acid" 12 987s number of chain ids: 3 987s histogram of chain id frequency: 987s "A" 1 987s "A-2" 1 987s "A-5" 1 987s number of alt. conf. ids: 0 987s number of residue names: 4 987s histogram of residue name frequency: 987s "ASN" 3 987s "PHE" 3 987s "SER" 3 987s "THR" 3 987s Can not initialize monomer_library, skipping test. 987s OK. Time: 0.447 987s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_1.py" [OK] 0.7s 987s Time: 0.65 987s Return code: 0 987s OKs: 1 987s Standard out: 987s OK. Time: 0.407 988s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_2.py" [OK] 0.7s 988s Time: 0.67 988s Return code: 0 988s OKs: 1 988s Standard out: 988s Can not initialize monomer_library, skipping test. 988s OK. Time: 0.015 989s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_3.py" [OK] 0.7s 989s Time: 0.69 989s Return code: 0 989s OKs: 1 989s Standard out: 989s Can not initialize monomer_library, skipping test. 989s OK. Time: 0.020 989s Standard error: 989s *** buffer overflow detected ***: terminated 989s Aborted (core dumped) 989s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 989s 134 989s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 989s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_occupancies_rounding.py" [FAIL] 6.9s 989s Time: 6.93 989s Return code: 134 989s OKs: 0 989s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_copy_select.py" [OK] 0.3s 989s Time: 0.28 989s Return code: 0 989s OKs: 1 989s Standard out: 989s There is no info: pdb=" N " 989s And no parent: None 989s Info is gone: pdb=" N " 989s Info is still here: pdb=" N GLY A 1 " 989s OK. Time: 0.027 989s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_id_str.py" [OK] 0.3s 989s Time: 0.26 989s Return code: 0 989s OKs: 0 989s Standard out: 989s u+s,u,s: 0.21 0.17 0.04 990s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_long_resname_4.py" [OK] 0.7s 990s Time: 0.68 990s Return code: 0 990s OKs: 1 990s Standard out: 990s Can not initialize monomer_library, skipping test. 990s OK. Time: 0.014 990s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_altlocs.py" [OK] 0.3s 990s Time: 0.26 990s Return code: 0 990s OKs: 1 990s Standard out: 990s OK 993s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 993s 139 993s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 993s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_debug_write.py" [FAIL] 3.2s 993s Time: 3.19 993s Return code: 139 993s OKs: 0 993s Standard error: 993s Segmentation fault (core dumped) 997s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 997s 139 997s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 997s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_reordered_chains.py" [EXPECTED FAIL] 3.8s 997s Time: 3.81 997s Return code: 139 997s OKs: 0 997s Standard error: 997s Segmentation fault (core dumped) 1001s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1001s 134 1001s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1001s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_to_from_hierarchy.py" [EXPECTED FAIL] 4.6s 1001s Time: 4.56 1001s Return code: 134 1001s OKs: 0 1001s Standard error: 1001s *** buffer overflow detected ***: terminated 1001s Aborted (core dumped) 1001s libtbx.python "/usr/lib/python3/dist-packages/libtbx/metric_prefixes.py" [OK] 0.0s 1001s Time: 0.03 1001s Return code: 0 1001s OKs: 1 1001s Standard out: 1001s OK 1006s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_utils.py" [OK] 4.3s 1006s Time: 4.28 1006s Return code: 0 1006s OKs: 0 1006s Standard out: 1006s Skipping exercise_retrieve_unless_exists 1006s ### USER = ubuntu 1006s ### PID = 10129 1006s multiprocessing problem: None 1006s base36_timestamp(): 00m8k8obl9 now 1006s base36_timestamp(): zzydazd000 year 115855 CE 1006s get_svn_revision(): None 1006s get_build_tag(): None 1006s u+s,u,s: 0.10 0.08 0.02 1006s libtbx.python "/usr/lib/python3/dist-packages/libtbx/test_utils/__init__.py" [OK] 0.7s 1006s Time: 0.66 1006s Return code: 0 1006s OKs: 1 1006s Standard out: 1006s OK 1006s libtbx.python "/usr/lib/python3/dist-packages/libtbx/queuing_system_utils/pbs_utils.py" [OK] 0.0s 1006s Time: 0.03 1006s Return code: 0 1006s OKs: 1 1006s Standard out: 1006s *** MY_PBS_ARRAY_SIZE = None 1006s *** MY_PBS_ARRAYID_OFFSET = None 1006s *** PBS_ARRAYID = None 1006s *** OMPI_MCA_ns_nds_num_procs = None 1006s *** OMPI_MCA_ns_nds_vpid = None 1006s n,i: 1 0 1006s OK 1006s libtbx.python "/usr/lib/python3/dist-packages/libtbx/queuing_system_utils/sge_utils.py" [OK] 0.0s 1006s Time: 0.03 1006s Return code: 0 1006s OKs: 1 1006s Standard out: 1006s *** JOB_ID = None 1006s *** SGE_ARCH = None 1006s *** SGE_TASK_FIRST = None 1006s *** SGE_TASK_LAST = None 1006s *** SGE_TASK_ID = None 1006s OK 1006s libtbx.python "/usr/lib/python3/dist-packages/libtbx/introspection.py" [OK] 0.1s 1006s Time: 0.05 1006s Return code: 0 1006s OKs: 1 1006s Standard out: 1006s number of processors: 2 1006s Virtual memory size: 21,860,352 1006s Resident set size: 13,049,856 1006s Stack size: 139,264 1006s Virtual memory size: 21,983,232 exact max: 29,986,816 1006s Resident set size: 13,709,312 approx. max: 21,626,880 1006s Stack size: 139,264 approx. max: 139,264 1006s Memory total: 4,106,809,344 1006s Memory free: 134,905,856 1006s OK 1029s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_thread_utils.py" [OK] 23.0s 1029s Time: 23.00 1029s Return code: 0 1029s OKs: 1 1029s Standard out: 1029s OK 1033s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp.py" [OK] 3.4s 1033s Time: 3.37 1033s Return code: 0 1033s OKs: 1 1033s Standard out: 1033s multiprocessing pool size: 2 1033s wall clock time: 0.01 seconds 1033s OK 1034s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp_state.py" [OK] 0.8s 1034s Time: 0.83 1034s Return code: 0 1034s OKs: 3 1034s Standard out: 1034s Running threading test with 1 processes, 1 threads, 3 tasks 1034s (0x76f6d236aba0-11345) object in state -init- 1034s (0x76f6d236aba0-11345) changing state from -init- to D326P2 1034s (0x76f6d236aba0-11345) changing state from D326P2 to QKM7UK 1034s (0x76f6d236aba0-11345) changing state from QKM7UK to 842J2H 1034s (0x76f6d236aba0-11345) object in state 842J2H 1034s OK 1034s Running threading test with 2 processes, 1 threads, 3 tasks 1034s (0x76f6d2232210-11345) object in state -init- 1034s (0x76f6d2232210-11345) changing state from -init- to QJOX6R 1034s (0x76f6d2232210-11345) changing state from QJOX6R to 9I3O4A 1034s (0x76f6d2232210-11345) changing state from 9I3O4A to 5CUC3I 1034s (0x76f6d2232210-11345) object in state 5CUC3I 1034s OK 1034s Running multiprocessing test with 1 processes, 1 threads, 3 tasks 1034s (0x76f6d2232210-11345) object in state -init- 1034s (0x76f6d2232210-11345) changing state from -init- to 2FY2FH 1034s (0x76f6d2232210-11345) changing state from 2FY2FH to PH5K9W 1034s (0x76f6d2232210-11345) changing state from PH5K9W to ML4IDB 1034s (0x76f6d2232210-11345) object in state ML4IDB 1034s OK 1034s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_pickle.py" [OK] 0.1s 1034s Time: 0.06 1034s Return code: 0 1034s OKs: 1 1034s Standard out: 1034s test.dat 1034s dump: 0.00 s 1034s load buffered: 0.00 s 1034s load direct: 0.00 s 1034s test.dat.gz 1034s dump: 0.00 s 1034s load buffered: 0.00 s 1034s load direct: 0.00 s 1034s dumps/loads 1034s dump: 0.00 s 1034s load buffered: 0.00 s 1034s OK 1034s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_fully_buffered_timeout.py" [OK] 0.1s 1034s Time: 0.08 1034s Return code: 0 1034s OKs: 0 1034s Standard out: 1034s Skipping test: probe not configured 1041s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_fetch.py" [OK] 51.1s 1041s Time: 51.15 1041s Return code: 0 1041s OKs: 1 1041s Standard out: 1041s data_r1yjpsf 1041s # 1041s loop_ 1041s _audit.revision_id 1041s _audit.creation_date 1041s _audit.update_record 1041s 1_0 2005-06-14 'Initial release' 1041s 1_1 2013-05-08 'Status correction and format standardization' 1041s # 1041s _cell.entry_id 1yjp 1041s _cell.length_a 21.937 1041s _cell.length_b 4.866 1041s _cell.length_c 23.477 1041s _cell.angle_alpha 90.000 1041s _cell.angle_beta 107.080 1041s _cell.angle_gamma 90.000 1041s # 1041s _diffrn_radiation_wavelength.id 1 1041s _diffrn_radiation_wavelength.wavelength 0.97500 1041s # 1041s _entry.id 1yjp 1041s # 1041s _exptl_crystal.id 1 1041s # 1041s _reflns_scale.group_code 1 1041s # 1041s _symmetry.entry_id 1yjp 1041s _symmetry.space_group_name_H-M 'P 1 21 1' 1041s # 1041s # 1041s loop_ 1041s _refln.crystal_id 1041s _refln.wavelength_id 1041s _refln.scale_group_code 1041s _refln.index_h 1041s _refln.index_k 1041s _refln.index_l 1041s _refln.status 1041s _refln.F_meas_au 1041s _refln.F_meas_sigma_au 1041s 1 1 1 -12 0 2 o 3.49 2.34 1041s 1 1 1 -12 0 3 o 3.31 2.43 1041s 1 1 1 -12 0 4 o 7.32 4.25 1041s 1 1 1 -12 0 5 o 8.88 5.39 1041s 1 1 1 -11 0 1 o 9.46 4.13 1041s 1 1 1 -11 0 2 o 4.91 3.21 1041s 1 1 1 -11 0 3 o 6.37 3.70 1041s 1 1 1 -11 0 4 o 8.50 4.91 1041s 1 1 1 -11 0 5 o 17.44 8.06 1041s 1 1 1 -11 0 6 o 5.89 3.64 1041s 1 1 1 -11 0 8 o 6.39 3.90 1041s 1 1 1 -11 1 2 o 5.69 2.18 1041s 1 1 1 -11 1 3 o 6.53 2.53 1041s 1 1 1 -11 1 5 o 7.26 3.20 1041s 1 1 1 -11 1 6 o 11.05 3.47 1041s 1 1 1 -10 0 2 o 6.32 3.74 1041s 1 1 1 -10 0 3 o 9.36 4.67 1041s 1 1 1 -10 0 5 o 7.20 4.12 1041s 1 1 1 -10 0 6 o 4.88 3.25 1041s 1 1 1 -10 0 7 o 11.84 5.41 1041s 1 1 1 -10 0 8 o 14.49 6.53 1041s 1 1 1 -10 0 9 o 6.21 3.91 1041s 1 1 1 -10 0 10 o 5.55 3.37 1041s 1 1 1 -10 1 1 o 4.58 1.49 1041s 1 1 1 -10 1 3 o 12.40 3.65 1041s 1 1 1 -10 1 4 o 9.07 2.47 1041s 1 1 1 -10 1 5 o 17.23 6.02 1041s 1 1 1 -10 1 6 o 4.60 2.10 1041s 1 1 1 -10 1 7 o 6.34 2.43 1041s 1 1 1 -10 1 8 o 9.04 2.92 1041s 1 1 1 -9 0 2 o 8.10 3.98 1041s 1 1 1 -9 0 3 o 14.22 5.11 1041s 1 1 1 -9 0 5 o 6.01 3.78 1041s 1 1 1 -9 0 6 o 10.48 4.68 1041s 1 1 1 -9 0 7 o 8.79 4.52 1041s 1 1 1 -9 0 8 o 6.15 3.63 1041s 1 1 1 -9 0 9 o 10.27 4.16 1041s 1 1 1 -9 0 10 o 4.38 3.04 1041s 1 1 1 -9 0 11 o 7.27 4.16 1041s 1 1 1 -9 1 3 o 10.75 2.38 1041s 1 1 1 -9 1 4 o 11.86 1.95 1041s 1 1 1 -9 1 5 o 10.95 3.27 1041s 1 1 1 -9 1 6 o 13.31 2.59 1041s 1 1 1 -9 1 7 o 8.06 2.92 1041s 1 1 1 -9 1 8 o 14.75 2.87 1041s 1 1 1 -9 1 9 o 9.04 2.82 1041s 1 1 1 -8 0 2 f 15.88 3.97 1041s 1 1 1 -8 0 3 o 26.78 5.79 1041s 1 1 1 -8 0 5 o 32.83 7.52 1041s 1 1 1 -8 0 7 o 12.74 3.54 1041s 1 1 1 -8 0 8 o 29.46 9.29 1041s 1 1 1 -8 0 9 f 22.09 3.59 1041s 1 1 1 -8 0 10 o 18.81 5.24 1041s 1 1 1 -8 0 11 o 12.76 7.11 1041s 1 1 1 -8 1 1 o 6.26 2.08 1041s 1 1 1 -8 1 2 o 6.97 2.14 1041s 1 1 1 -8 1 4 o 19.24 4.18 1041s 1 1 1 -8 1 5 o 15.46 2.43 1041s 1 1 1 -8 1 6 o 16.87 2.78 1041s 1 1 1 -8 1 7 o 15.66 2.34 1041s 1 1 1 -8 1 8 o 7.07 2.43 1041s 1 1 1 -8 1 9 o 8.81 2.80 1041s 1 1 1 -8 1 10 o 8.61 3.09 1041s 1 1 1 -8 2 1 o 4.39 1.52 1041s 1 1 1 -8 2 2 o 4.20 1.87 1041s 1 1 1 -8 2 3 o 6.14 1.87 1041s 1 1 1 -8 2 4 o 9.38 2.80 1041s 1 1 1 -7 0 3 o 23.46 3.83 1041s 1 1 1 -7 0 4 o 37.35 7.40 1041s 1 1 1 -7 0 6 o 7.44 3.60 1041s 1 1 1 -7 0 7 o 43.94 5.36 1041s 1 1 1 -7 0 8 o 18.96 2.98 1041s 1 1 1 -7 0 9 o 4.95 3.22 1041s 1 1 1 -7 0 10 o 31.73 4.61 1041s 1 1 1 -7 0 11 o 6.31 3.82 1041s 1 1 1 -7 0 12 o 5.05 3.33 1041s 1 1 1 -7 1 1 o 8.89 1.60 1041s 1 1 1 -7 1 2 o 13.70 1.71 1041s 1 1 1 -7 1 3 o 21.03 2.45 1041s 1 1 1 -7 1 4 f 7.57 2.36 1041s 1 1 1 -7 1 5 o 11.31 3.34 1041s 1 1 1 -7 1 6 o 19.93 3.06 1041s 1 1 1 -7 1 7 o 22.86 3.28 1041s 1 1 1 -7 1 8 o 10.32 2.58 1041s 1 1 1 -7 1 9 f 5.13 2.34 1041s 1 1 1 -7 1 10 o 9.91 3.03 1041s 1 1 1 -7 1 11 o 5.61 2.33 1041s 1 1 1 -7 2 1 o 12.28 3.86 1041s 1 1 1 -7 2 2 o 11.29 3.50 1041s 1 1 1 -7 2 3 f 7.22 2.40 1041s 1 1 1 -7 2 4 o 11.13 2.74 1041s 1 1 1 -7 2 5 o 7.86 2.92 1041s 1 1 1 -7 2 6 o 5.23 2.15 1041s 1 1 1 -6 0 2 o 35.03 5.13 1041s 1 1 1 -6 0 3 o 15.64 3.61 1041s 1 1 1 -6 0 4 o 12.60 4.22 1041s 1 1 1 -6 0 5 o 21.36 2.47 1041s 1 1 1 -6 0 6 o 31.19 3.17 1041s 1 1 1 -6 0 7 o 33.66 3.99 1041s 1 1 1 -6 0 8 o 13.70 4.22 1041s 1 1 1 -6 0 9 o 10.99 4.16 1041s 1 1 1 -6 0 10 o 24.56 3.98 1041s 1 1 1 -6 0 11 o 4.41 3.08 1041s 1 1 1 -6 0 12 o 4.07 2.83 1041s 1 1 1 -6 1 1 o 10.24 1.40 1041s 1 1 1 -6 1 2 o 20.59 2.28 1041s 1 1 1 -6 1 3 o 32.14 3.57 1041s 1 1 1 -6 1 4 f 11.60 2.18 1041s 1 1 1 -6 1 5 o 22.15 2.66 1041s 1 1 1 -6 1 6 o 7.68 2.64 1041s 1 1 1 -6 1 7 o 6.39 2.58 1041s 1 1 1 -6 1 8 o 6.60 2.60 1041s 1 1 1 -6 1 9 o 8.21 2.82 1041s 1 1 1 -6 1 10 o 13.25 3.07 1041s 1 1 1 -6 1 11 o 10.62 3.80 1041s 1 1 1 -6 2 1 o 13.78 2.98 1041s 1 1 1 -6 2 2 o 5.95 2.11 1041s 1 1 1 -6 2 3 o 8.96 3.00 1041s 1 1 1 -6 2 4 o 4.88 2.17 1041s 1 1 1 -6 2 5 o 7.35 2.58 1041s 1 1 1 -6 2 6 o 6.93 2.91 1041s 1 1 1 -6 2 7 o 8.14 2.74 1041s 1 1 1 -5 0 2 o 44.04 6.46 1041s 1 1 1 -5 0 3 o 15.30 3.69 1041s 1 1 1 -5 0 4 o 16.95 2.51 1041s 1 1 1 -5 0 5 o 14.82 4.54 1041s 1 1 1 -5 0 6 o 29.73 3.15 1041s 1 1 1 -5 0 7 f 55.71 13.43 1041s 1 1 1 -5 0 8 o 15.06 3.67 1041s 1 1 1 -5 0 9 o 8.76 4.15 1041s 1 1 1 -5 0 10 o 4.69 3.13 1041s 1 1 1 -5 0 11 o 16.56 5.19 1041s 1 1 1 -5 0 12 o 5.59 3.77 1041s 1 1 1 -5 1 1 o 26.70 2.49 1041s 1 1 1 -5 1 2 o 38.67 3.63 1041s 1 1 1 -5 1 3 o 20.45 2.09 1041s 1 1 1 -5 1 4 o 6.46 2.54 1041s 1 1 1 -5 1 5 o 20.55 2.58 1041s 1 1 1 -5 1 6 o 28.68 2.67 1041s 1 1 1 -5 1 7 o 5.68 2.48 1041s 1 1 1 -5 1 8 o 6.99 2.70 1041s 1 1 1 -5 1 9 o 20.74 2.59 1041s 1 1 1 -5 1 10 o 14.70 3.00 1041s 1 1 1 -5 1 11 o 8.62 2.89 1041s 1 1 1 -5 2 1 o 6.26 2.16 1041s 1 1 1 -5 2 2 o 7.93 2.10 1041s 1 1 1 -5 2 3 o 19.90 4.18 1041s 1 1 1 -5 2 4 o 4.98 2.02 1041s 1 1 1 -5 2 5 o 16.85 3.60 1041s 1 1 1 -5 2 7 o 8.15 2.74 1041s 1 1 1 -5 2 8 o 8.89 2.75 1041s 1 1 1 -4 0 2 o 4.55 2.74 1041s 1 1 1 -4 0 3 o 23.50 2.52 1041s 1 1 1 -4 0 4 o 19.15 3.81 1041s 1 1 1 -4 0 7 o 20.06 2.98 1041s 1 1 1 -4 0 8 o 28.85 3.55 1041s 1 1 1 -4 0 9 o 5.36 3.45 1041s 1 1 1 -4 0 10 o 25.68 3.87 1041s 1 1 1 -4 0 11 o 23.28 3.81 1041s 1 1 1 -4 0 12 o 11.39 4.82 1041s 1 1 1 -4 0 13 o 7.07 3.96 1041s 1 1 1 -4 1 1 o 31.99 4.35 1041s 1 1 1 -4 1 2 o 18.48 1.94 1041s 1 1 1 -4 1 3 f 18.93 2.01 1041s 1 1 1 -4 1 4 o 38.05 3.65 1041s 1 1 1 -4 1 5 o 36.34 3.49 1041s 1 1 1 -4 1 6 o 18.08 3.24 1041s 1 1 1 -4 1 7 o 20.11 2.29 1041s 1 1 1 -4 1 8 o 11.25 2.61 1041s 1 1 1 -4 1 9 o 27.09 3.02 1041s 1 1 1 -4 1 10 o 17.78 3.55 1041s 1 1 1 -4 1 11 o 10.45 3.55 1041s 1 1 1 -4 1 12 o 7.42 2.61 1041s 1 1 1 -4 2 1 o 7.72 2.01 1041s 1 1 1 -4 2 2 o 30.88 3.36 1041s 1 1 1 -4 2 3 o 19.14 2.65 1041s 1 1 1 -4 2 4 o 4.44 2.00 1041s 1 1 1 -4 2 5 f 26.44 8.10 1041s 1 1 1 -4 2 6 o 10.83 3.21 1041s 1 1 1 -4 2 7 o 6.03 2.73 1041s 1 1 1 -4 2 8 o 12.78 2.87 1041s 1 1 1 -3 0 2 o 3.40 2.13 1041s 1 1 1 -3 0 3 o 5.40 2.78 1041s 1 1 1 -3 0 4 o 11.52 2.39 1041s 1 1 1 -3 0 5 o 55.13 5.36 1041s 1 1 1 -3 0 6 f 31.55 3.22 1041s 1 1 1 -3 0 7 o 6.95 4.11 1041s 1 1 1 -3 0 8 o 6.00 3.79 1041s 1 1 1 -3 0 9 o 23.03 3.41 1041s 1 1 1 -3 0 10 o 4.79 3.36 1041s 1 1 1 -3 0 11 o 10.46 5.21 1041s 1 1 1 -3 0 12 o 11.53 6.07 1041s 1 1 1 -3 0 13 o 3.22 2.15 1041s 1 1 1 -3 1 1 o 53.95 5.22 1041s 1 1 1 -3 1 2 o 21.50 3.03 1041s 1 1 1 -3 1 3 o 42.88 4.08 1041s 1 1 1 -3 1 4 o 42.70 6.13 1041s 1 1 1 -3 1 5 o 41.12 3.18 1041s 1 1 1 -3 1 6 o 17.31 2.67 1041s 1 1 1 -3 1 7 o 35.59 4.21 1041s 1 1 1 -3 1 8 o 18.53 2.36 1041s 1 1 1 -3 1 9 o 11.55 2.71 1041s 1 1 1 -3 1 10 o 11.41 2.79 1041s 1 1 1 -3 1 11 o 6.92 2.69 1041s 1 1 1 -3 1 12 o 7.03 2.45 1041s 1 1 1 -3 2 1 o 18.65 2.01 1041s 1 1 1 -3 2 2 o 16.33 1.93 1041s 1 1 1 -3 2 3 o 32.88 5.01 1041s 1 1 1 -3 2 4 o 9.99 2.93 1041s 1 1 1 -3 2 5 o 20.62 2.93 1041s 1 1 1 -3 2 6 o 9.18 3.06 1041s 1 1 1 -3 2 7 o 6.90 2.83 1041s 1 1 1 -3 2 8 o 5.26 2.23 1041s 1 1 1 -2 0 1 o 37.92 5.29 1041s 1 1 1 -2 0 2 o 25.98 3.53 1041s 1 1 1 -2 0 3 o 20.20 2.27 1041s 1 1 1 -2 0 4 o 43.74 4.27 1041s 1 1 1 -2 0 5 o 32.34 3.28 1041s 1 1 1 -2 0 6 o 61.28 6.06 1041s 1 1 1 -2 0 7 o 39.92 3.91 1041s 1 1 1 -2 0 8 o 5.73 3.51 1041s 1 1 1 -2 0 9 o 34.44 8.22 1041s 1 1 1 -2 0 10 o 5.00 3.24 1041s 1 1 1 -2 0 11 o 5.95 3.63 1041s 1 1 1 -2 0 12 o 7.57 4.58 1041s 1 1 1 -2 1 1 o 5.64 1.74 1041s 1 1 1 -2 1 2 o 27.80 2.66 1041s 1 1 1 -2 1 3 f 58.08 5.70 1041s 1 1 1 -2 1 4 o 17.13 2.16 1041s 1 1 1 -2 1 5 o 17.82 1.84 1041s 1 1 1 -2 1 6 o 38.29 4.36 1041s 1 1 1 -2 1 7 o 21.32 2.41 1041s 1 1 1 -2 1 8 o 14.24 2.30 1041s 1 1 1 -2 1 9 o 23.48 2.71 1041s 1 1 1 -2 1 10 f 12.02 2.17 1041s 1 1 1 -2 1 11 o 15.91 5.89 1041s 1 1 1 -2 1 12 o 7.00 2.53 1041s 1 1 1 -2 2 1 o 15.73 2.27 1041s 1 1 1 -2 2 2 o 24.74 2.59 1041s 1 1 1 -2 2 3 o 16.53 2.59 1041s 1 1 1 -2 2 4 o 6.46 2.78 1041s 1 1 1 -2 2 5 o 13.27 4.40 1041s 1 1 1 -2 2 6 o 5.58 2.29 1041s 1 1 1 -2 2 7 o 6.76 2.38 1041s 1 1 1 -2 2 8 o 5.29 2.14 1041s 1 1 1 -1 0 1 o 28.12 3.79 1041s 1 1 1 -1 0 2 o 21.59 2.21 1041s 1 1 1 -1 0 3 o 33.14 3.24 1041s 1 1 1 -1 0 4 o 43.39 4.18 1041s 1 1 1 -1 0 5 f 46.52 4.56 1041s 1 1 1 -1 0 6 o 76.28 14.50 1041s 1 1 1 -1 0 7 o 5.12 3.18 1041s 1 1 1 -1 0 9 o 37.08 8.90 1041s 1 1 1 -1 0 10 o 6.65 3.72 1041s 1 1 1 -1 0 11 o 6.86 4.45 1041s 1 1 1 -1 0 12 o 4.18 2.86 1041s 1 1 1 -1 1 1 o 36.99 3.46 1041s 1 1 1 -1 1 2 o 40.11 3.76 1041s 1 1 1 -1 1 3 o 15.12 3.05 1041s 1 1 1 -1 1 4 o 11.44 2.42 1041s 1 1 1 -1 1 5 f 7.66 2.37 1041s 1 1 1 -1 1 6 o 37.21 3.40 1041s 1 1 1 -1 1 7 o 13.99 2.19 1041s 1 1 1 -1 1 8 o 23.42 2.40 1041s 1 1 1 -1 1 9 o 12.59 2.48 1041s 1 1 1 -1 1 10 o 14.84 2.83 1041s 1 1 1 -1 1 11 o 13.90 3.02 1041s 1 1 1 -1 2 1 o 7.71 2.59 1041s 1 1 1 -1 2 2 o 5.95 2.09 1041s 1 1 1 -1 2 3 o 25.96 3.59 1041s 1 1 1 -1 2 4 o 16.53 2.52 1041s 1 1 1 -1 2 5 o 12.51 2.97 1041s 1 1 1 -1 2 6 o 12.40 3.34 1041s 1 1 1 -1 2 7 o 5.97 2.01 1041s 1 1 1 -1 2 8 o 8.24 2.40 1041s 1 1 1 0 0 1 o 40.04 3.82 1041s 1 1 1 0 0 2 o 58.22 5.69 1041s 1 1 1 0 0 3 o 47.47 4.60 1041s 1 1 1 0 0 4 o 7.98 2.75 1041s 1 1 1 0 0 5 o 50.74 7.60 1041s 1 1 1 0 0 6 o 14.87 1.94 1041s 1 1 1 0 0 7 o 3.62 2.41 1041s 1 1 1 0 0 8 o 36.19 7.98 1041s 1 1 1 0 0 9 o 10.11 5.01 1041s 1 1 1 0 0 10 o 18.08 3.24 1041s 1 1 1 0 0 11 o 12.35 4.26 1041s 1 1 1 0 0 12 o 9.41 4.38 1041s 1 1 1 0 1 1 o 92.10 11.26 1041s 1 1 1 0 1 2 o 47.48 4.50 1041s 1 1 1 0 1 3 o 22.08 2.22 1041s 1 1 1 0 1 4 o 8.62 2.51 1041s 1 1 1 0 1 5 o 24.16 1.98 1041s 1 1 1 0 1 6 o 16.72 1.95 1041s 1 1 1 0 1 7 o 5.50 2.46 1041s 1 1 1 0 1 8 o 21.06 2.19 1041s 1 1 1 0 1 9 o 5.99 2.45 1041s 1 1 1 0 1 10 o 8.62 3.03 1041s 1 1 1 0 1 11 o 9.15 3.06 1041s 1 1 1 0 2 0 o 27.82 5.58 1041s 1 1 1 0 2 1 o 29.68 4.10 1041s 1 1 1 0 2 2 o 37.82 4.30 1041s 1 1 1 0 2 3 o 14.42 1.91 1041s 1 1 1 0 2 4 o 13.55 2.70 1041s 1 1 1 0 2 5 o 8.67 3.07 1041s 1 1 1 0 2 6 o 22.77 5.53 1041s 1 1 1 0 2 7 o 5.74 2.12 1041s 1 1 1 0 2 8 o 9.78 2.64 1041s 1 1 1 1 0 1 o 10.19 1.09 1041s 1 1 1 1 0 2 o 20.07 1.88 1041s 1 1 1 1 0 3 o 28.76 2.81 1041s 1 1 1 1 0 4 o 3.16 2.18 1041s 1 1 1 1 0 5 o 35.75 3.54 1041s 1 1 1 1 0 6 f 52.32 5.12 1041s 1 1 1 1 0 7 o 37.09 5.54 1041s 1 1 1 1 0 8 o 6.52 3.32 1041s 1 1 1 1 0 9 o 3.67 2.45 1041s 1 1 1 1 0 10 o 6.03 3.17 1041s 1 1 1 1 0 11 o 3.13 2.20 1041s 1 1 1 1 0 12 o 4.06 2.74 1041s 1 1 1 1 1 0 o 34.97 2.64 1041s 1 1 1 1 1 1 o 15.45 1.46 1041s 1 1 1 1 1 2 o 27.96 2.66 1041s 1 1 1 1 1 3 o 55.14 5.35 1041s 1 1 1 1 1 4 o 14.46 1.65 1041s 1 1 1 1 1 5 o 7.23 2.19 1041s 1 1 1 1 1 6 o 10.31 2.54 1041s 1 1 1 1 1 7 o 11.70 2.22 1041s 1 1 1 1 1 8 o 11.24 2.14 1041s 1 1 1 1 1 9 o 7.60 2.88 1041s 1 1 1 1 1 10 o 8.83 2.34 1041s 1 1 1 1 1 11 o 12.55 3.17 1041s 1 1 1 1 2 0 o 24.36 5.60 1041s 1 1 1 1 2 1 o 13.12 2.09 1041s 1 1 1 1 2 2 o 10.37 2.52 1041s 1 1 1 1 2 3 o 14.39 1.98 1041s 1 1 1 1 2 4 o 26.67 8.23 1041s 1 1 1 1 2 5 o 22.53 5.20 1041s 1 1 1 1 2 6 o 13.94 2.61 1041s 1 1 1 1 2 7 o 7.45 2.38 1041s 1 1 1 1 2 8 o 4.51 2.05 1041s 1 1 1 2 0 1 o 13.06 1.30 1041s 1 1 1 2 0 2 o 10.37 1.36 1041s 1 1 1 2 0 3 o 20.89 2.04 1041s 1 1 1 2 0 4 o 45.12 4.31 1041s 1 1 1 2 0 5 o 15.37 1.91 1041s 1 1 1 2 0 6 o 28.38 2.79 1041s 1 1 1 2 0 7 o 16.02 2.31 1041s 1 1 1 2 0 8 o 3.40 2.35 1041s 1 1 1 2 0 9 o 4.23 2.72 1041s 1 1 1 2 0 10 o 3.89 2.43 1041s 1 1 1 2 0 11 o 10.26 3.01 1041s 1 1 1 2 1 0 o 34.61 2.64 1041s 1 1 1 2 1 1 o 53.93 5.22 1041s 1 1 1 2 1 2 o 20.62 2.08 1041s 1 1 1 2 1 3 o 44.45 3.37 1041s 1 1 1 2 1 4 o 24.41 2.00 1041s 1 1 1 2 1 5 o 40.33 4.58 1041s 1 1 1 2 1 6 o 41.76 5.03 1041s 1 1 1 2 1 7 o 28.20 3.43 1041s 1 1 1 2 1 8 o 33.56 3.76 1041s 1 1 1 2 1 9 o 4.41 1.97 1041s 1 1 1 2 1 10 o 15.24 3.10 1041s 1 1 1 2 2 0 o 25.09 3.38 1041s 1 1 1 2 2 1 o 9.96 2.30 1041s 1 1 1 2 2 2 o 15.79 2.28 1041s 1 1 1 2 2 3 f 23.73 2.57 1041s 1 1 1 2 2 4 o 31.55 3.47 1041s 1 1 1 2 2 5 o 22.42 5.53 1041s 1 1 1 2 2 6 o 21.84 3.98 1041s 1 1 1 2 2 7 o 11.92 3.24 1041s 1 1 1 3 0 1 o 20.22 2.60 1041s 1 1 1 3 0 2 o 15.58 1.67 1041s 1 1 1 3 0 3 o 43.75 4.24 1041s 1 1 1 3 0 4 o 53.24 5.13 1041s 1 1 1 3 0 5 o 9.04 2.60 1041s 1 1 1 3 0 6 o 16.05 2.16 1041s 1 1 1 3 0 7 o 10.18 3.61 1041s 1 1 1 3 0 8 f 21.57 2.93 1041s 1 1 1 3 0 9 o 5.10 2.75 1041s 1 1 1 3 0 10 o 9.06 4.48 1041s 1 1 1 3 0 11 o 7.20 4.29 1041s 1 1 1 3 1 0 o 6.01 1.35 1041s 1 1 1 3 1 1 o 38.17 5.32 1041s 1 1 1 3 1 2 o 88.61 10.65 1041s 1 1 1 3 1 3 o 46.76 4.49 1041s 1 1 1 3 1 4 o 21.38 1.98 1041s 1 1 1 3 1 5 o 10.82 1.68 1041s 1 1 1 3 1 6 o 9.92 1.96 1041s 1 1 1 3 1 7 o 13.79 1.74 1041s 1 1 1 3 1 8 o 18.26 2.25 1041s 1 1 1 3 1 9 o 10.74 2.36 1041s 1 1 1 3 1 10 o 4.53 1.95 1041s 1 1 1 3 2 0 o 36.54 6.90 1041s 1 1 1 3 2 1 o 7.87 2.79 1041s 1 1 1 3 2 2 o 18.30 2.61 1041s 1 1 1 3 2 3 o 17.39 2.45 1041s 1 1 1 3 2 4 o 17.18 2.74 1041s 1 1 1 3 2 5 o 13.02 2.60 1041s 1 1 1 3 2 6 o 4.72 1.98 1041s 1 1 1 4 0 1 o 3.64 2.08 1041s 1 1 1 4 0 2 o 63.80 6.24 1041s 1 1 1 4 0 3 o 19.19 1.93 1041s 1 1 1 4 0 4 o 63.44 6.28 1041s 1 1 1 4 0 5 o 30.78 6.03 1041s 1 1 1 4 0 6 o 9.03 2.53 1041s 1 1 1 4 0 7 o 18.16 2.40 1041s 1 1 1 4 0 8 o 8.94 3.14 1041s 1 1 1 4 0 9 o 6.87 3.36 1041s 1 1 1 4 0 10 o 9.58 4.40 1041s 1 1 1 4 1 0 o 24.37 2.38 1041s 1 1 1 4 1 1 o 49.48 4.80 1041s 1 1 1 4 1 2 o 10.45 1.03 1041s 1 1 1 4 1 3 o 15.01 1.64 1041s 1 1 1 4 1 4 o 4.52 1.88 1041s 1 1 1 4 1 5 f 35.40 3.27 1041s 1 1 1 4 1 6 o 8.15 2.10 1041s 1 1 1 4 1 7 o 9.72 1.59 1041s 1 1 1 4 1 8 o 5.93 1.88 1041s 1 1 1 4 1 9 o 13.31 3.66 1041s 1 1 1 4 2 0 o 12.03 2.31 1041s 1 1 1 4 2 1 o 13.76 1.98 1041s 1 1 1 4 2 2 o 10.87 2.55 1041s 1 1 1 4 2 3 o 7.78 2.40 1041s 1 1 1 4 2 4 o 19.45 4.53 1041s 1 1 1 4 2 5 o 11.32 4.24 1041s 1 1 1 4 2 6 o 7.29 3.50 1041s 1 1 1 5 0 1 o 67.42 11.14 1041s 1 1 1 5 0 2 o 13.50 3.13 1041s 1 1 1 5 0 3 o 22.37 2.21 1041s 1 1 1 5 0 4 o 56.42 6.72 1041s 1 1 1 5 0 5 o 25.46 3.07 1041s 1 1 1 5 0 6 o 38.61 4.82 1041s 1 1 1 5 0 7 o 14.33 2.65 1041s 1 1 1 5 0 8 f 4.56 2.78 1041s 1 1 1 5 0 9 o 8.50 3.26 1041s 1 1 1 5 1 0 o 21.65 2.85 1041s 1 1 1 5 1 1 o 12.29 1.67 1041s 1 1 1 5 1 2 o 11.21 3.27 1041s 1 1 1 5 1 3 o 9.29 2.49 1041s 1 1 1 5 1 4 o 12.76 2.42 1041s 1 1 1 5 1 5 o 4.61 0.86 1041s 1 1 1 5 1 6 o 21.81 2.38 1041s 1 1 1 5 1 7 o 11.05 2.11 1041s 1 1 1 5 1 8 o 4.27 1.64 1041s 1 1 1 5 2 0 o 17.82 3.76 1041s 1 1 1 5 2 1 o 13.94 3.96 1041s 1 1 1 5 2 2 o 14.67 2.97 1041s 1 1 1 5 2 3 o 12.27 4.35 1041s 1 1 1 5 2 4 o 12.90 2.88 1041s 1 1 1 5 2 5 o 8.21 2.77 1041s 1 1 1 6 0 1 o 4.02 2.51 1041s 1 1 1 6 0 2 o 14.11 3.04 1041s 1 1 1 6 0 4 o 44.86 5.41 1041s 1 1 1 6 0 5 f 22.85 4.74 1041s 1 1 1 6 0 6 o 41.69 6.63 1041s 1 1 1 6 0 7 o 7.42 2.96 1041s 1 1 1 6 0 8 o 13.47 5.61 1041s 1 1 1 6 1 0 o 25.42 2.26 1041s 1 1 1 6 1 1 o 9.87 3.01 1041s 1 1 1 6 1 2 o 28.37 5.85 1041s 1 1 1 6 1 3 o 16.66 3.91 1041s 1 1 1 6 1 4 o 23.02 5.62 1041s 1 1 1 6 1 6 o 26.51 4.88 1041s 1 1 1 6 1 7 o 3.67 1.58 1041s 1 1 1 6 2 0 o 8.22 2.50 1041s 1 1 1 6 2 2 o 9.67 2.35 1041s 1 1 1 6 2 3 o 3.73 1.60 1041s 1 1 1 7 0 1 o 10.99 3.37 1041s 1 1 1 7 0 2 o 17.23 3.99 1041s 1 1 1 7 0 3 o 5.15 2.69 1041s 1 1 1 7 0 4 o 5.19 3.01 1041s 1 1 1 7 0 5 o 23.76 3.00 1041s 1 1 1 7 0 6 o 5.48 3.05 1041s 1 1 1 7 0 7 o 6.05 3.12 1041s 1 1 1 7 0 8 o 7.94 3.69 1041s 1 1 1 7 1 0 o 33.08 3.93 1041s 1 1 1 7 1 1 o 8.43 3.00 1041s 1 1 1 7 1 2 o 10.12 3.61 1041s 1 1 1 7 1 3 o 14.66 3.85 1041s 1 1 1 7 1 4 o 9.43 3.13 1041s 1 1 1 7 1 6 o 14.64 4.20 1041s 1 1 1 7 2 0 o 14.80 3.92 1041s 1 1 1 7 2 1 o 6.02 2.00 1041s 1 1 1 8 0 2 o 29.07 8.06 1041s 1 1 1 8 0 3 o 5.29 2.84 1041s 1 1 1 8 0 4 o 22.81 5.95 1041s 1 1 1 8 0 5 o 4.11 2.70 1041s 1 1 1 8 1 0 o 7.24 1.50 1041s 1 1 1 8 1 1 o 8.85 3.06 1041s 1 1 1 8 1 2 o 6.83 3.09 1041s 1 1 1 8 1 3 o 18.14 5.99 1041s 1 1 1 9 0 1 o 13.49 3.22 1041s 1 1 1 9 0 2 o 11.72 3.95 1041s 1 1 1 10 0 2 o 7.39 3.73 1041s 1 1 1 10 1 0 o 16.08 6.44 1041s #END OF REFLECTIONS 1041s 1041s Starting iotbx.fetch_pdb 1041s on Sat Mar 22 13:22:38 2025 by ubuntu 1041s =============================================================================== 1041s 1041s Processing files: 1041s ------------------------------------------------------------------------------- 1041s 1041s No files found 1041s 1041s Processing PHIL parameters: 1041s ------------------------------------------------------------------------------- 1041s 1041s Adding command-line PHIL: 1041s ------------------------- 1041s action=all 1041s 1041s Final processed PHIL parameters: 1041s ------------------------------------------------------------------------------- 1041s fetch { 1041s pdb_ids = "6yvd" 1041s action = model data sequence half_maps *all 1041s } 1041s 1041s 1041s Starting job 1041s =============================================================================== 1041s Validating inputs: 1041s 1041s Model in PDB format saved to /tmp/autopkgtest.gw2uST/autopkgtest_tmp/python3.13/6yvd.pdb 1041s Model in mmCIF format saved to /tmp/autopkgtest.gw2uST/autopkgtest_tmp/python3.13/6yvd.cif 1041s Couldn't download sf for 6yvd at https://files.rcsb.org/download/6yvd-sf.cif.gz. 1041s Cryo-EM map saved to /tmp/autopkgtest.gw2uST/autopkgtest_tmp/python3.13/emd_10944.map.gz 1041s Cryo-EM half map 1 saved to /tmp/autopkgtest.gw2uST/autopkgtest_tmp/python3.13/emd_10944_half_map_1.map.gz 1041s Cryo-EM half map 2 saved to /tmp/autopkgtest.gw2uST/autopkgtest_tmp/python3.13/emd_10944_half_map_2.map.gz 1041s Sequence saved to /tmp/autopkgtest.gw2uST/autopkgtest_tmp/python3.13/6yvd.fa 1041s 1041s =============================================================================== 1041s Job complete 1041s Total CPU time: 0.52 seconds 1041s Starting iotbx.fetch_pdb 1041s on Sat Mar 22 13:22:50 2025 by ubuntu 1041s =============================================================================== 1041s 1041s Processing files: 1041s ------------------------------------------------------------------------------- 1041s 1041s No files found 1041s 1041s Processing PHIL parameters: 1041s ------------------------------------------------------------------------------- 1041s 1041s Adding command-line PHIL: 1041s ------------------------- 1041s action=model 1041s 1041s Final processed PHIL parameters: 1041s ------------------------------------------------------------------------------- 1041s fetch { 1041s pdb_ids = "6yvd" 1041s } 1041s 1041s 1041s Starting job 1041s =============================================================================== 1041s Validating inputs: 1041s 1041s Model in PDB format saved to /tmp/autopkgtest.gw2uST/autopkgtest_tmp/python3.13/6yvd.pdb 1041s Model in mmCIF format saved to /tmp/autopkgtest.gw2uST/autopkgtest_tmp/python3.13/6yvd.cif 1041s 1041s =============================================================================== 1041s Job complete 1041s Total CPU time: 0.43 seconds 1041s Starting iotbx.fetch_pdb 1041s on Sat Mar 22 13:22:53 2025 by ubuntu 1041s =============================================================================== 1041s 1041s Processing files: 1041s ------------------------------------------------------------------------------- 1041s 1041s No files found 1041s 1041s Processing PHIL parameters: 1041s ------------------------------------------------------------------------------- 1041s 1041s Adding command-line PHIL: 1041s ------------------------- 1041s action=model 1041s 1041s Final processed PHIL parameters: 1041s ------------------------------------------------------------------------------- 1041s fetch { 1041s pdb_ids = "6yvd" 1041s } 1041s 1041s 1041s Starting job 1041s =============================================================================== 1041s Validating inputs: 1041s 1041s Model in PDB format saved to /tmp/autopkgtest.gw2uST/autopkgtest_tmp/python3.13/6yvd.pdb 1041s Model in mmCIF format saved to /tmp/autopkgtest.gw2uST/autopkgtest_tmp/python3.13/6yvd.cif 1041s 1041s =============================================================================== 1041s Job complete 1041s Total CPU time: 0.43 seconds 1041s Starting iotbx.fetch_pdb 1041s on Sat Mar 22 13:22:58 2025 by ubuntu 1041s =============================================================================== 1041s 1041s Processing files: 1041s ------------------------------------------------------------------------------- 1041s 1041s No files found 1041s 1041s Processing PHIL parameters: 1041s ------------------------------------------------------------------------------- 1041s 1041s Adding command-line PHIL: 1041s ------------------------- 1041s action=data 1041s 1041s Final processed PHIL parameters: 1041s ------------------------------------------------------------------------------- 1041s fetch { 1041s pdb_ids = "6yvd" 1041s action = model *data sequence half_maps all 1041s } 1041s 1041s 1041s Starting job 1041s =============================================================================== 1041s Validating inputs: 1041s 1041s Couldn't download sf for 6yvd at https://files.rcsb.org/download/6yvd-sf.cif.gz. 1041s Cryo-EM map saved to /tmp/autopkgtest.gw2uST/autopkgtest_tmp/python3.13/emd_10944.map.gz 1041s 1041s =============================================================================== 1041s Job complete 1041s Total CPU time: 0.41 seconds 1041s Starting iotbx.fetch_pdb 1041s on Sat Mar 22 13:23:02 2025 by ubuntu 1041s =============================================================================== 1041s 1041s Processing files: 1041s ------------------------------------------------------------------------------- 1041s 1041s No files found 1041s 1041s Processing PHIL parameters: 1041s ------------------------------------------------------------------------------- 1041s 1041s Adding command-line PHIL: 1041s ------------------------- 1041s action=half_maps 1041s 1041s Final processed PHIL parameters: 1041s ------------------------------------------------------------------------------- 1041s fetch { 1041s pdb_ids = "6yvd" 1041s action = model data sequence *half_maps all 1041s } 1041s 1041s 1041s Starting job 1041s =============================================================================== 1041s Validating inputs: 1041s 1041s Cryo-EM half map 1 saved to /tmp/autopkgtest.gw2uST/autopkgtest_tmp/python3.13/emd_10944_half_map_1.map.gz 1041s Cryo-EM half map 2 saved to /tmp/autopkgtest.gw2uST/autopkgtest_tmp/python3.13/emd_10944_half_map_2.map.gz 1041s 1041s =============================================================================== 1041s Job complete 1041s Total CPU time: 0.51 seconds 1041s Starting iotbx.fetch_pdb 1041s on Sat Mar 22 13:23:09 2025 by ubuntu 1041s =============================================================================== 1041s 1041s Processing files: 1041s ------------------------------------------------------------------------------- 1041s 1041s No files found 1041s 1041s Processing PHIL parameters: 1041s ------------------------------------------------------------------------------- 1041s 1041s Adding command-line PHIL: 1041s ------------------------- 1041s action=sequence 1041s 1041s Final processed PHIL parameters: 1041s ------------------------------------------------------------------------------- 1041s fetch { 1041s pdb_ids = "6yvd" 1041s action = model data *sequence half_maps all 1041s } 1041s 1041s 1041s Starting job 1041s =============================================================================== 1041s Validating inputs: 1041s 1041s Sequence saved to /tmp/autopkgtest.gw2uST/autopkgtest_tmp/python3.13/6yvd.fa 1041s 1041s =============================================================================== 1041s Job complete 1041s Total CPU time: 0.40 seconds 1041s Starting iotbx.fetch_pdb 1041s on Sat Mar 22 13:23:10 2025 by ubuntu 1041s =============================================================================== 1041s 1041s Processing files: 1041s ------------------------------------------------------------------------------- 1041s 1041s No files found 1041s 1041s Processing PHIL parameters: 1041s ------------------------------------------------------------------------------- 1041s 1041s Adding command-line PHIL: 1041s ------------------------- 1041s action=all 1041s 1041s Final processed PHIL parameters: 1041s ------------------------------------------------------------------------------- 1041s fetch { 1041s pdb_ids = "6yvd" 1041s action = model data sequence half_maps *all 1041s } 1041s 1041s 1041s Starting job 1041s =============================================================================== 1041s Validating inputs: 1041s 1041s Model in PDB format saved to /tmp/autopkgtest.gw2uST/autopkgtest_tmp/python3.13/6yvd.pdb 1041s Model in mmCIF format saved to /tmp/autopkgtest.gw2uST/autopkgtest_tmp/python3.13/6yvd.cif 1041s Couldn't download sf for 6yvd at https://files.rcsb.org/download/6yvd-sf.cif.gz. 1041s Cryo-EM map saved to /tmp/autopkgtest.gw2uST/autopkgtest_tmp/python3.13/emd_10944.map.gz 1041s Cryo-EM half map 1 saved to /tmp/autopkgtest.gw2uST/autopkgtest_tmp/python3.13/emd_10944_half_map_1.map.gz 1041s Cryo-EM half map 2 saved to /tmp/autopkgtest.gw2uST/autopkgtest_tmp/python3.13/emd_10944_half_map_2.map.gz 1041s Sequence saved to /tmp/autopkgtest.gw2uST/autopkgtest_tmp/python3.13/6yvd.fa 1041s 1041s =============================================================================== 1041s Job complete 1041s Total CPU time: 0.54 seconds 1041s OK 1041s u+s,u,s: 0.32 0.26 0.06 1041s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_scheduling.py" [OK] 7.3s 1041s Time: 7.31 1041s Return code: 0 1041s OKs: 0 1041s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_containers.py" [OK] 0.0s 1041s Time: 0.03 1041s Return code: 0 1041s OKs: 1 1041s Standard out: 1041s OK 1041s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_path.py" [OK] 0.1s 1041s Time: 0.07 1041s Return code: 0 1041s OKs: 1 1041s Standard out: 1041s OK 1041s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_math_utils.py" [OK] 0.3s 1041s Time: 0.31 1041s Return code: 0 1041s OKs: 1 1041s Standard out: 1041s OK 1042s libtbx.python "/usr/lib/python3/dist-packages/libtbx/assert_utils.py" [OK] 0.1s 1042s Time: 0.14 1042s Return code: 0 1042s OKs: 1 1042s Standard out: 1042s OK 1042s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_str_utils.py" [OK] 0.3s 1042s Time: 0.28 1042s Return code: 0 1042s OKs: 1 1042s Standard out: 1042s OK 1042s libtbx.python "/usr/lib/python3/dist-packages/libtbx/table_utils.py" [OK] 0.0s 1042s Time: 0.04 1042s Return code: 0 1042s OKs: 1 1042s Standard out: 1042s OK 1043s libtbx.python "/usr/lib/python3/dist-packages/libtbx/easy_run.py" [OK] 2.1s 1043s Time: 2.08 1043s Return code: 0 1043s OKs: 1 1043s Standard out: 1043s OK 1043s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_tokenizer.py" [OK] 0.1s 1043s Time: 0.06 1043s Return code: 0 1043s OKs: 1 1043s Standard out: 1043s OK 1043s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst.py" [OK] 0.3s 1043s Time: 0.28 1043s Return code: 0 1043s OKs: 1 1043s Standard out: 1043s OK 1043s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_experimental.py" [OK] 0.1s 1043s Time: 0.06 1043s Return code: 0 1043s OKs: 1 1043s Standard out: 1043s OK 1043s libtbx.python "/usr/lib/python3/dist-packages/libtbx/phil/tst_interface.py" [OK] 0.1s 1043s Time: 0.10 1043s Return code: 0 1043s OKs: 1 1043s Standard out: 1043s phenix module not available: skipping advanced tests 1043s phaser module not available: skipping advanced tests 1043s OK 1043s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_object_oriented_patterns.py" [OK] 0.1s 1043s Time: 0.08 1043s Return code: 0 1043s OKs: 0 1043s libtbx.python "/usr/lib/python3/dist-packages/libtbx/find_reference_cycles.py" [OK] 0.0s 1043s Time: 0.04 1043s Return code: 0 1043s OKs: 1 1043s Standard out: 1043s OK 1043s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_binary_search.py" [OK] 0.0s 1043s Time: 0.03 1043s Return code: 0 1043s OKs: 1 1043s Standard out: 1043s OK 1043s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_topological_sort.py" [OK] 0.0s 1043s Time: 0.03 1043s Return code: 0 1043s OKs: 1 1043s Standard out: 1043s OK 1044s libtbx.python "/usr/lib/python3/dist-packages/libtbx/clusterTests.py" [OK] 0.2s 1044s Time: 0.16 1044s Return code: 0 1044s OKs: 1 1044s Standard out: 1044s ---------------------------------------------------------------------- 1044s Ran 13 tests in 0.105s 1044s 1044s OK 1044s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_citations.py" [OK] 0.2s 1044s Time: 0.17 1044s Return code: 0 1044s OKs: 1 1044s Standard out: 1044s OK 1044s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_python_code_parsing.py" [OK] 0.0s 1044s Time: 0.04 1044s Return code: 0 1044s OKs: 1 1044s Standard out: 1044s OK 1044s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_representation.py" [OK] 0.0s 1044s Time: 0.03 1044s Return code: 0 1044s OKs: 0 1044s Standard out: 1044s 99999999999999950039963891867 1044s 99999999999999963917751699682 1044s 99999999999999977795539507496 1044s 99999999999999991673327315311 1044s 100000000000000005551115123125 1044s 100000000000000019428902930940 1044s 100000000000000033306690738754 1044s 100000000000000047184478546569 1044s 100000000000000061062266354383 1044s 100000000000000074940054162198 1044s 100000000000000088817841970012 1044s 100000000000000102695629777826 1044s 100000000000000116573417585641 1044s 100000000000000130451205393455 1044s 100000000000000144328993201270 1044s 100000000000000158206781009084 1044s 100000000000000172084568816899 1044s 100000000000000185962356624713 1044s 100000000000000199840144432528 1044s 100000000000000213717932240342 1044s 100000000000000227595720048157 1044s 100000000000000241473507855971 1044s 100000000000000255351295663786 1044s 100000000000000269229083471600 1044s 100000000000000283106871279414 1044s 100000000000000296984659087229 1044s 100000000000000310862446895043 1044s 100000000000000324740234702858 1044s 100000000000000338618022510672 1044s 100000000000000352495810318487 1044s BEst 450359962737049.6 1044s 900719925474099.2 1044s 55.32192809488736 1044s 56.32192809488736 1044s True 1044s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_find_unused_imports.py" [OK] 0.0s 1044s Time: 0.03 1044s Return code: 0 1044s OKs: 1 1044s Standard out: 1044s OK 1044s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_dlite.py" [OK] 2.1s 1044s Time: 2.06 1044s Return code: 0 1044s OKs: 1 1044s Standard out: 1044s OK 1044s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_version.py" [OK] 0.1s 1044s Time: 0.07 1044s Return code: 0 1044s OKs: 0 1044s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_program_template.py" [OK] 0.3s 1044s Time: 0.29 1044s Return code: 0 1044s OKs: 0 1044s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_easy_mp_multicore.py" [OK] 0.3s 1044s Time: 0.32 1044s Return code: 0 1044s OKs: 0 1044s Standard out: 1044s [1] 1 1044s [2] 2 1044s [3] 6 1044s [4] 24 1044s [5] 120 1044s [6] 720 1044s [7] 5040 1047s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1047s 1 1047s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1047s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_xmlrpc_utils.py" [EXPECTED FAIL] 2.5s 1047s Time: 2.50 1047s Return code: 1 1047s OKs: 0 1047s Standard error: 1047s Traceback (most recent call last): 1047s File "/usr/lib/python3/dist-packages/libtbx/tst_xmlrpc_utils.py", line 42, in 1047s exercise() 1047s ~~~~~~~~^^ 1047s File "/usr/lib/python3/dist-packages/libtbx/tst_xmlrpc_utils.py", line 15, in exercise 1047s server = xmlrpc_utils.external_program_server(command=full_cmd, 1047s program_id="TEST", 1047s timeout=None, 1047s cache_requests=True, 1047s log=log) 1047s TypeError: external_program_server.__init__() got an unexpected keyword argument 'command' 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/tests/tst_smoothing.py" [FAIL] 3.4s 1050s Time: 3.40 1050s Return code: 139 1050s OKs: 0 1050s Standard error: 1050s Segmentation fault (core dumped) 1051s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_runtime_utils.py" [OK] 6.6s 1051s Time: 6.57 1051s Return code: 0 1051s OKs: 1 1051s Standard out: 1051s OK 1054s Standard error: 1054s Segmentation fault (core dumped) 1054s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1054s 139 1054s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1054s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_genetic_algorithm_with_mp.py" [FAIL] 3.3s 1054s Time: 3.29 1054s Return code: 139 1054s OKs: 0 1054s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_1" [OK] 0.0s 1054s Time: 0.01 1054s Return code: 0 1054s OKs: 1 1054s Standard out: 1054s Total OK: 511 1054s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_2" [OK] 0.0s 1054s Time: 0.01 1054s Return code: 0 1054s OKs: 1 1054s Standard out: 1054s Total OK: 268 1054s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_3" [OK] 0.0s 1054s Time: 0.00 1054s Return code: 0 1054s OKs: 1 1054s Standard out: 1054s Total OK: 164 1054s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_4" [OK] 0.0s 1054s Time: 0.01 1054s Return code: 0 1054s OKs: 1 1054s Standard out: 1054s Total OK: 1420 1054s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_5" [OK] 0.0s 1054s Time: 0.00 1054s Return code: 0 1054s OKs: 1 1054s Standard out: 1054s Total OK: 23 1054s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_vec3" [OK] 0.0s 1054s Time: 0.00 1054s Return code: 0 1054s OKs: 1 1054s Standard out: 1054s Total OK: 83 1054s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_unsigned_float_arithmetic" [OK] 0.0s 1054s Time: 0.00 1054s Return code: 0 1054s OKs: 1 1054s Standard out: 1054s OK 1054s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_mat3" [OK] 0.0s 1054s Time: 0.01 1054s Return code: 0 1054s OKs: 1 1054s Standard out: 1054s Total OK: 129 1054s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_sym_mat3" [OK] 0.0s 1054s Time: 0.01 1054s Return code: 0 1054s OKs: 1 1054s Standard out: 1054s Total OK: 91 1054s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_ref_matrix_facet" [OK] 0.0s 1054s Time: 0.01 1054s Return code: 0 1054s OKs: 1 1054s Standard out: 1054s OK 1054s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_accessors" [OK] 0.0s 1054s Time: 0.01 1054s Return code: 0 1054s OKs: 1 1054s Standard out: 1054s Total OK: 1730 1054s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_optional_copy" [OK] 0.0s 1054s Time: 0.01 1054s Return code: 0 1054s OKs: 1 1054s Standard out: 1054s OK 1054s "/usr/lib/cctbx/python3.13/scitbx/array_family/tst_rectangular_full_packed" [OK] 0.0s 1054s Time: 0.01 1054s Return code: 0 1054s OKs: 0 1054s Standard out: 1054s Test of accessor for rectangular full packed format skipped 1054s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex_argument_passing.py" [OK] 0.1s 1054s Time: 0.14 1054s Return code: 0 1054s OKs: 1 1054s Standard out: 1054s OK 1054s "/usr/lib/cctbx/python3.13/scitbx/serialization/tst_base_256" [OK] 0.2s 1054s Time: 0.19 1054s Return code: 0 1054s OKs: 1 1054s Standard out: 1054s OK 1056s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1056s 139 1056s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1056s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_basic.py" [FAIL] 5.7s 1056s Time: 5.73 1056s Return code: 139 1056s OKs: 1 1056s Standard out: 1056s 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' 1056s Size of an empty container. 1056s Some of those containers store a pointer to a raw storage: 1056s the 'cumulative' entry refers to the total memory footprint 1056s whereas the other entry does not include the raw storage. 1056s 1056s int : 4 1056s af::ref : 32 1056s scitbx::auto_array : 8 1056s boost::shared_array : 16 1056s boost::ptr_vector : 24 1056s std::vector : 24 1056s af::shared : 16 1056s af::shared [cumulative] : 64 1056s std::valarray : 16 1056s af::versa : 24 1056s af::versa > : 280 1056s af::versa > [cumulative] : 328 1056s 1056s double : 8 1056s af::ref : 32 1056s scitbx::auto_array : 8 1056s boost::shared_array : 16 1056s boost::ptr_vector : 24 1056s std::vector : 24 1056s af::shared : 16 1056s af::shared [cumulative] : 64 1056s std::valarray : 16 1056s af::versa : 24 1056s af::versa > : 280 1056s af::versa > [cumulative] : 328 1056s 1056s OK 1056s Standard error: 1056s Segmentation fault (core dumped) 1060s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1060s 139 1060s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1060s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_minimum_covering_ellipsoid.py" [FAIL] 5.8s 1060s Time: 5.78 1060s Return code: 139 1060s OKs: 0 1060s Standard error: 1060s Segmentation fault (core dumped) 1063s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1063s 139 1063s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1063s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian_fit_1d_analytical.py" [FAIL] 6.4s 1063s Time: 6.38 1063s Return code: 139 1063s OKs: 0 1063s Standard error: 1063s Segmentation fault (core dumped) 1063s "/usr/lib/cctbx/python3.13/scitbx/math/tests/tst" [OK] 0.0s 1063s Time: 0.01 1063s Return code: 0 1063s OKs: 2 1063s Standard out: 1063s copysign(3.f, +0.f) = 3 instead of 0.f as per C99 1063s copysign(3.f, -0.f) = -3 instead of -0.f as per C99 1063s linear interpolation test OK 1063s OK 1063s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_givens" [OK] 0.0s 1063s Time: 0.01 1063s Return code: 0 1063s OKs: 1 1063s Standard out: 1063s OK 1063s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_householder" [OK] 0.0s 1063s Time: 0.01 1063s Return code: 0 1063s OKs: 1 1063s Standard out: 1063s OK 1063s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_svd" [OK] 0.0s 1063s Time: 0.01 1063s Return code: 0 1063s OKs: 1 1063s Standard out: 1063s OK 1063s "/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_cholesky" [OK] 0.1s 1063s Time: 0.11 1063s Return code: 0 1063s OKs: 1 1063s Standard out: 1063s Exercising sizes up to 100 1063s Hilbert 1063s Condition 1 1063s Condition 2 1063s Condition 3 1063s Condition 4 1063s OK 1063s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/tests/tst_row_echelon.py" [OK] 0.1s 1063s Time: 0.08 1063s Return code: 0 1063s OKs: 1 1063s Standard out: 1063s OK 1063s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/tests/tst_householder.py" [OK] 0.2s 1063s Time: 0.17 1063s Return code: 0 1063s OKs: 1 1063s Standard out: 1063s OK 1063s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_matrix.py" [OK] 0.2s 1063s Time: 0.16 1063s Return code: 0 1063s OKs: 1 1063s Standard out: 1063s OK 1066s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1066s 139 1066s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1066s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_cubic_equation.py" [FAIL] 6.2s 1066s Time: 6.21 1066s Return code: 139 1066s OKs: 0 1066s Standard error: 1066s Segmentation fault (core dumped) 1069s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1069s 139 1069s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1069s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_cholesky.py" [FAIL] 5.6s 1069s Time: 5.56 1069s Return code: 139 1069s OKs: 0 1069s Standard error: 1069s Segmentation fault (core dumped) 1072s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1072s 139 1072s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1072s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_svd.py" [FAIL] 6.0s 1072s Time: 6.04 1072s Return code: 139 1072s OKs: 0 1072s Standard error: 1072s Segmentation fault (core dumped) 1075s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1075s 139 1075s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1075s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_eigensystem.py" [FAIL] 6.0s 1075s Time: 5.98 1075s Return code: 139 1075s OKs: 0 1075s Standard error: 1075s Segmentation fault (core dumped) 1078s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1078s 139 1078s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1078s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_svd.py" [FAIL] 6.0s 1078s Time: 5.98 1078s Return code: 139 1078s OKs: 0 1078s Standard error: 1078s Segmentation fault (core dumped) 1078s libtbx.python "/usr/lib/python3/dist-packages/scitbx/error/tst_error.py" [OK] 0.1s 1078s Time: 0.08 1078s Return code: 0 1078s OKs: 1 1078s Standard out: 1078s OK 1078s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_map.py" [OK] 0.1s 1078s Time: 0.06 1078s Return code: 0 1078s OKs: 1 1078s Standard out: 1078s OK 1078s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_set.py" [OK] 0.1s 1078s Time: 0.06 1078s Return code: 0 1078s OKs: 1 1078s Standard out: 1078s OK 1078s libtbx.python "/usr/lib/python3/dist-packages/scitbx/stl/tst_vector.py" [OK] 0.1s 1078s Time: 0.06 1078s Return code: 0 1078s OKs: 1 1078s Standard out: 1078s OK 1081s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1081s 139 1081s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1081s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_dsyev.py" [FAIL] 6.1s 1081s Time: 6.06 1081s Return code: 139 1081s OKs: 0 1081s Standard error: 1081s Segmentation fault (core dumped) 1084s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1084s 139 1084s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1084s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/regression_test.py" [FAIL] 5.8s 1084s Time: 5.83 1084s Return code: 139 1084s OKs: 0 1084s Standard error: 1084s Segmentation fault (core dumped) 1087s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1087s 139 1087s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1087s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex.py" [FAIL] 6.4s 1087s Time: 6.36 1087s Return code: 139 1087s OKs: 0 1087s Standard error: 1087s Segmentation fault (core dumped) 1090s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1090s 139 1090s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1090s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_numpy_bridge.py" [FAIL] 6.3s 1090s Time: 6.25 1090s Return code: 139 1090s OKs: 0 1090s Standard error: 1090s Segmentation fault (core dumped) 1093s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1093s 139 1093s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1093s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_smart_selection.py" [FAIL] 6.0s 1093s Time: 6.04 1093s Return code: 139 1093s OKs: 0 1093s Standard error: 1093s Segmentation fault (core dumped) 1096s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1096s 139 1096s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1096s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_shared.py" [FAIL] 6.1s 1096s Time: 6.11 1096s Return code: 139 1096s OKs: 0 1096s Standard error: 1096s Segmentation fault (core dumped) 1099s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_cost_of_m_handle_in_af_shared.py" [OK] 2.3s 1099s Time: 2.30 1099s Return code: 0 1099s OKs: 1 1099s Standard out: 1099s Loop over af::shared: 1099s data_size=1000, n_repeats=30000 1099s size+begin inside loop: 0.16 s 1099s begin outside loop: 0.12 s 1099s size+begin outside loop: 0.09 s 1099s 1099s data_size=10000, n_repeats=3000 1099s size+begin inside loop: 0.17 s 1099s begin outside loop: 0.12 s 1099s size+begin outside loop: 0.09 s 1099s 1099s data_size=100000, n_repeats=300 1099s size+begin inside loop: 0.17 s 1099s begin outside loop: 0.12 s 1099s size+begin outside loop: 0.09 s 1099s 1099s data_size=1000000, n_repeats=30 1099s size+begin inside loop: 0.17 s 1099s begin outside loop: 0.12 s 1099s size+begin outside loop: 0.10 s 1099s 1099s data_size=10000000, n_repeats=3 1099s size+begin inside loop: 0.24 s 1099s begin outside loop: 0.12 s 1099s size+begin outside loop: 0.09 s 1099s 1099s OK 1099s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_cubicle_neighbors.py" [OK] 0.2s 1099s Time: 0.15 1099s Return code: 0 1099s OKs: 1 1099s Standard out: 1099s OK 1099s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_r3_utils.py" [OK] 0.2s 1099s Time: 0.17 1099s Return code: 0 1099s OKs: 1 1099s Standard out: 1099s OK 1100s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_regular_grid_on_unit_sphere.py" [OK] 0.6s 1100s Time: 0.61 1100s Return code: 0 1100s OKs: 0 1103s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1103s 139 1103s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1103s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/__init__.py" [FAIL] 3.4s 1103s Time: 3.40 1103s Return code: 139 1103s OKs: 0 1103s Standard error: 1103s Segmentation fault (core dumped) 1106s Standard error: 1106s Segmentation fault (core dumped) 1106s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1106s 139 1106s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1106s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_random_transform.py" [FAIL] 3.3s 1106s Time: 3.30 1106s Return code: 139 1106s OKs: 0 1106s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_graph.py" [OK] 0.1s 1106s Time: 0.05 1106s Return code: 0 1106s OKs: 1 1106s Standard out: 1106s OK 1106s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_robust.py" [OK] 0.1s 1106s Time: 0.13 1106s Return code: 0 1106s OKs: 1 1106s Standard out: 1106s OK 1110s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1110s 139 1110s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1110s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/superpose.py" [FAIL] 3.1s 1110s Time: 3.14 1110s Return code: 139 1110s OKs: 0 1110s Standard error: 1110s Segmentation fault (core dumped) 1113s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1113s 139 1113s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1113s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/spe.py" [FAIL] 3.0s 1113s Time: 3.02 1113s Return code: 139 1113s OKs: 0 1113s Standard error: 1113s Segmentation fault (core dumped) 1114s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_integer_offsets_vs_pointers.py" [OK] 20.2s 1114s Time: 20.20 1114s Return code: 0 1114s OKs: 1 1114s Standard out: 1114s data_size = 1000 n_repeats = 30000 1114s use_pointers = False 1114s use_iterators = 0 time = 0.42 s overhead = 0.00 s (d[p[i]] 3.10862e-15) 1114s use_iterators = 1 time = 0.22 s overhead = 0.00 s (d[*p++] 3.10862e-15) 1114s use_pointers = True 1114s use_iterators = 0 time = 0.20 s overhead = 0.00 s (*dp[i] 3.10862e-15) 1114s use_iterators = 1 time = 0.49 s overhead = 0.00 s (**dpi++ 3.10862e-15) 1114s use_iterators = 2 time = 0.05 s overhead = 0.00 s (**dpp++ 3.10862e-15) 1114s data_size = 10000 n_repeats = 3000 1114s use_pointers = False 1114s use_iterators = 0 time = 0.42 s overhead = 0.00 s (d[p[i]] -3.81983e-08) 1114s use_iterators = 1 time = 0.22 s overhead = 0.00 s (d[*p++] -3.81983e-08) 1114s use_pointers = True 1114s use_iterators = 0 time = 0.20 s overhead = 0.00 s (*dp[i] -3.81983e-08) 1114s use_iterators = 1 time = 0.49 s overhead = 0.00 s (**dpi++ -3.81983e-08) 1114s use_iterators = 2 time = 0.05 s overhead = 0.00 s (**dpp++ -3.81983e-08) 1114s data_size = 100000 n_repeats = 300 1114s use_pointers = False 1114s use_iterators = 0 time = 0.43 s overhead = 0.00 s (d[p[i]] 1.02595e-07) 1114s use_iterators = 1 time = 0.23 s overhead = 0.00 s (d[*p++] 1.02595e-07) 1114s use_pointers = True 1114s use_iterators = 0 time = 0.21 s overhead = 0.00 s (*dp[i] 1.02595e-07) 1114s use_iterators = 1 time = 0.54 s overhead = 0.00 s (**dpi++ 1.02595e-07) 1114s use_iterators = 2 time = 0.06 s overhead = 0.00 s (**dpp++ 1.02595e-07) 1114s data_size = 1000000 n_repeats = 30 1114s use_pointers = False 1114s use_iterators = 0 time = 1.06 s overhead = 0.02 s (d[p[i]] 3.80598e-07) 1114s use_iterators = 1 time = 0.40 s overhead = 0.02 s (d[*p++] 3.80598e-07) 1114s use_pointers = True 1114s use_iterators = 0 time = 0.41 s overhead = 0.02 s (*dp[i] 3.80598e-07) 1114s use_iterators = 1 time = 0.97 s overhead = 0.02 s (**dpi++ 3.80598e-07) 1114s use_iterators = 2 time = 0.18 s overhead = 0.02 s (**dpp++ 3.80598e-07) 1114s data_size = 10000000 n_repeats = 3 1114s use_pointers = False 1114s use_iterators = 0 time = 3.04 s overhead = 0.21 s (d[p[i]] 2.06526e-06) 1114s use_iterators = 1 time = 1.47 s overhead = 0.21 s (d[*p++] 2.06526e-06) 1114s use_pointers = True 1114s use_iterators = 0 time = 1.44 s overhead = 0.21 s (*dp[i] 2.06526e-06) 1114s use_iterators = 1 time = 3.22 s overhead = 0.21 s (**dpi++ 2.06526e-06) 1114s use_iterators = 2 time = 0.53 s overhead = 0.21 s (**dpp++ 2.06526e-06) 1114s OK 1117s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1117s 139 1117s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1117s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/incremental_SO3_sampling.py" [FAIL] 4.3s 1117s Time: 4.33 1117s Return code: 139 1117s OKs: 0 1117s Standard error: 1117s Segmentation fault (core dumped) 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_curve_fitting.py" [FAIL] 6.4s 1120s Time: 6.39 1120s Return code: 139 1120s OKs: 0 1120s Standard error: 1120s Segmentation fault (core dumped) 1120s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_similarity_indices.py" [OK] 0.2s 1120s Time: 0.15 1120s Return code: 0 1120s OKs: 1 1120s Standard out: 1120s OK 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_weighted_correlation.py" [FAIL] 6.1s 1123s Time: 6.06 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_fit_quadratic_function.py" [OK] 0.2s 1123s Time: 0.20 1123s Return code: 0 1123s OKs: 1 1123s Standard out: 1123s OK 1124s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gcd.py" [OK] 0.6s 1124s Time: 0.60 1124s Return code: 0 1124s OKs: 1 1124s Standard out: 1124s compare_with_boost_rational_gcd(gcd_int_simple) 1124s compare_with_boost_rational_gcd(gcd_long_simple) 1124s compare_with_boost_rational_gcd(gcd_long_binary) 1124s gcd_int_boost 999 w=0.04 u+s=0.03 1124s gcd_int_simple 999 w=0.03 u+s=0.04 1124s gcd_long_boost 999 w=0.04 u+s=0.03 1124s gcd_long_simple 999 w=0.03 u+s=0.03 1124s gcd_unsigned_long_binary 999 w=0.10 u+s=0.10 1124s gcd_long_binary 999 w=0.10 u+s=0.11 1124s OK 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_exp_functions.py" [FAIL] 6.1s 1126s Time: 6.11 1126s Return code: 139 1126s OKs: 0 1126s Standard error: 1126s Segmentation fault (core dumped) 1129s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_r3_rotation.py" [OK] 2.7s 1129s Time: 2.70 1129s Return code: 0 1129s OKs: 0 1129s Standard out: 1129s times unit quaternion <-> matrix 1129s py: 0.04 0.03 s 1129s c++: 0.06 0.06 s 1129s ratio: 0.69 0.44 1129s u+s,u,s: 2.65 2.62 0.03 1130s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1130s 139 1130s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1130s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_math.py" [FAIL] 5.7s 1130s Standard error: 1130s Segmentation fault (core dumped) 1130s Time: 5.70 1130s Return code: 139 1130s OKs: 0 1130s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_line_search.py" [OK] 0.2s 1130s Time: 0.17 1130s Return code: 0 1130s OKs: 1 1130s Standard out: 1130s OK 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/math/tests/tst_resample.py" [FAIL] 3.5s 1132s Time: 3.49 1132s Return code: 139 1132s OKs: 0 1132s Standard error: 1132s Segmentation fault (core dumped) 1136s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1136s 139 1136s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1136s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian.py" [FAIL] 5.8s 1136s Time: 5.84 1136s Return code: 139 1136s OKs: 0 1136s Standard error: 1136s Segmentation fault (core dumped) 1136s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_bessel.py" [OK] 0.2s 1136s Time: 0.19 1136s Return code: 0 1136s OKs: 0 1139s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1139s 139 1139s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1139s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_quadrature.py" [FAIL] 6.2s 1139s Time: 6.17 1139s Return code: 139 1139s OKs: 0 1139s Standard error: 1139s Segmentation fault (core dumped) 1140s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_euler_angles.py" [OK] 0.9s 1140s Time: 0.91 1140s Return code: 0 1140s OKs: 0 1140s Standard out: 1140s u+s,u,s: 0.79 0.76 0.03 1140s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_superpose.py" [OK] 0.3s 1140s Time: 0.26 1140s Return code: 0 1140s OKs: 1 1140s Standard out: 1140s OK 1140s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_uniform_rotation_matrix.py" [OK] 0.2s 1140s Time: 0.19 1140s Return code: 0 1140s OKs: 1 1140s Standard out: 1140s OK 1142s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1142s 139 1142s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1142s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_halton.py" [FAIL] 6.0s 1142s Time: 6.01 1142s Return code: 139 1142s OKs: 0 1142s Standard error: 1142s Segmentation fault (core dumped) 1142s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike_mom.py" [OK] 0.2s 1142s Time: 0.18 1142s Return code: 0 1142s OKs: 1 1142s Standard out: 1142s OK 1142s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/sieve_of_eratosthenes.py" [OK] 0.0s 1142s Time: 0.03 1142s Return code: 0 1142s OKs: 1 1142s Standard out: 1142s OK 1142s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/besselk.py" [OK] 0.0s 1142s Time: 0.03 1142s Return code: 0 1142s OKs: 1 1142s Standard out: 1142s OK 1145s Standard error: 1145s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1145s 139 1145s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1145s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/scale_curves.py" [FAIL] 3.2s 1145s Time: 3.20 1145s Return code: 139 1145s OKs: 0 1145s 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/math/tests/tst_fit_peak.py" [FAIL] 3.3s 1148s Time: 3.28 1148s Return code: 139 1148s OKs: 0 1148s Standard error: 1148s Segmentation fault (core dumped) 1153s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1153s 139 1153s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1153s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike.py" [FAIL] 12.6s 1153s Time: 12.62 1153s Return code: 139 1153s OKs: 0 1153s Standard error: 1153s Segmentation fault (core dumped) 1153s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_orthonormal_basis.py" [OK] 0.2s 1153s Time: 0.19 1153s Return code: 0 1153s OKs: 1 1153s Standard out: 1153s OK 1153s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_g_function.py" [OK] 0.2s 1153s Time: 0.18 1153s Return code: 0 1153s OKs: 0 1153s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_angle_derivative.py" [OK] 0.2s 1153s Time: 0.18 1153s Return code: 0 1153s OKs: 1 1153s Standard out: 1153s OK 1156s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1156s 139 1156s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1156s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_clustering.py" [FAIL] 7.2s 1156s Time: 7.15 1156s Return code: 139 1156s OKs: 0 1156s Standard error: 1156s Segmentation fault (core dumped) 1159s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1159s 139 1159s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1159s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_periodogram.py" [FAIL] 5.5s 1159s Time: 5.52 1159s Return code: 139 1159s OKs: 0 1159s Standard error: 1159s Segmentation fault (core dumped) 1159s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_tetrahedron.py" [OK] 0.3s 1159s Time: 0.25 1159s Return code: 0 1159s OKs: 1 1159s Standard out: 1159s OK 1159s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_undirected_graph.py" [OK] 0.2s 1159s Time: 0.22 1159s Return code: 0 1159s OKs: 0 1159s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_so3_lie_algebra.py" [OK] 0.2s 1159s Time: 0.17 1159s Return code: 0 1159s OKs: 0 1159s libtbx.python "/usr/lib/python3/dist-packages/scitbx/minpack/tst.py" [OK] 0.2s 1159s Time: 0.17 1159s Return code: 0 1159s OKs: 1 1159s Standard out: 1159s OK 1160s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_ext.py" [OK] 0.2s 1160s Time: 0.17 1160s Return code: 0 1160s OKs: 1 1160s Standard out: 1160s OK 1162s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1162s 139 1162s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1162s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_error_propagation_matrix_inverse.py" [FAIL] 6.4s 1162s Time: 6.39 1162s Return code: 139 1162s OKs: 0 1162s Standard error: 1162s Segmentation fault (core dumped) 1165s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1165s 139 1165s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1165s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_curvatures.py" [FAIL] 5.5s 1165s Standard error: 1165s Segmentation fault (core dumped) 1165s Time: 5.46 1165s Return code: 139 1165s OKs: 0 1165s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_func_free_line_search.py" [OK] 0.2s 1165s Time: 0.17 1165s Return code: 0 1165s OKs: 1 1165s Standard out: 1165s The answer is: [2, -5, 500] 1165s The start value is: [-100, 203, 999] 1165s scitbx.lbfgs: use gradient_only line search: True 1165s scitbx.lbfgs: use gradient_only line search: False 1165s OK 1165s "/usr/lib/cctbx/python3.13/scitbx/lbfgs/tst_lbfgs" [OK] 0.0s 1165s Time: 0.01 1165s Return code: 0 1165s OKs: 0 1165s Standard out: 1165s n: 100 1165s m: 5 1165s xtol: 1e-16 1165s f: 254.065 gnorm: 325.365 1165s 1 2 0.000607303 1165s f: 207.819 gnorm: 54.5204 1165s 2 3 1 1165s f: 206.329 gnorm: 12.6873 1165s 3 4 1 1165s f: 206.158 gnorm: 12.9705 1165s 4 5 1 1165s f: 204.568 gnorm: 36.0649 1165s 5 6 1 1165s f: 201.009 gnorm: 69.9702 1165s 6 7 1 1165s f: 132.076 gnorm: 99.1014 1165s 7 11 2.30835 1165s f: 131.557 gnorm: 80.1033 1165s 8 13 0.152436 1165s f: 120.196 gnorm: 66.244 1165s 9 15 5 1165s f: 105.948 gnorm: 116.627 1165s 10 16 1 1165s f: 87.4002 gnorm: 17.1325 1165s 11 17 1 1165s f: 72.7773 gnorm: 32.6968 1165s 12 18 1 1165s f: 67.7306 gnorm: 49.5851 1165s 13 20 0.213662 1165s f: 60.0913 gnorm: 52.8678 1165s 14 21 1 1165s f: 45.9493 gnorm: 28.0796 1165s 15 22 1 1165s f: 37.3669 gnorm: 39.3487 1165s 16 23 1 1165s f: 23.0492 gnorm: 14.5867 1165s 17 24 1 1165s f: 19.8468 gnorm: 17.9762 1165s 18 26 0.156708 1165s f: 17.6677 gnorm: 48.6045 1165s 19 27 1 1165s f: 13.9465 gnorm: 22.2498 1165s 20 28 1 1165s f: 9.11604 gnorm: 28.0105 1165s 21 29 1 1165s f: 5.82159 gnorm: 10.2151 1165s 22 30 1 1165s f: 4.75971 gnorm: 28.511 1165s 23 32 0.436181 1165s f: 2.35807 gnorm: 22.65 1165s 24 33 1 1165s f: 1.55734 gnorm: 15.4752 1165s 25 34 1 1165s f: 0.810498 gnorm: 2.3865 1165s 26 36 0.404632 1165s f: 0.508703 gnorm: 9.94499 1165s 27 38 0.247512 1165s f: 0.363447 gnorm: 15.2129 1165s 28 39 1 1165s f: 0.167247 gnorm: 9.7728 1165s 29 40 1 1165s f: 0.0372373 gnorm: 1.32586 1165s 30 41 1 1165s f: 0.0098316 gnorm: 4.14194 1165s 31 42 1 1165s f: 0.000471098 gnorm: 0.567595 1165s 32 43 1 1165s f: 3.2788e-06 gnorm: 0.027547 1165s 33 44 1 1165s f: 2.34044e-08 gnorm: 0.00607363 1165s 34 45 1 1165s f: 2.09469e-13 gnorm: 1.31535e-05 1165s 35 46 1 1169s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1169s 139 1169s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1169s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgsb/boost_python/tst_lbfgsb.py" [FAIL] 3.3s 1169s Time: 3.30 1169s Return code: 139 1169s OKs: 0 1169s Standard error: 1169s Segmentation fault (core dumped) 1172s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1172s 139 1172s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1172s libtbx.python "/usr/lib/python3/dist-packages/scitbx/fftpack/boost_python/tst_fftpack.py" [FAIL] 3.3s 1172s Time: 3.32 1172s Return code: 139 1172s OKs: 0 1172s Standard error: 1172s Segmentation fault (core dumped) 1173s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" [OK] 10.5s 1173s Time: 10.53 1173s Return code: 0 1173s OKs: 1 1173s Standard out: 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 5 -1 0 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 5 -1 0 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 5 -1 0 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 4 -1 1 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 4 -1 1 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 4 -1 1 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 5 -1 2 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 5 -1 2 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 5 -1 2 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 5 -1 3 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 5 -1 3 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 5 -1 3 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 6 0 0 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 6 0 0 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 6 0 0 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 6 0 1 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 6 0 1 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 6 0 1 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 4 0 2 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 4 0 2 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 4 0 2 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 2 0 3 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 2 0 3 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 2 0 3 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 6 1 0 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 6 1 0 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 6 1 0 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 4 1 1 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 4 1 1 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 4 1 1 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 7 1 2 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 7 1 2 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 7 1 2 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 7 1 3 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 7 1 3 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 7 1 3 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 5 2 0 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 5 2 0 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 5 2 0 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 4 2 1 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 4 2 1 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 4 2 1 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 4 2 2 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 4 2 2 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 4 2 2 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 6 2 3 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 6 2 3 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 6 2 3 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 5 3 0 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 5 3 0 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 5 3 0 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 4 2 3 1 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 4 2 3 1 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 4 2 3 1 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 100 2 3 2 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 100 2 3 2 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 100 2 3 2 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 2 7 3 3 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 2 7 3 3 1173s scitbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_lbfgs_fem.py" raw 2 7 3 3 1173s usr+sys time: 0.34 seconds 1173s wall clock time: 10.36 seconds 1173s OK 1173s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_array_loops.py" [OK] 0.1s 1173s Time: 0.13 1173s Return code: 0 1173s OKs: 1 1173s Standard out: 1173s 10.0 1173s 11.0 1173s 12.0 1173s 1173s 10.0 1173s 11.0 1173s 12.0 1173s 1173s 0 10.0 1173s 1 11.0 1173s 2 12.0 1173s 1173s 100.0 1173s 110.0 1173s 120.0 1173s 1173s 200.0 1173s 210.0 1173s 220.0 1173s 1173s OK 1173s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/principal_axes_of_inertia.py" [OK] 0.1s 1173s Time: 0.15 1173s Return code: 0 1173s OKs: 0 1173s Standard out: 1173s (7.796692307692308, 1.365076923076923, 8.357692307692307) 1173s (38.140037692307715, 97.02526753846156, 79.02221969230771, -19.808558307692305, 35.14258523076924, 7.662036692307694) 1173s [104.22746487361262, 97.26642591377531, 12.693634135689017] 1173s [-0.4390539716746839, 0.8222124337102901, -0.36221309171382476, 0.303721679623708, 0.515239851411788, 0.8014243799908461, 0.8455677094610694, 0.24185658843488292, -0.47594184450140553] 1173s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_recipe.py" [OK] 0.1s 1173s Time: 0.14 1173s Return code: 0 1173s OKs: 1 1173s Standard out: 1173s refinery 1173s compute_functional_and_gradients 1173s callback_after_step 1173s OK 1175s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1175s 139 1175s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1175s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_grid.py" [FAIL] 3.1s 1175s Time: 3.08 1175s Return code: 139 1175s OKs: 0 1175s Standard error: 1175s Segmentation fault (core dumped) 1178s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1178s 139 1178s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1178s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_linear_least_squares_fit.py" [FAIL] 5.0s 1178s Time: 4.98 1178s Return code: 139 1178s OKs: 0 1178s Standard error: 1178s Segmentation fault (core dumped) 1181s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1181s 139 1181s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1181s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/chebyshev_lsq_example.py" [FAIL] 6.0s 1181s Time: 6.01 1181s Return code: 139 1181s OKs: 0 1181s Standard error: 1181s Segmentation fault (core dumped) 1181s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/rigid_body_refinement_core.py" [OK] 0.1s 1181s Time: 0.15 1181s Return code: 0 1181s OKs: 1 1181s Standard out: 1181s an ea: [0.0, 0.0, 0.0] 1181s fd ea: [2.9856131013692537e-15, 8.482502921596884e-16, 3.956636706594845e-15] 1181s an lt: [-0.0, -0.0, -0.0] 1181s fd lt: [0.0, 0.0, 0.0] 1181s 1181s an ea: [1.4293798315070272, -4.7699199336056015, -3.2848275925325994] 1181s fd ea: [1.4293798327180696, -4.769919932368083, -3.284827593041939] 1181s an lt: [-2.6395370381698946, 3.8546779254822816, -3.7648774634679576] 1181s fd lt: [-2.639537036053241, 3.8546779261849906, -3.764877463563465] 1181s 1181s an ea: [-4.386454471339835, 2.1848899436111178, 5.0802158076235635] 1181s fd ea: [-4.386454468985335, 2.184889945411328, 5.080215810693289] 1181s an lt: [-4.688132824683539, -10.874759921610867, -1.9393316543209416] 1181s fd lt: [-4.688132825947378, -10.874759922785415, -1.939331655265164] 1181s 1181s an ea: [-5.097458993694191, 2.0225151159319297, 4.479103261227751] 1181s fd ea: [-5.097458993574833, 2.0225151207142744, 4.479103258958617] 1181s an lt: [-2.8154365578392593, -5.157085781215166, -17.014046644874668] 1181s fd lt: [-2.8154365576682494, -5.157085780638226, -17.014046648000658] 1181s 1181s OK 1184s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1184s 139 1184s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1184s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/immoptibox_ports.py" [FAIL] 6.3s 1184s Time: 6.28 1184s Return code: 139 1184s OKs: 0 1184s Standard error: 1184s Segmentation fault (core dumped) 1187s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1187s 139 1187s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1187s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/integrating_a_weighted_sinc_function.py" [FAIL] 6.0s 1187s Time: 5.99 1187s Return code: 139 1187s OKs: 0 1187s Standard error: 1187s Segmentation fault (core dumped) 1187s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_utils.py" [OK] 0.0s 1187s Time: 0.03 1187s Return code: 0 1187s OKs: 1 1187s Standard out: 1187s OK 1187s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/rigidity.py" [OK] 0.0s 1187s Time: 0.04 1187s Return code: 0 1187s OKs: 0 1187s Standard out: 1187s double banana 3D dof (method=integer): 7 1187s double banana 3D dof (method=float): 7 1187s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_rigidity.py" [OK] 0.2s 1187s Time: 0.22 1187s Return code: 0 1187s OKs: 0 1187s Standard out: 1187s repeat_log = {0: 85} 1187s u+s,u,s: 0.20 0.20 0.00 1188s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/rigidity_matrix_symbolic.py" [OK] 0.2s 1188s Time: 0.23 1188s Return code: 0 1188s OKs: 0 1188s Standard out: 1188s u+s,u,s: 0.21 0.21 0.00 1190s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree_find_paths.py" [OK] 2.4s 1190s Time: 2.40 1190s Return code: 0 1190s OKs: 1 1190s Standard out: 1190s OK 1190s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1190s 139 1190s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1190s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/minimizer_comparisons.py" [FAIL] 5.9s 1190s Time: 5.92 1190s Return code: 139 1190s OKs: 0 1190s Standard error: 1190s Segmentation fault (core dumped) 1190s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/test_cases_tardy_pdb.py" [OK] 0.1s 1190s Time: 0.06 1190s Return code: 0 1190s OKs: 0 1194s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1194s 139 1194s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1194s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_basic.py" [FAIL] 3.5s 1194s Time: 3.50 1194s Return code: 139 1194s OKs: 0 1194s Standard error: 1194s Segmentation fault (core dumped) 1197s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1197s 139 1197s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1197s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree.py" [FAIL] 6.8s 1197s Time: 6.82 1197s Return code: 139 1197s OKs: 0 1197s Standard error: 1197s Segmentation fault (core dumped) 1200s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1200s 139 1200s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1200s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_tardy.py" [FAIL] 6.3s 1200s Time: 6.28 1200s Return code: 139 1200s OKs: 0 1200s Standard error: 1200s Segmentation fault (core dumped) 1203s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1203s 139 1203s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1203s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_energy_plots.py" [FAIL] 6.2s 1203s Time: 6.22 1203s Return code: 139 1203s OKs: 0 1203s Standard error: 1203s Segmentation fault (core dumped) 1203s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/free_motion_reference_impl.py" [OK] 0.0s 1203s Time: 0.04 1203s Return code: 0 1203s OKs: 1 1203s Standard out: 1203s e_kin tot ang lin: 0.04066059413038476 0.012310594130384761 0.02835 1203s e_pot: 0.6403087877704161 1203s e_tot: 0.6809693819008009 1203s ang acc 3D: (0.4499405243671747, -0.22736369685250066, -0.6859763000328927) 1203s lin acc 3D: (0.2108121283092794, 0.3044814367238479, -0.7824311428947446) 1203s 1203s e_kin tot ang lin: 0.043334386720177365 0.012335145793951681 0.030999240926225684 1203s e_pot: 0.6375204431681878 1203s e_tot: 0.6808548298883652 1203s ang acc 3D: (0.4491523283824315, -0.2233952828755118, -0.688364609039924) 1203s lin acc 3D: (0.2063305410676703, 0.3022012812609254, -0.7827791077048256) 1203s 1203s e_kin tot ang lin: 0.04624491637806352 0.012390841212545118 0.0338540751655184 1203s e_pot: 0.6344966498401754 1203s e_tot: 0.6807415662182389 1203s ang acc 3D: (0.4482905223840879, -0.2193464063160701, -0.6906197519803725) 1203s lin acc 3D: (0.20168867739512958, 0.299808900299363, -0.7830079270607541) 1203s 1203s e_kin tot ang lin: 0.049389854602061224 0.01247763222642335 0.036912222375637876 1203s e_pot: 0.6312398275384674 1203s e_tot: 0.6806296821405287 1203s ang acc 3D: (0.44735466644443667, -0.21521902126722914, -0.692740958483326) 1203s lin acc 3D: (0.19688964121862268, 0.29730414639378616, -0.7831155604559972) 1203s 1203s e_kin tot ang lin: 0.05276668787891577 0.012595448079626585 0.04017123979928919 1203s e_pot: 0.6277525800757479 1203s e_tot: 0.6805192679546637 1203s ang acc 3D: (0.4463443200247767, -0.2110151239756078, -0.694727476553102) 1203s lin acc 3D: (0.1919366941490876, 0.29468687861617315, -0.783099948460292) 1203s 1203s e_kin tot ang lin: 0.05637271969939971 0.012744195480724368 0.043628524218675344 1203s e_pot: 0.6240376932449352 1203s e_tot: 0.6804104129443349 1203s ang acc 3D: (0.4452590426839754, -0.2067367517215091, -0.6965785731789051) 1203s lin acc 3D: (0.18683325327725137, 0.29195696483157874, -0.7829590159403469) 1203s 1203s e_kin tot ang lin: 0.060205072713709167 0.012923758676161239 0.04728131403754793 1203s e_pot: 0.6200981325993219 1203s e_tot: 0.680303205313031 1203s ang acc 3D: (0.44409839480429714, -0.20238598167333133, -0.6982935349568492) 1203s lin acc 3D: (0.18158288880693388, 0.2891142841060344, -0.7826906753299725) 1203s 1203s e_kin tot ang lin: 0.06426069102522652 0.013133999536143382 0.051126691489083144 1203s e_pot: 0.6159370410950341 1203s e_tot: 0.6801977321202606 1203s ang acc 3D: (0.4428619383337592, -0.1979649297164907, -0.6998716687235316) 1203s lin acc 3D: (0.17618932152521946, 0.2861587292410898, -0.7822928299444691) 1203s 1203s e_kin tot ang lin: 0.06853634262082685 0.013374757653013635 0.05516158496781321 1203s e_pot: 0.6115577365976127 1203s e_tot: 0.6800940792184396 1203s ang acc 3D: (0.4415492375442347, -0.1934757492571058, -0.7013123022002559) 1203s lin acc 3D: (0.17065642010895676, 0.2830902094290727, -0.7817633773339945) 1203s 1203s e_kin tot ang lin: 0.07302862193581516 0.013645850452066947 0.059382771483748216 1203s e_pot: 0.6069637092547071 1203s e_tot: 0.6799923311905223 1203s ang acc 3D: (0.44015985980451133, -0.18892063000069204, -0.702614784647033) 1203s lin acc 3D: (0.16498819826718966, 0.2799086530227533, -0.7811002126706817) 1203s 1203s OK 1206s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1206s 139 1206s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1206s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/tst.py" [FAIL] 6.1s 1206s Time: 6.05 1206s Return code: 139 1206s OKs: 0 1206s Standard error: 1206s Segmentation fault (core dumped) 1209s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1209s 139 1209s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1209s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_featherstone.py" [FAIL] 5.9s 1209s Time: 5.89 1209s Return code: 139 1209s OKs: 0 1209s Standard error: 1209s Segmentation fault (core dumped) 1212s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1212s 139 1212s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1212s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion.py" [FAIL] 6.1s 1212s Time: 6.11 1212s Return code: 139 1212s OKs: 0 1212s Standard error: 1212s Segmentation fault (core dumped) 1215s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1215s 139 1215s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1215s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion_hard.py" [FAIL] 6.1s 1215s Time: 6.12 1215s Return code: 139 1215s OKs: 0 1215s Standard error: 1215s Segmentation fault (core dumped) 1218s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1218s 139 1218s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1218s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_joint_lib.py" [FAIL] 6.0s 1218s Time: 5.96 1218s Return code: 139 1218s OKs: 0 1218s Standard error: 1218s Segmentation fault (core dumped) 1218s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_spherical_refinement.py" [OK] 0.3s 1218s Time: 0.34 1218s Return code: 0 1218s OKs: 1 1218s Standard out: 1218s OK 1218s usr+sys time: 0.29 seconds 1218s wall clock time: 0.29 seconds 1221s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1221s 139 1221s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1221s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_singular.py" [FAIL] 6.0s 1221s Time: 6.00 1221s Return code: 139 1221s OKs: 0 1221s Standard error: 1221s Segmentation fault (core dumped) 1224s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1224s 139 1224s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1224s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_molecules.py" [FAIL] 5.7s 1224s Time: 5.73 1224s Return code: 139 1224s OKs: 0 1224s Standard error: 1224s Segmentation fault (core dumped) 1227s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1227s 139 1227s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1227s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_sparse.py" [FAIL] 6.0s 1227s Time: 6.04 1227s Return code: 139 1227s OKs: 0 1227s Standard error: 1227s Segmentation fault (core dumped) 1230s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1230s 139 1230s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1230s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_lu_factorization.py" [FAIL] 6.0s 1230s Time: 6.02 1230s Return code: 139 1230s OKs: 0 1230s Standard error: 1230s Segmentation fault (core dumped) 1233s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1233s 139 1233s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1233s libtbx.python "/usr/lib/python3/dist-packages/scitbx/iso_surface/tst_iso_surface.py" [FAIL] 6.0s 1233s Time: 5.99 1233s Return code: 139 1233s OKs: 0 1233s Standard error: 1233s Segmentation fault (core dumped) 1236s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1236s 139 1236s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1236s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/simplex.py" [FAIL] 6.0s 1236s Time: 5.96 1236s Return code: 139 1236s OKs: 0 1236s Standard error: 1236s Segmentation fault (core dumped) 1236s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/golden_section_search.py" [OK] 0.0s 1236s Time: 0.03 1236s Return code: 0 1236s OKs: 0 1239s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1239s 139 1239s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1239s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/differential_evolution.py" [FAIL] 5.9s 1239s Time: 5.94 1239s Return code: 139 1239s OKs: 0 1239s Standard error: 1239s Segmentation fault (core dumped) 1242s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1242s 139 1242s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1242s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/direct_search_simulated_annealing.py" [FAIL] 5.9s 1242s Time: 5.90 1242s Return code: 139 1242s OKs: 0 1242s Standard error: 1242s Segmentation fault (core dumped) 1246s Standard error: 1246s Segmentation fault (core dumped) 1246s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1246s 139 1246s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1246s libtbx.python "/usr/lib/python3/dist-packages/scitbx/random/tests/tst_random.py" [FAIL] 6.5s 1246s Time: 6.54 1246s Return code: 139 1246s OKs: 0 1246s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/test_problems.py" [OK] 0.2s 1246s Time: 0.16 1246s Return code: 0 1246s OKs: 0 1247s libtbx.python "/usr/lib/python3/dist-packages/scitbx/glmtbx/tests/tst.py" [OK] 0.8s 1247s Time: 0.75 1247s Return code: 0 1247s OKs: 2 1247s Standard out: 1247s OK 1247s OK 1249s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1249s 139 1249s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1249s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/tst_normal_equations.py" [FAIL] 6.5s 1249s Time: 6.55 1249s Return code: 139 1249s OKs: 0 1249s Standard error: 1249s Segmentation fault (core dumped) 1252s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1252s 139 1252s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1252s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_basic.py" [FAIL] 5.1s 1252s Time: 5.12 1252s Return code: 139 1252s OKs: 0 1252s Standard error: 1252s Segmentation fault (core dumped) 1255s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1255s 139 1255s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1255s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_booth.py" [FAIL] 6.0s 1255s Time: 5.99 1255s Return code: 139 1255s OKs: 0 1255s Standard error: 1255s Segmentation fault (core dumped) 1255s libtbx.python "/usr/lib/python3/dist-packages/scitbx/suffixtree/test/tst_single.py" [OK] 0.1s 1255s Time: 0.08 1255s Return code: 0 1255s OKs: 0 1258s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1258s 139 1258s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1258s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_twisted.py" [FAIL] 6.0s 1258s Time: 6.03 1258s Return code: 139 1258s OKs: 0 1258s Standard error: 1258s Segmentation fault (core dumped) 1261s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1261s 139 1261s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1261s libtbx.python "/usr/lib/python3/dist-packages/smtbx/absolute_structure/tests/tst_absolute_structure.py" --fix_random_seeds [FAIL] 6.5s 1261s Time: 6.52 1261s Return code: 139 1261s OKs: 0 1261s Standard error: 1261s Segmentation fault (core dumped) 1265s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1265s 139 1265s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1265s libtbx.python "/usr/lib/python3/dist-packages/smtbx/ab_initio/tests/tst_ab_initio_ext.py" [FAIL] 6.9s 1265s Time: 6.87 1265s Return code: 139 1265s OKs: 0 1265s Standard error: 1265s Segmentation fault (core dumped) 1268s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1268s 139 1268s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1268s libtbx.python "/usr/lib/python3/dist-packages/smtbx/ab_initio/tests/tst_charge_flipping.py" --fix_seed --on=E "hall: P 1" "hall: P 3" "hall: -P 2ybc" [FAIL] 6.7s 1268s Time: 6.73 1268s Return code: 139 1268s OKs: 0 1268s Standard error: 1268s Segmentation fault (core dumped) 1272s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1272s 139 1272s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1272s libtbx.python "/usr/lib/python3/dist-packages/smtbx/masks/tests/tst_masks.py" [FAIL] 6.9s 1272s Time: 6.93 1272s Return code: 139 1272s OKs: 0 1272s Standard error: 1272s Segmentation fault (core dumped) 1275s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1275s 139 1275s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1275s libtbx.python "/usr/lib/python3/dist-packages/smtbx/structure_factors/direct/tests/tst_standard_xray.py" [FAIL] 7.1s 1275s Time: 7.12 1275s Return code: 139 1275s OKs: 0 1275s Standard error: 1275s 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_weighting_schemes.py" --fix_random_seeds [FAIL] 7.0s 1279s Standard error: 1279s Segmentation fault (core dumped) 1279s Time: 7.02 1279s Return code: 139 1279s OKs: 0 1279s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_reparametrisation" [OK] 0.0s 1279s Time: 0.01 1279s Return code: 0 1279s OKs: 1 1279s Standard out: 1279s sizeof(parameter) = 32 1279s OK 1282s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1282s 139 1282s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1282s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_lbfgs.py" [FAIL] 7.0s 1282s Time: 6.96 1282s Return code: 139 1282s OKs: 0 1282s Standard error: 1282s Segmentation fault (core dumped) 1282s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens" [OK] 0.0s 1282s Time: 0.01 1282s Return code: 0 1282s OKs: 1 1282s Standard out: 1282s OK 1286s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1286s 139 1286s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1286s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_occupancies.py" [FAIL] 7.1s 1286s Time: 7.12 1286s Return code: 139 1286s OKs: 0 1286s Standard error: 1286s Segmentation fault (core dumped) 1286s "/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_special_position" [OK] 0.0s 1286s Time: 0.01 1286s Return code: 0 1286s OKs: 1 1286s Standard out: 1286s OK 1289s Standard error: 1289s Segmentation fault (core dumped) 1289s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1289s 139 1289s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1289s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_same_group.py" [FAIL] 7.1s 1289s Time: 7.07 1289s Return code: 139 1289s OKs: 0 1293s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1293s 139 1293s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1293s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_reparametrisation.py" [FAIL] 7.0s 1293s Time: 7.02 1293s Return code: 139 1293s OKs: 0 1293s Standard error: 1293s Segmentation fault (core dumped) 1296s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1296s 139 1296s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1296s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=naive [FAIL] 7.0s 1296s Time: 7.04 1296s Return code: 139 1296s OKs: 0 1296s Standard error: 1296s Segmentation fault (core dumped) 1300s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1300s 139 1300s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1300s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_disorder.py" [FAIL] 7.1s 1300s Time: 7.06 1300s Return code: 139 1300s OKs: 0 1300s Standard error: 1300s Segmentation fault (core dumped) 1300s Standard error: 1300s Segmentation fault (core dumped) 1300s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1300s 139 1300s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1300s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=levenberg-marquardt [FAIL] 3.7s 1300s Time: 3.65 1300s Return code: 139 1300s OKs: 0 1304s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1304s 139 1304s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1304s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_rigid.py" [FAIL] 3.9s 1304s Time: 3.89 1304s Return code: 139 1304s OKs: 0 1304s Standard error: 1304s Segmentation fault (core dumped) 1307s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1307s 139 1307s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1307s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_direction.py" [FAIL] 7.1s 1307s Time: 7.15 1307s Return code: 139 1307s OKs: 0 1307s Standard error: 1307s Segmentation fault (core dumped) 1310s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1310s 139 1310s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1310s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_adp_restraints.py" [FAIL] 6.7s 1310s Standard error: 1310s Segmentation fault (core dumped) 1310s Time: 6.66 1310s Return code: 139 1310s OKs: 0 1314s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1314s 139 1314s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1314s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_manager.py" [FAIL] 6.7s 1314s Time: 6.65 1314s Return code: 139 1314s OKs: 0 1314s Standard error: 1314s Segmentation fault (core dumped) 1317s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1317s 139 1317s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1317s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_restraints.py" --verbose --scatterers=5 --resolution=0.2 [FAIL] 6.6s 1317s Time: 6.57 1317s Return code: 139 1317s OKs: 0 1317s Standard error: 1317s Segmentation fault (core dumped) 1321s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1321s 139 1321s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1321s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_refine.py" [FAIL] 6.9s 1321s Time: 6.92 1321s Return code: 139 1321s OKs: 0 1321s Standard error: 1321s Segmentation fault (core dumped) 1327s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1327s 1 1327s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1327s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py" [FAIL] 9.7s 1327s Time: 9.67 1327s Return code: 1 1327s OKs: 0 1327s Standard out: 1327s 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 1327s Standard error: 1327s Traceback (most recent call last): 1327s File "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py", line 37, in 1327s run() 1327s ~~~^^ 1327s File "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py", line 27, in run 1327s run_buf.raise_if_errors() 1327s ~~~~~~~~~~~~~~~~~~~~~~~^^ 1327s File "/usr/lib/python3/dist-packages/libtbx/easy_run.py", line 46, in raise_if_errors 1327s raise Error(msg) 1327s RuntimeError: child process stderr output: 1327s 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' 1327s Segmentation fault (core dumped) 1328s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1328s 139 1328s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1328s libtbx.python "/usr/lib/python3/dist-packages/smtbx/tests/tst_utils.py" [FAIL] 7.1s 1328s Time: 7.14 1328s Return code: 139 1328s OKs: 0 1328s Standard error: 1328s Segmentation fault (core dumped) 1331s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1331s 139 1331s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1331s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_least_squares.py" [EXPECTED UNSTABLE] 4.7s 1331s Time: 4.65 1331s Return code: 139 1331s OKs: 0 1331s Standard error: 1331s Segmentation fault (core dumped) 1332s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_predict.py" [OK] 0.2s 1332s Time: 0.24 1332s Return code: 0 1332s OKs: 1 1332s Standard out: 1332s OK 1332s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_ewald_sphere.py" [OK] 0.2s 1332s Time: 0.20 1332s Return code: 0 1332s OKs: 1 1332s Standard out: 1332s OK 1332s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/tst_partial_derivatives.py" [OK] 0.2s 1332s Time: 0.18 1332s Return code: 0 1332s OKs: 1 1332s Standard out: 1332s OK 1335s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1335s 139 1335s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1335s libtbx.python "/usr/lib/python3/dist-packages/rstbx/dps_core/tst_iotbx_converter.py" [FAIL] 6.9s 1335s Time: 6.87 1335s Return code: 139 1335s OKs: 0 1335s Standard error: 1335s Segmentation fault (core dumped) 1338s Standard error: 1338s Segmentation fault (core dumped) 1338s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1338s 139 1338s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1338s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/fastbragg/tst_bragg_minimal.py" [FAIL] 6.2s 1338s Time: 6.18 1338s Return code: 139 1338s OKs: 0 1341s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1341s 139 1341s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1341s libtbx.python "/usr/lib/python3/dist-packages/rstbx/sublattice_support/tst_sublattice.py" [FAIL] 6.8s 1341s Time: 6.84 1341s Return code: 139 1341s OKs: 0 1341s Standard error: 1341s Segmentation fault (core dumped) 1342s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/core_toolbox/boost_python/tst_small_image.py" [OK] 0.4s 1342s Time: 0.42 1342s Return code: 0 1342s OKs: 1 1342s Standard out: 1342s OK 1342s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/diffraction/geometry.py" [OK] 0.2s 1342s Time: 0.18 1342s Return code: 0 1342s OKs: 1 1342s Standard out: 1342s OK 1342s libtbx.python "/usr/lib/python3/dist-packages/spotfinder/math_support/sphere_formulae.py" [OK] 0.0s 1342s Time: 0.03 1342s Return code: 0 1342s OKs: 1 1342s Standard out: 1342s OK 1343s RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN RETURN CODE BEGIN 1343s 139 1343s RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- RETURN CODE -END- 1343s libtbx.python -c "from rstbx.run_tests import run; run()" [FAIL] 5.0s 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Time: 4.98 1343s Return code: 139 1343s OKs: 0 1343s ================================================================================ 1343s 1343s Tests finished. Elapsed time: 1019.97s 1343s 1343s Distribution of test runtimes: 1343s 0.0s - 5.1s: 288 1343s 5.1s - 10.2s: 250 1343s 10.2s - 15.3s: 5 1343s 15.3s - 20.5s: 1 1343s 20.5s - 25.6s: 1 1343s 25.6s - 30.7s: 0 1343s 30.7s - 35.8s: 0 1343s 35.8s - 40.9s: 0 1343s 40.9s - 46.0s: 0 1343s 46.0s - 51.1s: 1 1343s 1343s 1343s Warning: the following are 5 longest jobs: 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_fetch.py": 51.1s 1343s libtbx.python "/usr/lib/python3/dist-packages/libtbx/tst_thread_utils.py": 23.0s 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_integer_offsets_vs_pointers.py": 20.2s 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py": 13.0s 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike.py": 12.6s 1343s Please try to reduce overall runtime - consider splitting up these tests. 1343s 1343s 1343s Error: the following jobs returned non-zero exit codes or suspicious stderr output: 1343s 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sf_low_res_accuracy.py" [FAIL] 4.3s 1343s Time: 4.34 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_double_step_filtration.py" [FAIL] 4.4s 1343s Time: 4.43 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_is_periodic.py" [FAIL] 6.8s 1343s Time: 6.76 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/tst_reindexing.py" [FAIL] 6.8s 1343s Time: 6.77 1343s Return code: 139 1343s OKs: 0 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_data_manipulation.py" [FAIL] 6.2s 1343s Time: 6.23 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_bfgs.py" [FAIL] 6.5s 1343s Time: 6.54 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/omz/tst_dev.py" P31 [FAIL] 6.6s 1343s Time: 6.61 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry/tests/tst_geometry.py" [FAIL] 6.8s 1343s Time: 6.79 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/covariance/tests/tst_covariance.py" [FAIL] 6.8s 1343s Time: 6.84 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_goodness_of_symmetry.py" [FAIL] 6.7s 1343s Time: 6.70 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/symmetry_search/tests/tst_from_map.py" P312 [FAIL] 6.8s 1343s Time: 6.84 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_xray.py" [FAIL] 6.4s 1343s Time: 6.38 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray.py" I41/acd [FAIL] 7.0s 1343s Time: 6.98 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_r1.py" [FAIL] 6.9s 1343s Time: 6.90 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/targets/tst_shelxl_wght_ls.py" [FAIL] 6.8s 1343s Time: 6.77 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/xray/boost_python/tst_f_model.py" [FAIL] 6.5s 1343s Time: 6.50 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/array_family/boost_python/tst_flex.py" [FAIL] 6.4s 1343s Time: 6.45 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_uctbx.py" [FAIL] 6.5s 1343s Time: 6.48 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/uctbx/boost_python/tst_crystal_orientation.py" [FAIL] 6.3s 1343s Time: 6.32 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/boost_python/tst_sgtbx.py" [FAIL] 6.4s 1343s Time: 6.43 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_ext.py" [FAIL] 6.4s 1343s Time: 6.44 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_distance_based_connectivity.py" [FAIL] 6.5s 1343s Time: 6.49 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/crystal/tst_super_cell.py" [FAIL] 7.2s 1343s Time: 7.25 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adptbx/boost_python/tst_adptbx.py" [FAIL] 7.4s 1343s Time: 7.42 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/miller/boost_python/tst_miller.py" [FAIL] 6.6s 1343s Time: 6.65 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_xray_scattering.py" [FAIL] 6.4s 1343s Time: 6.37 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_formula.py" [FAIL] 5.5s 1343s Time: 5.50 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/eltbx/tests/tst_attenuation_coefficient.py" [FAIL] 6.0s 1343s Time: 5.95 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/boost_python/tst_maptbx.py" [FAIL] 6.3s 1343s Time: 6.32 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_bcr.py" [FAIL] 7.4s 1343s Time: 7.36 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_loft.py" [FAIL] 7.4s 1343s Time: 7.42 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/dmtbx/boost_python/tst_dmtbx.py" [FAIL] 6.4s 1343s Time: 6.42 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/translation_search/boost_python/tst_translation_search.py" [FAIL] 6.1s 1343s Time: 6.13 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_ext.py" [FAIL] 6.5s 1343s Time: 6.52 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/geometry_restraints/tst_angle_derivs.py" [FAIL] 4.9s 1343s Time: 4.91 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/adp_restraints/tst_ext.py" [FAIL] 6.2s 1343s Time: 6.16 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_krivy_gruber.py" --Quick [FAIL] 6.2s 1343s Time: 6.19 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx.py" [FAIL] 6.1s 1343s Time: 6.10 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_space_group_type_tidy_cb_op_t.py" [FAIL] 5.9s 1343s Time: 5.94 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_denominators.py" P31 [FAIL] 6.1s 1343s Time: 6.11 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_subgroups.py" [FAIL] 6.1s 1343s Time: 6.05 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_lattice_symmetry.py" [FAIL] 6.0s 1343s Time: 5.97 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints.py" P3 [FAIL] 6.1s 1343s Time: 6.13 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_adp_constraints_cartesian.py" [FAIL] 6.2s 1343s Time: 6.19 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reflection_statistics.py" [FAIL] 5.8s 1343s Time: 5.83 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_harker.py" [FAIL] 6.2s 1343s Time: 6.18 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_special_op_simplifier.py" [FAIL] 6.2s 1343s Time: 6.24 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_twin_target.py" [FAIL] 6.5s 1343s Time: 6.46 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/symbol_confidence.py" [FAIL] 6.2s 1343s Time: 6.21 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/bravais_types.py" [FAIL] 6.0s 1343s Time: 6.02 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_lookup_utils.py" [FAIL] 6.2s 1343s Time: 6.24 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal.py" I41/acd [FAIL] 6.4s 1343s Time: 6.40 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_direct_space_asu.py" I41/acd [FAIL] 6.4s 1343s Time: 6.40 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pair_asu_table.py" [FAIL] 6.4s 1343s Time: 6.43 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_asu_clusters.py" [FAIL] 6.3s 1343s Time: 6.30 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_crystal_close_packing.py" R-3mr [FAIL] 5.9s 1343s Time: 5.92 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fourier_transform_real_part_at_x.py" P31 [FAIL] 6.2s 1343s Time: 6.16 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller.py" P31 [FAIL] 6.4s 1343s Time: 6.43 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_mem.py" [FAIL] 6.8s 1343s Time: 6.83 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_reciprocal_space_asu.py" P312 [FAIL] 6.2s 1343s Time: 6.23 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_triplet_generator.py" P41 [FAIL] 6.3s 1343s Time: 6.32 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_emma.py" P31 [FAIL] 6.7s 1343s Time: 6.66 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_expand_to_p1.py" P31 [FAIL] 6.8s 1343s Time: 6.82 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_change_basis.py" P31 [FAIL] 6.5s 1343s Time: 6.54 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_wilson_plot.py" P31 [FAIL] 6.3s 1343s Time: 6.33 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_derivatives.py" P31 [FAIL] 6.3s 1343s Time: 6.31 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_fast_gradients.py" P31 [FAIL] 6.5s 1343s Time: 6.46 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F P31 [FAIL] 6.4s 1343s Time: 6.44 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_xray_minimization.py" --F_sq P31 [FAIL] 3.2s 1343s Time: 3.17 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_maptbx_structure_factors.py" P31 [FAIL] 3.6s 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Traceback (most recent call last): 1343s File "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py", line 140, in 1343s exercise() 1343s ~~~~~~~~^^ 1343s File "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py", line 126, in exercise 1343s assert not easy_run.call(cmd) 1343s ^^^^^^^^^^^^^^^^^^^^^^ 1343s AssertionError 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Traceback (most recent call last): 1343s File "/usr/lib/python3.13/urllib/request.py", line 1541, in ftp_open 1343s fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout) 1343s File "/usr/lib/python3.13/urllib/request.py", line 1561, in connect_ftp 1343s return ftpwrapper(user, passwd, host, port, dirs, timeout, 1343s persistent=False) 1343s File "/usr/lib/python3.13/urllib/request.py", line 2409, in __init__ 1343s self.init() 1343s ~~~~~~~~~^^ 1343s File "/usr/lib/python3.13/urllib/request.py", line 2418, in init 1343s self.ftp.connect(self.host, self.port, self.timeout) 1343s ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1343s File "/usr/lib/python3.13/ftplib.py", line 158, in connect 1343s self.sock = socket.create_connection((self.host, self.port), self.timeout, 1343s ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1343s source_address=self.source_address) 1343s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1343s File "/usr/lib/python3.13/socket.py", line 864, in create_connection 1343s raise exceptions[0] 1343s File "/usr/lib/python3.13/socket.py", line 849, in create_connection 1343s sock.connect(sa) 1343s ~~~~~~~~~~~~^^^^ 1343s TimeoutError: timed out 1343s 1343s The above exception was the direct cause of the following exception: 1343s 1343s Traceback (most recent call last): 1343s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 327, in 1343s exercise(sys.argv[1:]) 1343s ~~~~~~~~^^^^^^^^^^^^^^ 1343s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 26, in exercise 1343s exercise_validation() 1343s ~~~~~~~~~~~~~~~~~~~^^ 1343s File "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py", line 29, in exercise_validation 1343s cd = validation.smart_load_dictionary(name="cif_core.dic") 1343s File "/usr/lib/python3/dist-packages/iotbx/cif/validation.py", line 111, in smart_load_dictionary 1343s url = locate_dictionary(name, registry_location=registry_location) 1343s File "/usr/lib/python3/dist-packages/iotbx/cif/validation.py", line 129, in locate_dictionary 1343s cm = cif.reader(file_object=urlopen(registry_location)).model() 1343s ~~~~~~~^^^^^^^^^^^^^^^^^^^ 1343s File "/usr/lib/python3.13/urllib/request.py", line 189, in urlopen 1343s return opener.open(url, data, timeout) 1343s ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1343s File "/usr/lib/python3.13/urllib/request.py", line 489, in open 1343s response = self._open(req, data) 1343s File "/usr/lib/python3.13/urllib/request.py", line 506, in _open 1343s result = self._call_chain(self.handle_open, protocol, protocol + 1343s '_open', req) 1343s File "/usr/lib/python3.13/urllib/request.py", line 466, in _call_chain 1343s result = func(*args) 1343s File "/usr/lib/python3.13/urllib/request.py", line 1558, in ftp_open 1343s raise URLError(exp) from exp 1343s urllib.error.URLError: 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s *** buffer overflow detected ***: terminated 1343s Aborted (core dumped) 1343s Standard error: 1343s *** buffer overflow detected ***: terminated 1343s Aborted (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s *** buffer overflow detected ***: terminated 1343s Aborted (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s /usr/lib/python3/dist-packages/ccp4io_adaptbx/__init__.py:25: UserWarning: ccp4io_adaptbx: cannot locate syminfo.lib 1343s warnings.warn("ccp4io_adaptbx: cannot locate syminfo.lib") 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Traceback (most recent call last): 1343s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 477, in 1343s exercise(sys.argv[1:]) 1343s ~~~~~~~~^^^^^^^^^^^^^^ 1343s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 22, in exercise 1343s run_and_compare( 1343s ~~~~~~~~~~~~~~~^ 1343s ['iotbx.lattice_symmetry' 1343s ^^^^^^^^^^^^^^^^^^^^^^^^^ 1343s ...<31 lines>... 1343s 1343s 1343s """) 1343s ^^^^ 1343s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py", line 17, in run_and_compare 1343s command=command).raise_if_errors().stdout_lines 1343s ~~~~~~~~~~~~~~~^^ 1343s File "/usr/lib/python3/dist-packages/libtbx/easy_run.py", line 46, in raise_if_errors 1343s raise Error(msg) 1343s RuntimeError: child process stderr output: 1343s command: 'iotbx.lattice_symmetry --unit_cell="12.7923,12.8923,29.4356,102.846,103.846,22.7475"' 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s *** buffer overflow detected ***: terminated 1343s Aborted (core dumped) 1343s Traceback (most recent call last): 1343s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py", line 138, in 1343s exercise() 1343s ~~~~~~~~^^ 1343s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py", line 48, in exercise 1343s assert not easy_run.call("iotbx.pdb.box_around_molecule %s.pdb" % ( 1343s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1343s prefix)) 1343s ^^^^^^^^ 1343s AssertionError 1343s Standard error: 1343s *** buffer overflow detected ***: terminated 1343s Aborted (core dumped) 1343s Standard error: 1343s *** buffer overflow detected ***: terminated 1343s Aborted (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Traceback (most recent call last): 1343s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py", line 60, in 1343s exercise() 1343s ~~~~~~~~^^ 1343s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py", line 48, in exercise 1343s assert (len(out.stdout_lines) == 2) and (len(out.stderr_lines) == 0) 1343s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1343s AssertionError 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Traceback (most recent call last): 1343s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py", line 815, in 1343s exercise_1() 1343s ~~~~~~~~~~^^ 1343s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py", line 806, in exercise_1 1343s assert not easy_run.call(cmd) 1343s ^^^^^^^^^^^^^^^^^^^^^^ 1343s AssertionError 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Time: 3.60 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_map_weights_for_symmetry_summation.py" Pmmm [FAIL] 6.9s 1343s Time: 6.85 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_real_space_refinement_simple.py" [FAIL] 6.6s 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s *** buffer overflow detected ***: terminated 1343s Aborted (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Traceback (most recent call last): 1343s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py", line 395, in 1343s tst_1() 1343s ~~~~~^^ 1343s File "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py", line 370, in tst_1 1343s assert os.path.isfile('%s.cif_%s_000.mtz' % (prefix, bn)) 1343s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1343s AssertionError 1343s Standard error: 1343s *** buffer overflow detected ***: terminated 1343s Aborted (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s *** buffer overflow detected ***: terminated 1343s Aborted (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Time: 6.60 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation.py" [FAIL] 6.4s 1343s Time: 6.41 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_interpolation_2.py" [FAIL] 6.5s 1343s Time: 6.54 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_loc_res.py" [FAIL] 7.5s 1343s Time: 7.50 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_target_and_gradients.py" [FAIL] 7.2s 1343s Time: 7.24 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_merge_equivalents.py" P31 [FAIL] 6.4s 1343s Time: 6.45 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_grouped_data.py" P31 [FAIL] 6.5s 1343s Time: 6.49 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_fft_map.py" P31 [FAIL] 6.5s 1343s Time: 6.54 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sampled_model_density.py" P31 [FAIL] 6.6s 1343s Time: 6.64 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_fast_nv1995.py" F222 [FAIL] 6.6s 1343s Time: 6.58 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_lbfgs.py" [FAIL] 6.0s 1343s Time: 5.98 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_geometry_restraints_2.py" [FAIL] 7.0s 1343s Time: 7.04 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_french_wilson.py" [FAIL] 6.5s 1343s Time: 6.47 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/development/make_cns_input.py" P31 [FAIL] 6.5s 1343s Time: 6.49 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_pointgroup_tools.py" [FAIL] 5.8s 1343s Time: 5.75 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/sub_lattice_tools.py" [FAIL] 6.3s 1343s Time: 6.32 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/rational_matrices_point_groups.py" [FAIL] 6.4s 1343s Time: 6.37 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/cosets.py" [FAIL] 6.4s 1343s Time: 6.38 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_pg_tools.py" [FAIL] 6.2s 1343s Time: 6.22 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/reticular_twin_laws.py" [FAIL] 6.3s 1343s Time: 6.29 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_find_best_cell.py" [FAIL] 6.4s 1343s Time: 6.42 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_amplitude_normalisation.py" [FAIL] 6.6s 1343s Time: 6.60 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_statistics_graphs.py" [FAIL] 6.6s 1343s Time: 6.61 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_web_change_basis.py" [FAIL] 6.3s 1343s Time: 6.28 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/sgtbx/direct_space_asu/proto/tst_asu.py" [FAIL] 6.1s 1343s Time: 6.15 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sgtbx_tidy_pickling.py" [FAIL] 6.5s 1343s Time: 6.51 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/masks/tests/tst_flood_fill.py" [FAIL] 6.6s 1343s Time: 6.59 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_r_free_utils.py" [FAIL] 6.5s 1343s Time: 6.51 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_ccp.py" [FAIL] 6.4s 1343s Time: 6.44 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_mask.py" [FAIL] 6.7s 1343s Time: 6.72 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_map_peak_3d_as_2d.py" [FAIL] 6.7s 1343s Time: 6.67 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_asymmetric_map.py" [FAIL] 6.6s 1343s Time: 6.60 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_peak_volume_estimate.py" [FAIL] 6.6s 1343s Time: 6.62 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_resolution_from_map_and_model.py" [FAIL] 6.7s 1343s Time: 6.67 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_curves.py" [FAIL] 6.7s 1343s Time: 6.68 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_atom_radius_as_central_peak_width.py" [FAIL] 6.6s 1343s Time: 6.59 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/maptbx/tst_get_percentile_cutoffs.py" [FAIL] 6.6s 1343s Time: 6.62 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_sphericity.py" [FAIL] 5.3s 1343s Time: 5.32 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_miller_statistics.py" [FAIL] 6.6s 1343s Time: 6.58 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity.py" [FAIL] 6.3s 1343s Time: 6.25 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_connectivity_allsym.py" [FAIL] 6.7s 1343s Time: 6.68 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_diffuse.py" [FAIL] 9.5s 1343s Time: 9.49 1343s Return code: 1 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cctbx/regression/tst_prepare_map_for_docking.py" [FAIL] 7.2s 1343s Time: 7.16 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/cma_es/tst_cma_es.py" [FAIL] 5.9s 1343s Time: 5.86 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mrc_io.py" [FAIL] 3.5s 1343s Time: 3.45 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/gui_tools/tst.py" [FAIL] 3.7s 1343s Time: 3.71 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phil.py" [FAIL] 5.4s 1343s Time: 5.45 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_data_manager.py" [FAIL] 7.0s 1343s Time: 6.96 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager_wrapping.py" [FAIL] 7.5s 1343s Time: 7.47 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_manager.py" [FAIL] 6.8s 1343s Time: 6.77 1343s Return code: 139 1343s OKs: 0 1343s 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 1343s Time: 4.84 1343s Return code: 139 1343s OKs: 0 1343s 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] 8.2s 1343s Time: 8.22 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_map_tools.py" [FAIL] 6.7s 1343s Time: 6.70 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_atom_selections_10k.py" [FAIL] 6.2s 1343s Time: 6.23 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_crystal_symmetry_from_any.py" [FAIL] 6.6s 1343s Time: 6.62 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/kriber/tst_strudat.py" [FAIL] 6.6s 1343s Time: 6.63 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_geometry.py" [FAIL] 6.6s 1343s Time: 6.61 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_lex_parse_build.py" [FAIL] 6.8s 1343s Time: 6.81 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_model.py" [FAIL] 6.8s 1343s Time: 6.82 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_restraints.py" [FAIL] 6.6s 1343s Time: 6.61 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_lex_parse_build.py" [FAIL] 3.8s 1343s Time: 3.81 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_hklf.py" [FAIL] 3.5s 1343s Time: 3.52 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cif/tests/tst_validation.py" [FAIL] 13.0s 1343s Time: 12.99 1343s Return code: 1 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_writer.py" [FAIL] 3.7s 1343s Time: 3.66 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/shelx/tst_fvar_encoding.py" [FAIL] 5.3s 1343s Time: 5.26 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_pdb.py" [FAIL] 6.8s 1343s Time: 6.81 1343s Return code: 134 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_mmcif_hierarchy.py" [FAIL] 7.5s 1343s Time: 7.51 1343s Return code: 134 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_hierarchy.py" [FAIL] 4.2s 1343s Time: 4.15 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_ext.py" [FAIL] 6.8s 1343s Time: 6.81 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection.py" [FAIL] 6.9s 1343s Time: 6.93 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/secondary_structure/tst_annotation.py" [FAIL] 5.9s 1343s Time: 5.86 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_atom_selection_string.py" [FAIL] 6.6s 1343s Time: 6.63 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_utils.py" [FAIL] 6.0s 1343s Time: 6.02 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/examples/pdb_truncate_to_ala/tst.py" [FAIL] 4.3s 1343s Time: 4.27 1343s Return code: 134 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_examples.py" [FAIL] 7.3s 1343s Time: 7.29 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/space_group_symbols.py" [FAIL] 7.1s 1343s Time: 7.11 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/cns/tst_cns.py" [FAIL] 6.2s 1343s Time: 6.21 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_merge.py" P31 [FAIL] 6.5s 1343s Time: 6.45 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/no_merge_original_index.py" [FAIL] 6.4s 1343s Time: 6.39 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/ccp4_map/tst.py" [FAIL] 6.4s 1343s Time: 6.37 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_ext.py" [FAIL] 6.9s 1343s Time: 6.89 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_extract_from_symmetry_lib.py" [FAIL] 7.2s 1343s Time: 7.24 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst_dano.py" [FAIL] 6.9s 1343s Time: 6.92 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/mtz/tst.py" P31 [FAIL] 6.2s 1343s Time: 6.16 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_utils.py" [FAIL] 6.6s 1343s Time: 6.62 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xplor/tst_xplormap.py" [FAIL] 6.6s 1343s Time: 6.59 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_phases.py" P31 [FAIL] 6.6s 1343s Time: 6.63 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_lattice_symmetry.py" [FAIL] 9.4s 1343s Time: 9.36 1343s Return code: 1 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_statistics.py" Fdd2 P31m [FAIL] 7.1s 1343s Time: 7.08 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_file_reader.py" [FAIL] 4.2s 1343s Time: 4.25 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_box_around_molecule.py" [FAIL] 10.1s 1343s Time: 10.08 1343s Return code: 1 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_mmcif_segids.py" [FAIL] 7.7s 1343s Time: 7.70 1343s Return code: 134 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_forward_compatible_pdb.py" [FAIL] 4.1s 1343s Time: 4.09 1343s Return code: 134 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_symmetry.py" [FAIL] 5.5s 1343s Time: 5.49 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_reflection_file_editor.py" [FAIL] 6.3s 1343s Time: 6.33 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_models.py" [FAIL] 9.2s 1343s Time: 9.24 1343s Return code: 1 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_simple_map_coefficients.py" [FAIL] 5.8s 1343s Time: 5.76 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_sort_atoms.py" [FAIL] 7.3s 1343s Time: 7.34 1343s Return code: 1 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/xds/tests/tst_integrate_hkl.py" [FAIL] 7.6s 1343s Time: 7.60 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/scalepack/tst_no_merge_original_index.py" [FAIL] 4.1s 1343s Time: 4.07 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_export_scalepack_unmerged.py" [FAIL] 7.0s 1343s Time: 7.04 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/dsn6/tst.py" P31 [FAIL] 6.9s 1343s Time: 6.88 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_ligs.py" [FAIL] 5.9s 1343s Time: 5.90 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_broken_chain.py" [FAIL] 7.1s 1343s Time: 7.11 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_search_shortcut_1.py" [FAIL] 7.0s 1343s Time: 6.98 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_groups_preprocessing.py" [FAIL] 7.6s 1343s Time: 7.62 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_input.py" [FAIL] 7.6s 1343s Time: 7.60 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_user_selections.py" [FAIL] 7.0s 1343s Time: 7.01 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs.py" [FAIL] 7.8s 1343s Time: 7.79 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_without_validation.py" [FAIL] 7.7s 1343s Time: 7.66 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/pdb/tst_read_mtrix_records_from_cif.py" [FAIL] 7.5s 1343s Time: 7.47 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_show_systematic_absences.py" [FAIL] 7.6s 1343s Time: 7.60 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_miller_sort_asu.py" [FAIL] 6.9s 1343s Time: 6.95 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_xray_scale.py" [FAIL] 7.1s 1343s Time: 7.10 1343s Return code: 134 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_as_pdb_1atom.py" [FAIL] 7.4s 1343s Time: 7.36 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cif_1.py" [FAIL] 8.2s 1343s Time: 8.17 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_split_data_cif.py" [FAIL] 10.7s 1343s Time: 10.66 1343s Return code: 1 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_all_chain_ids.py" [FAIL] 8.3s 1343s Time: 8.31 1343s Return code: 134 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_extract_xtal_data.py" [FAIL] 5.3s 1343s Time: 5.28 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_cli_parser.py" [FAIL] 7.7s 1343s Time: 7.71 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/regression/tst_hierarchy_occupancies_rounding.py" [FAIL] 6.9s 1343s Time: 6.93 1343s Return code: 134 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/iotbx/detectors/tst_debug_write.py" [FAIL] 3.2s 1343s Time: 3.19 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_smoothing.py" [FAIL] 3.4s 1343s Time: 3.40 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_genetic_algorithm_with_mp.py" [FAIL] 3.3s 1343s Time: 3.29 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/tst_basic.py" [FAIL] 5.7s 1343s Time: 5.73 1343s Return code: 139 1343s OKs: 1 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_minimum_covering_ellipsoid.py" [FAIL] 5.8s 1343s Time: 5.78 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian_fit_1d_analytical.py" [FAIL] 6.4s 1343s Time: 6.38 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_cubic_equation.py" [FAIL] 6.2s 1343s Time: 6.21 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_cholesky.py" [FAIL] 5.6s 1343s Time: 5.56 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_svd.py" [FAIL] 6.0s 1343s Time: 6.04 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_eigensystem.py" [FAIL] 6.0s 1343s Time: 5.98 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_svd.py" [FAIL] 6.0s 1343s Time: 5.98 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/linalg/tests/tst_lapack_dsyev.py" [FAIL] 6.1s 1343s Time: 6.06 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/regression_test.py" [FAIL] 5.8s 1343s Time: 5.83 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_flex.py" [FAIL] 6.4s 1343s Time: 6.36 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_numpy_bridge.py" [FAIL] 6.3s 1343s Time: 6.25 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_smart_selection.py" [FAIL] 6.0s 1343s Time: 6.04 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/array_family/boost_python/tst_shared.py" [FAIL] 6.1s 1343s Time: 6.11 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/matrix/__init__.py" [FAIL] 3.4s 1343s Time: 3.40 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/python_utils/tst_random_transform.py" [FAIL] 3.3s 1343s Time: 3.30 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/superpose.py" [FAIL] 3.1s 1343s Time: 3.14 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/spe.py" [FAIL] 3.0s 1343s Time: 3.02 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/incremental_SO3_sampling.py" [FAIL] 4.3s 1343s Time: 4.33 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_curve_fitting.py" [FAIL] 6.4s 1343s Time: 6.39 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_weighted_correlation.py" [FAIL] 6.1s 1343s Time: 6.06 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_exp_functions.py" [FAIL] 6.1s 1343s Time: 6.11 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_math.py" [FAIL] 5.7s 1343s Time: 5.70 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_resample.py" [FAIL] 3.5s 1343s Time: 3.49 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_gaussian.py" [FAIL] 5.8s 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Time: 5.84 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_quadrature.py" [FAIL] 6.2s 1343s Time: 6.17 1343s Return code: 139 1343s OKs: 0 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Traceback (most recent call last): 1343s File "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py", line 37, in 1343s run() 1343s ~~~^^ 1343s File "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py", line 27, in run 1343s run_buf.raise_if_errors() 1343s ~~~~~~~~~~~~~~~~~~~~~~~^^ 1343s File "/usr/lib/python3/dist-packages/libtbx/easy_run.py", line 46, in raise_if_errors 1343s raise Error(msg) 1343s RuntimeError: child process stderr output: 1343s 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' 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s Standard error: 1343s Segmentation fault (core dumped) 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_halton.py" [FAIL] 6.0s 1343s Time: 6.01 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/scale_curves.py" [FAIL] 3.2s 1343s Time: 3.20 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_fit_peak.py" [FAIL] 3.3s 1343s Time: 3.28 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tst_zernike.py" [FAIL] 12.6s 1343s Time: 12.62 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_clustering.py" [FAIL] 7.2s 1343s Time: 7.15 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_periodogram.py" [FAIL] 5.5s 1343s Time: 5.52 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/math/tests/tst_error_propagation_matrix_inverse.py" [FAIL] 6.4s 1343s Time: 6.39 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgs/tst_curvatures.py" [FAIL] 5.5s 1343s Time: 5.46 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lbfgsb/boost_python/tst_lbfgsb.py" [FAIL] 3.3s 1343s Time: 3.30 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/fftpack/boost_python/tst_fftpack.py" [FAIL] 3.3s 1343s Time: 3.32 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/flex_grid.py" [FAIL] 3.1s 1343s Time: 3.08 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/lbfgs_linear_least_squares_fit.py" [FAIL] 5.0s 1343s Time: 4.98 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/chebyshev_lsq_example.py" [FAIL] 6.0s 1343s Time: 6.01 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/immoptibox_ports.py" [FAIL] 6.3s 1343s Time: 6.28 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/integrating_a_weighted_sinc_function.py" [FAIL] 6.0s 1343s Time: 5.99 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/examples/minimizer_comparisons.py" [FAIL] 5.9s 1343s Time: 5.92 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_basic.py" [FAIL] 3.5s 1343s Time: 3.50 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/graph/tst_tardy_tree.py" [FAIL] 6.8s 1343s Time: 6.82 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_tardy.py" [FAIL] 6.3s 1343s Time: 6.28 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/essence/tst_energy_plots.py" [FAIL] 6.2s 1343s Time: 6.22 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/tst.py" [FAIL] 6.1s 1343s Time: 6.05 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_featherstone.py" [FAIL] 5.9s 1343s Time: 5.89 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion.py" [FAIL] 6.1s 1343s Time: 6.11 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_free_motion_hard.py" [FAIL] 6.1s 1343s Time: 6.12 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_joint_lib.py" [FAIL] 6.0s 1343s Time: 5.96 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_singular.py" [FAIL] 6.0s 1343s Time: 6.00 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/rigid_body/proto/tst_molecules.py" [FAIL] 5.7s 1343s Time: 5.73 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_sparse.py" [FAIL] 6.0s 1343s Time: 6.04 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/sparse/tests/tst_lu_factorization.py" [FAIL] 6.0s 1343s Time: 6.02 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/iso_surface/tst_iso_surface.py" [FAIL] 6.0s 1343s Time: 5.99 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/simplex.py" [FAIL] 6.0s 1343s Time: 5.96 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/differential_evolution.py" [FAIL] 5.9s 1343s Time: 5.94 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/tests/direct_search_simulated_annealing.py" [FAIL] 5.9s 1343s Time: 5.90 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/random/tests/tst_random.py" [FAIL] 6.5s 1343s Time: 6.54 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/lstbx/tests/tst_normal_equations.py" [FAIL] 6.5s 1343s Time: 6.55 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_basic.py" [FAIL] 5.1s 1343s Time: 5.12 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_booth.py" [FAIL] 6.0s 1343s Time: 5.99 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/scitbx/dtmin/regression/tst_dtmin_twisted.py" [FAIL] 6.0s 1343s Time: 6.03 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/absolute_structure/tests/tst_absolute_structure.py" --fix_random_seeds [FAIL] 6.5s 1343s Time: 6.52 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/ab_initio/tests/tst_ab_initio_ext.py" [FAIL] 6.9s 1343s Time: 6.87 1343s Return code: 139 1343s OKs: 0 1343s 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] 6.7s 1343s Time: 6.73 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/masks/tests/tst_masks.py" [FAIL] 6.9s 1343s Time: 6.93 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/structure_factors/direct/tests/tst_standard_xray.py" [FAIL] 7.1s 1343s Time: 7.12 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/tests/tst_weighting_schemes.py" --fix_random_seeds [FAIL] 7.0s 1343s Time: 7.02 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_lbfgs.py" [FAIL] 7.0s 1343s Time: 6.96 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_occupancies.py" [FAIL] 7.1s 1343s Time: 7.12 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_same_group.py" [FAIL] 7.1s 1343s Time: 7.07 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_reparametrisation.py" [FAIL] 7.0s 1343s Time: 7.02 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=naive [FAIL] 7.0s 1343s Time: 7.04 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_disorder.py" [FAIL] 7.1s 1343s Time: 7.06 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_constrained_structure.py" --normal_eqns_solving_method=levenberg-marquardt [FAIL] 3.7s 1343s Time: 3.65 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_rigid.py" [FAIL] 3.9s 1343s Time: 3.89 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/constraints/tests/tst_direction.py" [FAIL] 7.1s 1343s Time: 7.15 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_adp_restraints.py" [FAIL] 6.7s 1343s Time: 6.66 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_manager.py" [FAIL] 6.7s 1343s Time: 6.65 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/refinement/restraints/tests/tst_restraints.py" --verbose --scatterers=5 --resolution=0.2 [FAIL] 6.6s 1343s Time: 6.57 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_refine.py" [FAIL] 6.9s 1343s Time: 6.92 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/regression/tst_commandline_anomrefine.py" [FAIL] 9.7s 1343s Time: 9.67 1343s Return code: 1 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/smtbx/tests/tst_utils.py" [FAIL] 7.1s 1343s Time: 7.14 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/rstbx/dps_core/tst_iotbx_converter.py" [FAIL] 6.9s 1343s Time: 6.87 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/rstbx/diffraction/fastbragg/tst_bragg_minimal.py" [FAIL] 6.2s 1343s Time: 6.18 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python "/usr/lib/python3/dist-packages/rstbx/sublattice_support/tst_sublattice.py" [FAIL] 6.8s 1343s Time: 6.84 1343s Return code: 139 1343s OKs: 0 1343s libtbx.python -c "from rstbx.run_tests import run; run()" [FAIL] 5.0s 1343s Time: 4.98 1343s Return code: 139 1343s OKs: 0 1343s 1343s Please verify these tests manually. 1343s 1343s Summary: 1343s Tests run : 546 1343s Failures : 284 1343s Warnings (possible failures) : 0 1343s Known Failures ( 4) : 4 1343s Known Unstable ( 3) : 2 1343s Stderr output (discouraged) : 291 1343s 1343s See run_tests_parallel_zlog for full output. 1343s 1343s 1343s ******************************************************************************** 1343s ERROR: 284 TEST FAILURES. PLEASE FIX BEFORE COMMITTING CODE. 1343s ******************************************************************************** 1343s 1344s autopkgtest [13:28:26]: test cctbx: -----------------------] 1344s autopkgtest [13:28:26]: test cctbx: - - - - - - - - - - results - - - - - - - - - - 1344s cctbx FAIL non-zero exit status 1 1344s autopkgtest [13:28:26]: test dxtbx: preparing testbed 1414s autopkgtest [13:29:36]: testbed dpkg architecture: amd64 1414s autopkgtest [13:29:36]: testbed apt version: 2.9.31ubuntu1 1414s autopkgtest [13:29:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup 1414s autopkgtest [13:29:36]: testbed release detected to be: plucky 1414s autopkgtest [13:29:36]: updating testbed package index (apt update) 1414s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 1414s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 1414s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 1414s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 1414s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [1232 B] 1414s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [11.5 kB] 1414s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [288 kB] 1414s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [29.9 kB] 1414s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [36.9 kB] 1414s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [43.5 kB] 1414s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1320 B] 1414s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [1256 B] 1414s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 1414s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [102 kB] 1414s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [196 kB] 1414s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [12.4 kB] 1414s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [3536 B] 1414s Get:18 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [7592 B] 1414s Get:19 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [424 B] 1416s Fetched 862 kB in 0s (4960 kB/s) 1417s Reading package lists... 1417s autopkgtest [13:29:39]: upgrading testbed (apt dist-upgrade and autopurge) 1417s Reading package lists... 1418s Building dependency tree... 1418s Reading state information... 1418s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 1418s Starting 2 pkgProblemResolver with broken count: 0 1418s Done 1419s Entering ResolveByKeep 1419s 1419s Calculating upgrade... 1419s The following packages were automatically installed and are no longer required: 1419s libnl-genl-3-200 python3.12-gdbm 1419s Use 'sudo apt autoremove' to remove them. 1419s The following NEW packages will be installed: 1419s linux-headers-6.14.0-11 linux-headers-6.14.0-11-generic 1419s linux-image-6.14.0-11-generic linux-modules-6.14.0-11-generic 1419s linux-modules-extra-6.14.0-11-generic pnp.ids 1419s The following packages will be upgraded: 1419s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 1419s cloud-init cloud-init-base cron cron-daemon-common curl dbus dbus-bin 1419s dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session 1419s dhcpcd-base diffutils dosfstools dpkg dpkg-dev fwupd gcc-14-base gcc-15-base 1419s gir1.2-girepository-2.0 gir1.2-glib-2.0 grub-common grub-efi-amd64-bin 1419s grub-efi-amd64-signed grub-efi-amd64-unsigned grub-pc grub-pc-bin 1419s grub2-common htop hwdata ibverbs-providers libapparmor1 libapt-pkg7.0 1419s libatomic1 libaudit-common libaudit1 libbinutils libbrotli1 libc-bin 1419s libc-dev-bin libc6 libc6-dev libcap-ng0 libctf-nobfd0 libctf0 1419s libcurl3t64-gnutls libcurl4t64 libdbus-1-3 libdpkg-perl libdw1t64 libelf1t64 1419s libestr0 libfwupd3 libgcc-s1 libgirepository-1.0-1 libglib2.0-0t64 1419s libglib2.0-data libgnutls30t64 libgprofng0 libibverbs1 libjemalloc2 1419s libjson-glib-1.0-0 libjson-glib-1.0-common libldap-common libldap2 liblz4-1 1419s liblzma5 libmm-glib0 libncurses6 libncursesw6 libnl-3-200 libnl-genl-3-200 1419s libnl-route-3-200 libnss-systemd libpam-systemd libpci3 libpng16-16t64 1419s libpython3-stdlib libpython3.13 libpython3.13-minimal libpython3.13-stdlib 1419s libselinux1 libsframe1 libsqlite3-0 libssl3t64 libstdc++6 libsystemd-shared 1419s libsystemd0 libtinfo6 libudev1 libxml2 libxmlb2 linux-firmware linux-generic 1419s linux-headers-generic linux-headers-virtual linux-image-generic 1419s linux-image-virtual linux-libc-dev linux-tools-common linux-virtual locales 1419s media-types ncurses-base ncurses-bin ncurses-term openssl 1419s openssl-provider-legacy pci.ids pciutils pinentry-curses python-apt-common 1419s python3 python3-apt python3-cffi-backend python3-dbus python3-gdbm 1419s python3-gi python3-jaraco.context python3-jinja2 python3-lazr.uri 1419s python3-markupsafe python3-minimal python3-passlib python3-systemd 1419s python3-urllib3 python3-yaml python3.13 python3.13-gdbm python3.13-minimal 1419s rsync rsyslog strace systemd systemd-cryptsetup systemd-resolved 1419s systemd-sysv systemd-timesyncd ubuntu-pro-client ubuntu-pro-client-l10n udev 1419s xz-utils 1419s 148 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 1419s Need to get 841 MB of archives. 1419s After this operation, 300 MB of additional disk space will be used. 1419s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 diffutils amd64 1:3.10-3 [192 kB] 1419s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 1419s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 1419s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-11.11 [1724 kB] 1419s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250315-1ubuntu1 [10.4 kB] 1419s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250315-1ubuntu1 [53.5 kB] 1419s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250315-1ubuntu1 [77.7 kB] 1419s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250315-1ubuntu1 [804 kB] 1419s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 1419s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 1419s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 1419s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 openssl-provider-legacy amd64 3.4.1-1ubuntu2 [39.0 kB] 1419s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libssl3t64 amd64 3.4.1-1ubuntu2 [2334 kB] 1419s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.4-1ubuntu1 [596 kB] 1419s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.4-1ubuntu1 [199 kB] 1419s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.4-1ubuntu1 [11.9 kB] 1419s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.4-1ubuntu1 [345 kB] 1419s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.4-1ubuntu1 [302 kB] 1419s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.4-1ubuntu1 [2372 kB] 1420s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.4-1ubuntu1 [3052 kB] 1420s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.4-1ubuntu1 [42.1 kB] 1420s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.4-1ubuntu1 [124 kB] 1420s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.4-1ubuntu1 [1404 kB] 1420s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.4-1ubuntu1 [216 kB] 1420s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 dbus-session-bus-common all 1.16.2-2ubuntu1 [54.2 kB] 1420s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 dbus-user-session amd64 1.16.2-2ubuntu1 [9692 B] 1420s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu11 [55.2 kB] 1420s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 1420s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 1420s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 1420s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 1420s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 dbus-system-bus-common all 1.16.2-2ubuntu1 [55.7 kB] 1420s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 dbus-bin amd64 1.16.2-2ubuntu1 [46.5 kB] 1420s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 dbus amd64 1.16.2-2ubuntu1 [24.8 kB] 1420s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 dbus-daemon amd64 1.16.2-2ubuntu1 [123 kB] 1420s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libdbus-1-3 amd64 1.16.2-2ubuntu1 [195 kB] 1420s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.34 [1143 kB] 1420s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 dpkg amd64 1.22.18ubuntu2 [1359 kB] 1420s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 1420s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 1420s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 1420s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 1420s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.34 [1440 kB] 1420s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.34 [222 kB] 1420s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 1420s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 1420s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 1420s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 1420s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 1420s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 1420s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 1420s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 1420s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 1420s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 1420s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 1420s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 1420s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 1420s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 cron amd64 3.0pl1-194ubuntu1 [93.9 kB] 1420s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 1420s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-base amd64 14.2.0-19ubuntu1 [53.9 kB] 1420s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 dhcpcd-base amd64 1:10.1.0-8 [250 kB] 1420s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.84.0-1 [25.3 kB] 1420s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 1420s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 1420s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.84.0-1 [89.5 kB] 1420s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libdw1t64 amd64 0.192-4ubuntu1 [277 kB] 1420s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libelf1t64 amd64 0.192-4ubuntu1 [58.6 kB] 1420s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 1420s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 1420s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libgnutls30t64 amd64 3.8.9-2ubuntu3 [1093 kB] 1420s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 1420s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 1420s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 openssl amd64 3.4.1-1ubuntu2 [1189 kB] 1420s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 1420s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 1420s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 1420s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 1420s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 1420s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 1420s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 1420s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-pro-client-l10n amd64 35 [19.7 kB] 1420s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-pro-client amd64 35 [257 kB] 1420s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu11 [702 kB] 1420s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 cron-daemon-common all 3.0pl1-194ubuntu1 [14.6 kB] 1420s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 1420s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-2 [12.2 kB] 1420s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-2 [192 kB] 1420s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-2 [64.9 kB] 1420s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libibverbs1 amd64 56.0-3ubuntu1 [68.6 kB] 1420s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 ibverbs-providers amd64 56.0-3ubuntu1 [388 kB] 1420s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 1420s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 1420s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 1420s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 libpng16-16t64 amd64 1.6.47-1.1 [217 kB] 1420s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 1420s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gdbm amd64 3.13.2-1 [8708 B] 1420s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 1420s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 1420s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 1420s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 1420s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 1420s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 1420s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 1420s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 1420s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 1420s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 1420s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 1420s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 1420s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 1420s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 1420s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 libldap-common all 2.6.9+dfsg-2ubuntu1 [35.5 kB] 1420s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 libldap2 amd64 2.6.9+dfsg-2ubuntu1 [212 kB] 1420s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 1420s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 1420s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 dpkg-dev all 1.22.18ubuntu2 [1089 kB] 1420s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libdpkg-perl all 1.22.18ubuntu2 [281 kB] 1420s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 1420s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 libjson-glib-1.0-common all 1.10.6+ds-2 [5698 B] 1420s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 libjson-glib-1.0-0 amd64 1.10.6+ds-2 [73.4 kB] 1420s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-7 [5408 kB] 1420s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-7 [137 kB] 1420s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 1420s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 libxmlb2 amd64 0.3.22-1 [74.8 kB] 1420s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc amd64 2.12-5ubuntu9 [137 kB] 1420s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 grub2-common amd64 2.12-5ubuntu9 [674 kB] 1420s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc-bin amd64 2.12-5ubuntu9 [1131 kB] 1420s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-common amd64 2.12-5ubuntu9 [2115 kB] 1420s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-efi-amd64-unsigned amd64 2.12-5ubuntu9 [1393 kB] 1420s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-efi-amd64-signed amd64 1.211+2.12-5ubuntu9 [1395 kB] 1420s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-efi-amd64-bin amd64 2.12-5ubuntu9 [783 kB] 1420s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 1420s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 1420s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 1420s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 1420s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250317.git1d4c88ee-0ubuntu1 [573 MB] 1424s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-11-generic amd64 6.14.0-11.11 [41.2 MB] 1424s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-11-generic amd64 6.14.0-11.11 [15.3 MB] 1424s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-11-generic amd64 6.14.0-11.11 [120 MB] 1425s Get:139 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-11.11 [1730 B] 1425s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-11.11 [11.2 kB] 1425s Get:141 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-11.11 [1724 B] 1425s Get:142 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-11.11 [11.1 kB] 1425s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-11.11 [1646 B] 1425s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-11 all 6.14.0-11.11 [14.2 MB] 1425s Get:145 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-11-generic amd64 6.14.0-11.11 [3915 kB] 1425s Get:146 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-11.11 [11.0 kB] 1425s Get:147 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-11.11 [296 kB] 1425s Get:148 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 1425s Get:149 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jaraco.context all 6.0.1-1 [8272 B] 1425s Get:150 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 1425s Get:151 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 1425s Get:152 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-urllib3 all 2.3.0-2 [94.1 kB] 1425s Get:153 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-passlib all 1.7.4-6ubuntu1 [375 kB] 1425s Get:154 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 1425s Preconfiguring packages ... 1426s Fetched 841 MB in 6s (147 MB/s) 1426s (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 ... 109138 files and directories currently installed.) 1426s Preparing to unpack .../diffutils_1%3a3.10-3_amd64.deb ... 1426s Unpacking diffutils (1:3.10-3) over (1:3.10-2) ... 1426s Setting up diffutils (1:3.10-3) ... 1426s (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 ... 109138 files and directories currently installed.) 1426s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 1426s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 1426s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 1426s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 1426s Preparing to unpack .../linux-libc-dev_6.14.0-11.11_amd64.deb ... 1426s Unpacking linux-libc-dev:amd64 (6.14.0-11.11) over (6.12.0-16.16) ... 1426s Preparing to unpack .../libatomic1_15-20250315-1ubuntu1_amd64.deb ... 1426s Unpacking libatomic1:amd64 (15-20250315-1ubuntu1) over (15-20250222-0ubuntu1) ... 1427s Preparing to unpack .../gcc-15-base_15-20250315-1ubuntu1_amd64.deb ... 1427s Unpacking gcc-15-base:amd64 (15-20250315-1ubuntu1) over (15-20250222-0ubuntu1) ... 1427s Setting up gcc-15-base:amd64 (15-20250315-1ubuntu1) ... 1427s (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 ... 109143 files and directories currently installed.) 1427s Preparing to unpack .../libgcc-s1_15-20250315-1ubuntu1_amd64.deb ... 1427s Unpacking libgcc-s1:amd64 (15-20250315-1ubuntu1) over (15-20250222-0ubuntu1) ... 1427s Setting up libgcc-s1:amd64 (15-20250315-1ubuntu1) ... 1427s (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 ... 109143 files and directories currently installed.) 1427s Preparing to unpack .../libstdc++6_15-20250315-1ubuntu1_amd64.deb ... 1427s Unpacking libstdc++6:amd64 (15-20250315-1ubuntu1) over (15-20250222-0ubuntu1) ... 1427s Setting up libstdc++6:amd64 (15-20250315-1ubuntu1) ... 1427s (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 ... 109143 files and directories currently installed.) 1427s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 1427s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 1427s Setting up libc6:amd64 (2.41-1ubuntu2) ... 1427s (Reading database ... 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1452s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 1452s Setting up apparmor (4.1.0~beta5-0ubuntu11) ... 1452s Installing new version of config file /etc/apparmor.d/openvpn ... 1453s Removing obsolete conffile /etc/apparmor.d/unshare-userns-restrict ... 1453s Reloading AppArmor profiles 1455s Setting up libglib2.0-data (2.84.0-1) ... 1455s Setting up systemd-cryptsetup (257.4-1ubuntu1) ... 1455s Setting up libncurses6:amd64 (6.5+20250216-2) ... 1455s Setting up strace (6.13+ds-1ubuntu1) ... 1455s Setting up libdbus-1-3:amd64 (1.16.2-2ubuntu1) ... 1455s Setting up xz-utils (5.6.4-1) ... 1455s Setting up libpng16-16t64:amd64 (1.6.47-1.1) ... 1455s Setting up systemd-timesyncd (257.4-1ubuntu1) ... 1455s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 1455s Setting up libatomic1:amd64 (15-20250315-1ubuntu1) ... 1455s Setting up udev (257.4-1ubuntu1) ... 1456s Setting up dhcpcd-base (1:10.1.0-8) ... 1456s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 1456s Setting up libdpkg-perl (1.22.18ubuntu2) ... 1456s Setting up linux-headers-6.14.0-11-generic (6.14.0-11.11) ... 1456s Setting up libpci3:amd64 (1:3.13.0-2) ... 1456s Setting up python-apt-common (2.9.9build1) ... 1456s Setting up pnp.ids (0.393-3) ... 1456s Setting up dbus-session-bus-common (1.16.2-2ubuntu1) ... 1456s Setting up libnl-3-200:amd64 (3.7.0-2) ... 1456s Setting up python3.13-minimal (3.13.2-2) ... 1457s Setting up libjson-glib-1.0-common (1.10.6+ds-2) ... 1457s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 1457s Setting up dbus-system-bus-common (1.16.2-2ubuntu1) ... 1457s Setting up libc-dev-bin (2.41-1ubuntu2) ... 1457s Setting up openssl (3.4.1-1ubuntu2) ... 1457s Installing new version of config file /etc/ssl/openssl.cnf ... 1457s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 1457s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 1457s Setting up libldap2:amd64 (2.6.9+dfsg-2ubuntu1) ... 1457s Setting up dbus-bin (1.16.2-2ubuntu1) ... 1457s Setting up linux-modules-6.14.0-11-generic (6.14.0-11.11) ... 1459s Setting up rsync (3.4.1+ds1-3) ... 1459s rsync.service is a disabled or a static unit not running, not starting it. 1459s Setting up python3.13-gdbm (3.13.2-2) ... 1459s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 1459s Setting up ncurses-term (6.5+20250216-2) ... 1459s Setting up cron-daemon-common (3.0pl1-194ubuntu1) ... 1459s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 1459s Setting up libpython3.13:amd64 (3.13.2-2) ... 1459s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 1459s Setting up systemd-sysv (257.4-1ubuntu1) ... 1459s Setting up linux-modules-extra-6.14.0-11-generic (6.14.0-11.11) ... 1461s Setting up linux-image-6.14.0-11-generic (6.14.0-11.11) ... 1463s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 1463s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 1463s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-11-generic 1463s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-11-generic 1464s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 1464s Setting up python3.13 (3.13.2-2) ... 1464s Setting up htop (3.4.0-2) ... 1464s Setting up cron (3.0pl1-194ubuntu1) ... 1465s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 1465s Setting up libnss-systemd:amd64 (257.4-1ubuntu1) ... 1465s Setting up python3 (3.13.2-2) ... 1465s Setting up linux-headers-generic (6.14.0-11.11) ... 1465s Setting up dbus-daemon (1.16.2-2ubuntu1) ... 1465s Setting up python3-markupsafe (2.1.5-1build4) ... 1465s Setting up libnl-route-3-200:amd64 (3.7.0-2) ... 1465s Setting up hwdata (0.393-3) ... 1465s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 1466s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 1466s No schema files found: doing nothing. 1466s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 1466s Setting up dbus (1.16.2-2ubuntu1) ... 1466s A reboot is required to replace the running dbus-daemon. 1466s Please reboot the system when convenient. 1466s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 1466s Setting up pciutils (1:3.13.0-2) ... 1466s Setting up python3-urllib3 (2.3.0-2) ... 1466s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 1466s Setting up libnl-genl-3-200:amd64 (3.7.0-2) ... 1466s Setting up libpam-systemd:amd64 (257.4-1ubuntu1) ... 1466s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 1466s Setting up libgirepository-1.0-1:amd64 (1.84.0-1) ... 1466s Setting up curl (8.12.1-3ubuntu1) ... 1466s Setting up linux-image-virtual (6.14.0-11.11) ... 1466s Setting up linux-tools-common (6.14.0-11.11) ... 1466s Setting up python3-systemd (235-1build6) ... 1466s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 1466s Setting up systemd-resolved (257.4-1ubuntu1) ... 1467s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 1467s Setting up linux-image-generic (6.14.0-11.11) ... 1467s Setting up libibverbs1:amd64 (56.0-3ubuntu1) ... 1467s Setting up python3-dbus (1.3.2-5build5) ... 1467s Setting up linux-headers-virtual (6.14.0-11.11) ... 1467s Setting up linux-generic (6.14.0-11.11) ... 1467s Setting up python3-jaraco.context (6.0.1-1) ... 1467s Setting up python3-passlib (1.7.4-6ubuntu1) ... 1467s Setting up ibverbs-providers:amd64 (56.0-3ubuntu1) ... 1467s Setting up python3-gdbm:amd64 (3.13.2-1) ... 1467s Setting up python3-apt (2.9.9build1) ... 1467s Setting up libxmlb2:amd64 (0.3.22-1) ... 1467s Setting up python3-yaml (6.0.2-1build2) ... 1468s Setting up python3-lazr.uri (1.0.6-6) ... 1468s Setting up binutils (2.44-3ubuntu1) ... 1468s Setting up cloud-init-base (25.1-0ubuntu3) ... 1469s Setting up dpkg-dev (1.22.18ubuntu2) ... 1469s Setting up libjson-glib-1.0-0:amd64 (1.10.6+ds-2) ... 1469s Setting up linux-virtual (6.14.0-11.11) ... 1469s Setting up grub-common (2.12-5ubuntu9) ... 1469s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 1470s Setting up dbus-user-session (1.16.2-2ubuntu1) ... 1470s Setting up gir1.2-girepository-2.0:amd64 (1.84.0-1) ... 1470s Setting up python3-gi (3.50.0-4build1) ... 1470s Setting up ubuntu-pro-client (35) ... 1470s Installing new version of config file /etc/apparmor.d/ubuntu_pro_apt_news ... 1470s Installing new version of config file /etc/apt/apt.conf.d/20apt-esm-hook.conf ... 1472s Setting up ubuntu-pro-client-l10n (35) ... 1472s Setting up cloud-init (25.1-0ubuntu3) ... 1472s Setting up grub-efi-amd64-unsigned (2.12-5ubuntu9) ... 1472s Setting up grub2-common (2.12-5ubuntu9) ... 1472s Setting up libfwupd3:amd64 (2.0.6-7) ... 1472s Setting up grub-pc-bin (2.12-5ubuntu9) ... 1472s Setting up grub-pc (2.12-5ubuntu9) ... 1472s Installing for i386-pc platform. 1473s Installation finished. No error reported. 1473s Sourcing file `/etc/default/grub' 1473s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 1473s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 1473s Generating grub configuration file ... 1473s Found linux image: /boot/vmlinuz-6.14.0-11-generic 1473s Found linux image: /boot/vmlinuz-6.12.0-16-generic 1473s Found initrd image: /boot/initrd.img-6.12.0-16-generic 1473s Found linux image: /boot/vmlinuz-6.11.0-8-generic 1473s Found initrd image: /boot/initrd.img-6.11.0-8-generic 1473s Warning: os-prober will not be executed to detect other bootable partitions. 1473s Systems on them will not be added to the GRUB boot configuration. 1473s Check GRUB_DISABLE_OS_PROBER documentation entry. 1473s Adding boot menu entry for UEFI Firmware Settings ... 1473s done 1473s Setting up grub-efi-amd64-bin (2.12-5ubuntu9) ... 1473s Setting up fwupd (2.0.6-7) ... 1474s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 1474s fwupd.service is a disabled or a static unit not running, not starting it. 1474s Setting up grub-efi-amd64-signed (1.211+2.12-5ubuntu9) ... 1474s Installing for x86_64-efi platform. 1474s grub-install: warning: EFI variables cannot be set on this system. 1474s grub-install: warning: You will have to complete the GRUB setup manually. 1474s Installation finished. No error reported. 1474s Processing triggers for man-db (2.13.0-1) ... 1476s Processing triggers for shared-mime-info (2.4-5) ... 1476s Warning: program compiled against libxml 212 using older 209 1476s Processing triggers for install-info (7.1.1-1) ... 1476s Processing triggers for initramfs-tools (0.146ubuntu1) ... 1476s update-initramfs: Generating /boot/initrd.img-6.12.0-16-generic 1476s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 1486s Processing triggers for libc-bin (2.41-1ubuntu2) ... 1486s Processing triggers for linux-image-6.14.0-11-generic (6.14.0-11.11) ... 1486s /etc/kernel/postinst.d/initramfs-tools: 1486s update-initramfs: Generating /boot/initrd.img-6.14.0-11-generic 1486s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 1496s /etc/kernel/postinst.d/zz-update-grub: 1496s Sourcing file `/etc/default/grub' 1496s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 1496s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 1496s Generating grub configuration file ... 1496s Found linux image: /boot/vmlinuz-6.14.0-11-generic 1496s Found initrd image: /boot/initrd.img-6.14.0-11-generic 1496s Found linux image: /boot/vmlinuz-6.12.0-16-generic 1496s Found initrd image: /boot/initrd.img-6.12.0-16-generic 1496s Found linux image: /boot/vmlinuz-6.11.0-8-generic 1496s Found initrd image: /boot/initrd.img-6.11.0-8-generic 1497s Warning: os-prober will not be executed to detect other bootable partitions. 1497s Systems on them will not be added to the GRUB boot configuration. 1497s Check GRUB_DISABLE_OS_PROBER documentation entry. 1497s Adding boot menu entry for UEFI Firmware Settings ... 1497s done 1498s Reading package lists... 1498s Building dependency tree... 1498s Reading state information... 1499s Starting pkgProblemResolver with broken count: 0 1499s Starting 2 pkgProblemResolver with broken count: 0 1499s Done 1499s Solving dependencies... 1499s The following packages will be REMOVED: 1499s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 1499s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 1499s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 1499s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* python3.12-gdbm* 1499s 0 upgraded, 0 newly installed, 12 to remove and 0 not upgraded. 1499s After this operation, 225 MB disk space will be freed. 1499s (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 ... 148584 files and directories currently installed.) 1499s Removing libnl-genl-3-200:amd64 (3.7.0-2) ... 1499s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 1499s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 1499s Removing libpython3.12t64:amd64 (3.12.9-1) ... 1499s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 1500s Removing libnsl2:amd64 (1.3.0-3build3) ... 1500s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 1500s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 1500s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 1502s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 1502s /etc/kernel/postrm.d/initramfs-tools: 1502s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 1502s /etc/kernel/postrm.d/zz-update-grub: 1502s Sourcing file `/etc/default/grub' 1502s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 1502s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 1502s Generating grub configuration file ... 1502s Found linux image: /boot/vmlinuz-6.14.0-11-generic 1502s Found initrd image: /boot/initrd.img-6.14.0-11-generic 1503s Found linux image: /boot/vmlinuz-6.12.0-16-generic 1503s Found initrd image: /boot/initrd.img-6.12.0-16-generic 1503s Warning: os-prober will not be executed to detect other bootable partitions. 1503s Systems on them will not be added to the GRUB boot configuration. 1503s Check GRUB_DISABLE_OS_PROBER documentation entry. 1503s Adding boot menu entry for UEFI Firmware Settings ... 1503s done 1503s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 1503s Removing python3.12-gdbm (3.12.9-1) ... 1503s Processing triggers for libc-bin (2.41-1ubuntu2) ... 1503s (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 ... 115746 files and directories currently installed.) 1503s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 1503s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 1503s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 1503s autopkgtest [13:31:05]: rebooting testbed after setup commands that affected boot 1507s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 1519s Reading package lists... 1520s Building dependency tree... 1520s Reading state information... 1520s Starting pkgProblemResolver with broken count: 0 1520s Starting 2 pkgProblemResolver with broken count: 0 1520s Done 1520s The following NEW packages will be installed: 1520s adwaita-icon-theme at-spi2-common bitshuffle blt dconf-gsettings-backend 1520s dconf-service fontconfig fontconfig-config fonts-dejavu-core 1520s fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lyx 1520s gtk-update-icon-cache hicolor-icon-theme libaec0 libamd-comgr2 libamdhip64-5 1520s libann-cctbx-dev libann-cctbx0 libantlr3c-3.4-0 libasan8 1520s libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 libavahi-client3 1520s libavahi-common-data libavahi-common3 libblas3 libboost-numpy1.83.0 1520s libboost-python-dev libboost-python1.83-dev libboost-python1.83.0 1520s libboost-thread1.83.0 libboost-timer1.83.0 libboost1.83-dev 1520s libcairo-gobject2 libcairo2 libcbf1t64 libccp4-data libccp4-dev libccp4c0t64 1520s libccp4f0t64 libcctbx-dev libcctbx0 libcolord2 libcups2t64 libdatrie1 1520s libdconf1 libdeflate0 libdouble-conversion3 libdrm-intel1 libegl-mesa0 1520s libegl1 libepoxy0 libevent-pthreads-2.1-7t64 libexpat1-dev libfabric1 1520s libfontconfig1 libgbm1 libgcc-14-dev libgdk-pixbuf-2.0-0 1520s libgdk-pixbuf2.0-common libgfortran5 libgl1 libgl1-mesa-dri libglew2.2 1520s libglu1-mesa libglut3.12 libglvnd0 libglx-mesa0 libglx0 libgomp1 1520s libgraphite2-3 libgtk-3-0t64 libgtk-3-common libharfbuzz0b libhdf5-310 1520s libhdf5-hl-310 libhdf5-openmpi-310 libhsa-runtime64-1 libhsakmt1 libhwasan0 1520s libhwloc-plugins libhwloc15 libibmad5 libibumad3 libice6 libimagequant0 1520s libinput-bin libinput10 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 1520s libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 1520s liblbfgsb0 liblcms2-2 liblerc4 libllvm17t64 liblsan0 liblzf1 libmd4c0 1520s libmmdb2-0 libmtdev1t64 libmunge2 libnetcdf22 libnotify4 libopengl0 1520s libopenjp2-7 libopenmpi40 libpango-1.0-0 libpangocairo-1.0-0 1520s libpangoft2-1.0-0 libpciaccess0 libpcre2-16-0 libpcre2-32-0 libpixman-1-0 1520s libpmix2t64 libpsm-infinipath1 libpsm2-2 libpython3-dev libpython3.13-dev 1520s libqhull-r8.0 libqt5core5t64 libqt5dbus5t64 libqt5designer5 libqt5gui5t64 1520s libqt5help5 libqt5network5t64 libqt5opengl5t64 libqt5printsupport5t64 1520s libqt5sql5t64 libqt5test5t64 libqt5widgets5t64 libqt5xml5t64 libquadmath0 1520s libraqm0 librdmacm1t64 libsharpyuv0 libsm6 libssm2 libstdc++-14-dev libsz2 1520s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libtsan2 libubsan1 libucx0 1520s libvulkan1 libwacom-common libwacom9 libwayland-client0 libwayland-cursor0 1520s libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 libwebpmux3 1520s libwxbase3.2-1t64 libwxgtk-gl3.2-1t64 libwxgtk3.2-1t64 libx11-xcb1 1520s libxcb-dri3-0 libxcb-glx0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 1520s libxcb-present0 libxcb-randr0 libxcb-render-util0 libxcb-render0 1520s libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-util1 libxcb-xfixes0 1520s libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxcomposite1 libxcursor1 1520s libxdamage1 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon-x11-0 1520s libxnvctrl0 libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1 libxtst6 1520s libxxf86vm1 mesa-libgallium ocl-icd-libopencl1 pymol-data 1520s python-matplotlib-data python3-all python3-brotli python3-cctbx 1520s python3-contourpy python3-cycler python3-dateutil python3-decorator 1520s python3-dev python3-dials-data python3-flexcache python3-flexparser 1520s python3-fonttools python3-fs python3-h5py python3-h5py-serial 1520s python3-hdf5plugin python3-importlib-resources python3-iniconfig 1520s python3-kiwisolver python3-legacy-cgi python3-lxml python3-lz4 1520s python3-matplotlib python3-mpmath python3-mrcfile python3-natsort 1520s python3-numpy python3-numpy-dev python3-nxmx python3-opengl 1520s python3-ordered-set python3-packaging python3-pil python3-pil.imagetk 1520s python3-pint python3-platformdirs python3-pluggy python3-procrunner 1520s python3-pycbf python3-pymol python3-pyqt5 python3-pyqt5.qtopengl 1520s python3-pyqt5.sip python3-pytest python3-pytest-datadir python3-pytest-mock 1520s python3-pytest-regressions python3-scipy python3-six python3-sympy 1520s python3-tk python3-tqdm python3-ufolib2 python3-wxgtk4.0 python3.13-dev 1520s python3.13-tk sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data x11-common 1520s zlib1g-dev 1520s 0 upgraded, 268 newly installed, 0 to remove and 0 not upgraded. 1520s Need to get 271 MB of archives. 1520s After this operation, 1291 MB of additional disk space will be used. 1520s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-lato all 2.015-1 [2781 kB] 1521s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-5 [148 kB] 1521s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 1521s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250315-1ubuntu1 [925 kB] 1521s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 1521s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:2.2.3+ds-5 [5702 kB] 1521s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [8004 B] 1521s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 1521s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 1521s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 1521s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 1521s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 1521s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 1521s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 1521s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 1521s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [161 kB] 1521s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 gtk-update-icon-cache amd64 4.18.2+ds-1 [53.9 kB] 1521s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 hicolor-icon-theme all 0.18-2 [13.3 kB] 1521s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 adwaita-icon-theme all 48.0-1 [578 kB] 1521s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 at-spi2-common all 2.56.0-2 [9108 B] 1521s Get:21 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 1521s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 1521s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-310 amd64 1.14.5+repack-3 [1519 kB] 1521s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [62.6 kB] 1521s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 1521s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py-serial amd64 3.13.0-1 [1230 kB] 1521s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py all 3.13.0-1 [7978 B] 1521s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250315-1ubuntu1 [150 kB] 1521s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [7966 B] 1521s Get:30 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3build1 [178 kB] 1521s Get:31 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 1521s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 librdmacm1t64 amd64 56.0-3ubuntu1 [71.6 kB] 1521s Get:33 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfabric1 amd64 1.17.0-3.1 [789 kB] 1521s Get:34 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc15 amd64 2.12.0-1 [194 kB] 1521s Get:35 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmunge2 amd64 0.5.16-1 [16.5 kB] 1521s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 1521s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 1521s Get:38 http://ftpmaster.internal/ubuntu plucky/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1build1 [38.5 kB] 1521s Get:39 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc-plugins amd64 2.12.0-1 [16.0 kB] 1521s Get:40 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpmix2t64 amd64 5.0.6-5 [714 kB] 1521s Get:41 http://ftpmaster.internal/ubuntu plucky/universe amd64 libllvm17t64 amd64 1:17.0.6-21 [26.0 MB] 1521s Get:42 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build2 [14.4 MB] 1521s Get:43 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsakmt1 amd64 5.7.0-1build1 [62.9 kB] 1521s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsa-runtime64-1 amd64 5.7.1-2build1 [491 kB] 1521s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamdhip64-5 amd64 5.7.1-5build1 [9702 kB] 1521s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libibumad3 amd64 56.0-3ubuntu1 [31.1 kB] 1521s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libibmad5 amd64 56.0-3ubuntu1 [43.9 kB] 1521s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 libucx0 amd64 1.18.1+ds-2 [1293 kB] 1521s Get:49 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmpi40 amd64 5.0.7-1 [2526 kB] 1521s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-openmpi-310 amd64 1.14.5+repack-3 [1584 kB] 1521s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 bitshuffle amd64 0.5.2-1build2 [154 kB] 1521s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 1521s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 1521s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 1521s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2.1ubuntu1 [37.6 kB] 1521s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2.1ubuntu1 [164 kB] 1521s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 1521s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 1521s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 1521s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 1521s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 1521s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [694 kB] 1521s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-8 [4824 B] 1521s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libdconf1 amd64 0.40.0-5 [39.8 kB] 1521s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 dconf-service amd64 0.40.0-5 [28.4 kB] 1521s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [22.7 kB] 1521s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2.1ubuntu1 [180 kB] 1521s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 1521s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.3-1 [171 kB] 1521s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 libann-cctbx0 amd64 1.1.2+doc-9build1 [32.7 kB] 1521s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 libann-cctbx-dev amd64 1.1.2+doc-9build1 [45.1 kB] 1521s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 libantlr3c-3.4-0 amd64 3.4+dfsg-4build2 [44.9 kB] 1521s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 15-20250315-1ubuntu1 [3075 kB] 1521s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libatk1.0-0t64 amd64 2.56.0-2 [55.4 kB] 1521s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libxi6 amd64 2:1.8.2-1 [32.4 kB] 1521s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libatspi2.0-0t64 amd64 2.56.0-2 [91.1 kB] 1521s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libatk-bridge2.0-0t64 amd64 2.56.0-2 [69.0 kB] 1521s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common-data amd64 0.8-16ubuntu2 [31.0 kB] 1521s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common3 amd64 0.8-16ubuntu2 [23.6 kB] 1521s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-client3 amd64 0.8-16ubuntu2 [27.5 kB] 1521s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-python1.83.0 amd64 1.83.0-4.1ubuntu2 [314 kB] 1521s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 libboost-numpy1.83.0 amd64 1.83.0-4.1ubuntu2 [243 kB] 1521s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 15-20250315-1ubuntu1 [29.3 kB] 1521s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 15-20250315-1ubuntu1 [1362 kB] 1521s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 15-20250315-1ubuntu1 [2760 kB] 1521s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 15-20250315-1ubuntu1 [1211 kB] 1521s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 15-20250315-1ubuntu1 [1687 kB] 1521s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 15-20250315-1ubuntu1 [153 kB] 1521s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-19ubuntu1 [2815 kB] 1521s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-19ubuntu1 [2488 kB] 1521s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost1.83-dev amd64 1.83.0-4.1ubuntu2 [10.7 MB] 1521s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1-dev amd64 2.6.4-1 [148 kB] 1521s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 1521s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-dev amd64 3.13.2-2 [5503 kB] 1521s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-dev amd64 3.13.2-2 [10.7 kB] 1521s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-dev amd64 3.13.2-2 [509 kB] 1521s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 1521s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 1521s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 1521s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dev amd64 3.13.2-2 [26.7 kB] 1521s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 libboost-python1.83-dev amd64 1.83.0-4.1ubuntu2 [338 kB] 1521s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 libboost-python-dev amd64 1.83.0.2ubuntu1 [4516 B] 1521s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-thread1.83.0 amd64 1.83.0-4.1ubuntu2 [278 kB] 1521s Get:104 http://ftpmaster.internal/ubuntu plucky/universe amd64 libboost-timer1.83.0 amd64 1.83.0-4.1ubuntu2 [241 kB] 1521s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 1521s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 1521s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 1521s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.4-1 [662 kB] 1521s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo-gobject2 amd64 1.18.4-1 [127 kB] 1521s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcbf1t64 amd64 0.9.7+dfsg1-5build1 [361 kB] 1521s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccp4-data all 8.0.0-4 [65.2 kB] 1521s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccp4c0t64 amd64 8.0.0-4 [104 kB] 1521s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmmdb2-0 amd64 2.0.22-1 [363 kB] 1521s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccp4f0t64 amd64 8.0.0-4 [228 kB] 1521s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccp4-dev amd64 8.0.0-4 [42.4 kB] 1521s Get:116 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libcctbx0 amd64 2024.10+ds2+~3.22.1+ds1-4build2 [2077 kB] 1522s Get:117 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libcctbx-dev amd64 2024.10+ds2+~3.22.1+ds1-4build2 [1192 kB] 1522s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 1522s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 libcolord2 amd64 1.4.7-3 [155 kB] 1522s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 libcups2t64 amd64 2.4.11-0ubuntu2 [292 kB] 1522s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 1522s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 libdouble-conversion3 amd64 3.3.1-1 [41.7 kB] 1522s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 libdrm-intel1 amd64 2.4.123-1 [68.8 kB] 1522s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-server0 amd64 1.23.1-3 [37.2 kB] 1522s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [7944 B] 1522s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-dri3-0 amd64 1.17.0-2 [7508 B] 1522s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-present0 amd64 1.17.0-2 [6064 B] 1522s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-randr0 amd64 1.17.0-2 [17.9 kB] 1522s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-sync1 amd64 1.17.0-2 [9312 B] 1522s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xfixes0 amd64 1.17.0-2 [10.2 kB] 1522s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 libxshmfence1 amd64 1.3-1build5 [4764 B] 1522s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 mesa-libgallium amd64 25.0.1-2ubuntu2 [12.1 MB] 1522s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 libgbm1 amd64 25.0.1-2ubuntu2 [33.3 kB] 1522s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-client0 amd64 1.23.1-3 [29.7 kB] 1522s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 libegl-mesa0 amd64 25.0.1-2ubuntu2 [136 kB] 1522s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 libepoxy0 amd64 1.5.10-2 [218 kB] 1522s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 libvulkan1 amd64 1.4.304.0-1 [147 kB] 1522s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 libgl1-mesa-dri amd64 25.0.1-2ubuntu2 [35.7 kB] 1522s Get:139 http://ftpmaster.internal/ubuntu plucky/main amd64 libglvnd0 amd64 1.7.0-1build1 [69.6 kB] 1522s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-glx0 amd64 1.17.0-2 [24.8 kB] 1522s Get:141 http://ftpmaster.internal/ubuntu plucky/main amd64 libxxf86vm1 amd64 1:1.1.4-1build4 [9282 B] 1522s Get:142 http://ftpmaster.internal/ubuntu plucky/main amd64 libglx-mesa0 amd64 25.0.1-2ubuntu2 [146 kB] 1522s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 libglx0 amd64 1.7.0-1build1 [38.6 kB] 1522s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 libgl1 amd64 1.7.0-1build1 [102 kB] 1522s Get:145 http://ftpmaster.internal/ubuntu plucky/universe amd64 libglew2.2 amd64 2.2.0-4build1 [187 kB] 1522s Get:146 http://ftpmaster.internal/ubuntu plucky/universe amd64 libglut3.12 amd64 3.4.0-4 [111 kB] 1522s Get:147 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 1522s Get:148 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 1522s Get:149 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 1522s Get:150 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 1522s Get:151 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.3-1 [256 kB] 1522s Get:152 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.3-1 [52.9 kB] 1522s Get:153 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.3-1 [29.1 kB] 1522s Get:154 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-cursor0 amd64 1.23.1-3 [10.9 kB] 1522s Get:155 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-egl1 amd64 1.23.1-3 [6168 B] 1522s Get:156 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcomposite1 amd64 1:0.4.6-1 [6642 B] 1522s Get:157 http://ftpmaster.internal/ubuntu plucky/main amd64 libxfixes3 amd64 1:6.0.0-2build1 [10.8 kB] 1522s Get:158 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcursor1 amd64 1:1.2.3-1 [23.1 kB] 1522s Get:159 http://ftpmaster.internal/ubuntu plucky/main amd64 libxdamage1 amd64 1:1.1.6-1build1 [6150 B] 1522s Get:160 http://ftpmaster.internal/ubuntu plucky/main amd64 libxinerama1 amd64 2:1.1.4-3build1 [6396 B] 1522s Get:161 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrandr2 amd64 2:1.5.4-1 [19.6 kB] 1522s Get:162 http://ftpmaster.internal/ubuntu plucky/main amd64 libgtk-3-common all 3.24.49-2ubuntu1 [1424 kB] 1522s Get:163 http://ftpmaster.internal/ubuntu plucky/main amd64 libgtk-3-0t64 amd64 3.24.49-2ubuntu1 [3172 kB] 1522s Get:164 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 1522s Get:165 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 1522s Get:166 http://ftpmaster.internal/ubuntu plucky/main amd64 libwacom-common all 2.14.0-1 [103 kB] 1522s Get:167 http://ftpmaster.internal/ubuntu plucky/main amd64 libwacom9 amd64 2.14.0-1 [27.3 kB] 1522s Get:168 http://ftpmaster.internal/ubuntu plucky/main amd64 libinput-bin amd64 1.27.1-1 [23.4 kB] 1522s Get:169 http://ftpmaster.internal/ubuntu plucky/main amd64 libmtdev1t64 amd64 1.1.7-1 [16.3 kB] 1522s Get:170 http://ftpmaster.internal/ubuntu plucky/main amd64 libinput10 amd64 1.27.1-1 [155 kB] 1522s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 1522s Get:172 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 1522s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmd4c0 amd64 0.5.2-2 [50.1 kB] 1522s Get:174 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnetcdf22 amd64 1:4.9.3-1 [574 kB] 1522s Get:175 http://ftpmaster.internal/ubuntu plucky/main amd64 libnotify4 amd64 0.8.4-1 [26.9 kB] 1522s Get:176 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-16-0 amd64 10.45-1 [268 kB] 1522s Get:177 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-32-0 amd64 10.45-1 [251 kB] 1522s Get:178 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 1522s Get:179 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5core5t64 amd64 5.15.15+dfsg-4ubuntu1 [2038 kB] 1522s Get:180 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5dbus5t64 amd64 5.15.15+dfsg-4ubuntu1 [221 kB] 1522s Get:181 http://ftpmaster.internal/ubuntu plucky/main amd64 libegl1 amd64 1.7.0-1build1 [28.7 kB] 1522s Get:182 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5network5t64 amd64 5.15.15+dfsg-4ubuntu1 [725 kB] 1522s Get:183 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 1522s Get:184 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-icccm4 amd64 0.4.2-1 [11.1 kB] 1522s Get:185 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-util1 amd64 0.4.1-1 [11.2 kB] 1522s Get:186 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-image0 amd64 0.4.0-2build1 [10.8 kB] 1522s Get:187 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-keysyms1 amd64 0.4.1-1 [8738 B] 1522s Get:188 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render-util0 amd64 0.3.10-1 [10.8 kB] 1522s Get:189 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shape0 amd64 1.17.0-2 [6092 B] 1522s Get:190 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xinerama0 amd64 1.17.0-2 [5412 B] 1522s Get:191 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xinput0 amd64 1.17.0-2 [33.2 kB] 1522s Get:192 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xkb1 amd64 1.17.0-2 [32.3 kB] 1522s Get:193 http://ftpmaster.internal/ubuntu plucky/main amd64 libxkbcommon-x11-0 amd64 1.7.0-2 [15.2 kB] 1522s Get:194 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5gui5t64 amd64 5.15.15+dfsg-4ubuntu1 [3791 kB] 1522s Get:195 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5widgets5t64 amd64 5.15.15+dfsg-4ubuntu1 [2560 kB] 1522s Get:196 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5xml5t64 amd64 5.15.15+dfsg-4ubuntu1 [124 kB] 1522s Get:197 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5designer5 amd64 5.15.15-6build1 [2827 kB] 1522s Get:198 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5sql5t64 amd64 5.15.15+dfsg-4ubuntu1 [122 kB] 1522s Get:199 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5help5 amd64 5.15.15-6build1 [162 kB] 1522s Get:200 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5opengl5t64 amd64 5.15.15+dfsg-4ubuntu1 [150 kB] 1522s Get:201 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5printsupport5t64 amd64 5.15.15+dfsg-4ubuntu1 [208 kB] 1522s Get:202 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqt5test5t64 amd64 5.15.15+dfsg-4ubuntu1 [149 kB] 1522s Get:203 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 1522s Get:204 http://ftpmaster.internal/ubuntu plucky/universe amd64 libssm2 amd64 1.4.0-2build1 [87.7 kB] 1522s Get:205 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 1522s Get:206 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 1522s Get:207 http://ftpmaster.internal/ubuntu plucky/universe amd64 libwxbase3.2-1t64 amd64 3.2.6+dfsg-2ubuntu1 [980 kB] 1522s Get:208 http://ftpmaster.internal/ubuntu plucky/main amd64 libxtst6 amd64 2:1.2.5-1 [13.0 kB] 1522s Get:209 http://ftpmaster.internal/ubuntu plucky/universe amd64 libwxgtk3.2-1t64 amd64 3.2.6+dfsg-2ubuntu1 [4967 kB] 1522s Get:210 http://ftpmaster.internal/ubuntu plucky/universe amd64 libwxgtk-gl3.2-1t64 amd64 3.2.6+dfsg-2ubuntu1 [53.9 kB] 1522s Get:211 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu4 [176 kB] 1522s Get:212 http://ftpmaster.internal/ubuntu plucky/universe amd64 pymol-data all 3.1.0+dfsg-1 [1394 kB] 1522s Get:213 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-7build1 [2934 kB] 1522s Get:214 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.13.2-2 [884 B] 1522s Get:215 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build4 [367 kB] 1522s Get:216 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-legacy-cgi all 2.6.2-1 [16.6 kB] 1522s Get:217 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pycbf amd64 0.9.7+dfsg1-5build1 [166 kB] 1522s Get:218 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-hdf5plugin all 5.0.0-1 [23.1 kB] 1522s Get:219 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-4 [80.3 kB] 1522s Get:220 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.3-2 [218 kB] 1522s Get:221 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 11.1.0-5build1 [583 kB] 1522s Get:222 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.2-2 [107 kB] 1522s Get:223 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.13.2-1 [9818 B] 1522s Get:224 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 11.1.0-5build1 [9828 B] 1522s Get:225 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.1-1build1 [218 kB] 1522s Get:226 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 1522s Get:227 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-platformdirs all 4.3.6-1 [16.8 kB] 1522s Get:228 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-7 [90.8 kB] 1522s Get:229 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.1-1build1 [1408 kB] 1522s Get:230 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.4.0+dfsg-1build1 [27.0 kB] 1522s Get:231 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 1522s Get:232 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.14.1-4ubuntu2 [18.7 MB] 1522s Get:233 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 1522s Get:234 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-5 [4229 kB] 1523s Get:235 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 1523s Get:236 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 1523s Get:237 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.55.3-2build1 [1536 kB] 1523s Get:238 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-importlib-resources all 6.5.2-1 [24.5 kB] 1523s Get:239 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-3build1 [55.6 kB] 1523s Get:240 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 1523s Get:241 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-7build1 [17.4 MB] 1523s Get:242 http://ftpmaster.internal/ubuntu plucky/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 1523s Get:243 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mrcfile all 1.5.4-2 [116 kB] 1523s Get:244 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-natsort all 8.0.2-2 [33.8 kB] 1523s Get:245 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-flexcache all 0.3-2 [13.4 kB] 1523s Get:246 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-flexparser all 0.4-1 [43.8 kB] 1523s Get:247 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pint all 0.24.4-1 [203 kB] 1523s Get:248 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-nxmx all 0.0.4-1 [16.4 kB] 1523s Get:249 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ordered-set all 4.1.0-1 [9778 B] 1523s Get:250 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-procrunner all 2.3.3-2 [12.0 kB] 1523s Get:251 http://ftpmaster.internal/ubuntu plucky/main amd64 libopengl0 amd64 1.7.0-1build1 [32.8 kB] 1523s Get:252 http://ftpmaster.internal/ubuntu plucky/main amd64 libglu1-mesa amd64 9.0.2-1.1build1 [152 kB] 1523s Get:253 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-opengl all 3.1.9+dfsg-1syncable1 [631 kB] 1523s Get:254 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyqt5.sip amd64 12.17.0-1build1 [76.5 kB] 1523s Get:255 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyqt5 amd64 5.15.11+dfsg-2 [2725 kB] 1523s Get:256 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyqt5.qtopengl amd64 5.15.11+dfsg-2 [128 kB] 1523s Get:257 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pymol amd64 3.1.0+dfsg-1 [4171 kB] 1523s Get:258 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.17.0-1 [13.2 kB] 1523s Get:259 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-tqdm all 4.67.1-2 [92.5 kB] 1523s Get:260 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-wxgtk4.0 amd64 4.2.2+dfsg-3build1 [7838 kB] 1523s Get:261 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-cctbx amd64 2024.10+ds2+~3.22.1+ds1-4build2 [29.0 MB] 1523s Get:262 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 1523s Get:263 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 1523s Get:264 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.5-1 [252 kB] 1523s Get:265 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-dials-data all 2.4.0-2 [110 kB] 1523s Get:266 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-datadir all 1.4.1+ds-1 [5386 B] 1523s Get:267 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-mock all 3.14.0-2 [11.7 kB] 1523s Get:268 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-regressions all 2.5.0+ds-2 [39.2 kB] 1524s Fetched 271 MB in 3s (95.9 MB/s) 1524s Selecting previously unselected package fonts-lato. 1524s (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 ... 115743 files and directories currently installed.) 1524s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ... 1524s Unpacking fonts-lato (2.015-1) ... 1524s Selecting previously unselected package python3-numpy-dev:amd64. 1524s Preparing to unpack .../001-python3-numpy-dev_1%3a2.2.3+ds-5_amd64.deb ... 1524s Unpacking python3-numpy-dev:amd64 (1:2.2.3+ds-5) ... 1524s Selecting previously unselected package libblas3:amd64. 1524s Preparing to unpack .../002-libblas3_3.12.1-2_amd64.deb ... 1524s Unpacking libblas3:amd64 (3.12.1-2) ... 1524s Selecting previously unselected package libgfortran5:amd64. 1524s Preparing to unpack .../003-libgfortran5_15-20250315-1ubuntu1_amd64.deb ... 1524s Unpacking libgfortran5:amd64 (15-20250315-1ubuntu1) ... 1524s Selecting previously unselected package liblapack3:amd64. 1524s Preparing to unpack .../004-liblapack3_3.12.1-2_amd64.deb ... 1524s Unpacking liblapack3:amd64 (3.12.1-2) ... 1525s Selecting previously unselected package python3-numpy. 1525s Preparing to unpack .../005-python3-numpy_1%3a2.2.3+ds-5_amd64.deb ... 1525s Unpacking python3-numpy (1:2.2.3+ds-5) ... 1525s Selecting previously unselected package libgdk-pixbuf2.0-common. 1525s Preparing to unpack .../006-libgdk-pixbuf2.0-common_2.42.12+dfsg-2_all.deb ... 1525s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... 1525s Selecting previously unselected package libjpeg-turbo8:amd64. 1525s Preparing to unpack .../007-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 1525s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 1525s Selecting previously unselected package libjpeg8:amd64. 1525s Preparing to unpack .../008-libjpeg8_8c-2ubuntu11_amd64.deb ... 1525s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 1525s Selecting previously unselected package libdeflate0:amd64. 1525s Preparing to unpack .../009-libdeflate0_1.23-1_amd64.deb ... 1525s Unpacking libdeflate0:amd64 (1.23-1) ... 1525s Selecting previously unselected package libjbig0:amd64. 1525s Preparing to unpack .../010-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 1525s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 1525s Selecting previously unselected package liblerc4:amd64. 1525s Preparing to unpack .../011-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 1525s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 1525s Selecting previously unselected package libsharpyuv0:amd64. 1525s Preparing to unpack .../012-libsharpyuv0_1.5.0-0.1_amd64.deb ... 1525s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 1525s Selecting previously unselected package libwebp7:amd64. 1525s Preparing to unpack .../013-libwebp7_1.5.0-0.1_amd64.deb ... 1525s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 1525s Selecting previously unselected package libtiff6:amd64. 1525s Preparing to unpack .../014-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 1525s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 1525s Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. 1525s Preparing to unpack .../015-libgdk-pixbuf-2.0-0_2.42.12+dfsg-2_amd64.deb ... 1525s Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... 1525s Selecting previously unselected package gtk-update-icon-cache. 1525s Preparing to unpack .../016-gtk-update-icon-cache_4.18.2+ds-1_amd64.deb ... 1525s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 1525s 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. 1525s Unpacking gtk-update-icon-cache (4.18.2+ds-1) ... 1525s Selecting previously unselected package hicolor-icon-theme. 1525s Preparing to unpack .../017-hicolor-icon-theme_0.18-2_all.deb ... 1525s Unpacking hicolor-icon-theme (0.18-2) ... 1525s Selecting previously unselected package adwaita-icon-theme. 1525s Preparing to unpack .../018-adwaita-icon-theme_48.0-1_all.deb ... 1525s Unpacking adwaita-icon-theme (48.0-1) ... 1525s Selecting previously unselected package at-spi2-common. 1525s Preparing to unpack .../019-at-spi2-common_2.56.0-2_all.deb ... 1525s Unpacking at-spi2-common (2.56.0-2) ... 1525s Selecting previously unselected package libaec0:amd64. 1525s Preparing to unpack .../020-libaec0_1.1.3-1_amd64.deb ... 1525s Unpacking libaec0:amd64 (1.1.3-1) ... 1525s Selecting previously unselected package libsz2:amd64. 1525s Preparing to unpack .../021-libsz2_1.1.3-1_amd64.deb ... 1525s Unpacking libsz2:amd64 (1.1.3-1) ... 1525s Selecting previously unselected package libhdf5-310:amd64. 1525s Preparing to unpack .../022-libhdf5-310_1.14.5+repack-3_amd64.deb ... 1525s Unpacking libhdf5-310:amd64 (1.14.5+repack-3) ... 1525s Selecting previously unselected package libhdf5-hl-310:amd64. 1525s Preparing to unpack .../023-libhdf5-hl-310_1.14.5+repack-3_amd64.deb ... 1525s Unpacking libhdf5-hl-310:amd64 (1.14.5+repack-3) ... 1526s Selecting previously unselected package liblzf1:amd64. 1526s Preparing to unpack .../024-liblzf1_3.6-4_amd64.deb ... 1526s Unpacking liblzf1:amd64 (3.6-4) ... 1526s Selecting previously unselected package python3-h5py-serial. 1526s Preparing to unpack .../025-python3-h5py-serial_3.13.0-1_amd64.deb ... 1526s Unpacking python3-h5py-serial (3.13.0-1) ... 1526s Selecting previously unselected package python3-h5py. 1526s Preparing to unpack .../026-python3-h5py_3.13.0-1_all.deb ... 1526s Unpacking python3-h5py (3.13.0-1) ... 1526s Selecting previously unselected package libgomp1:amd64. 1526s Preparing to unpack .../027-libgomp1_15-20250315-1ubuntu1_amd64.deb ... 1526s Unpacking libgomp1:amd64 (15-20250315-1ubuntu1) ... 1526s Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. 1526s Preparing to unpack .../028-libevent-pthreads-2.1-7t64_2.1.12-stable-10_amd64.deb ... 1526s Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 1526s Selecting previously unselected package libpsm-infinipath1. 1526s Preparing to unpack .../029-libpsm-infinipath1_3.3+20.604758e7-6.3build1_amd64.deb ... 1526s Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 1526s Selecting previously unselected package libpsm2-2. 1526s Preparing to unpack .../030-libpsm2-2_11.2.185-2.1_amd64.deb ... 1526s Unpacking libpsm2-2 (11.2.185-2.1) ... 1526s Selecting previously unselected package librdmacm1t64:amd64. 1526s Preparing to unpack .../031-librdmacm1t64_56.0-3ubuntu1_amd64.deb ... 1526s Unpacking librdmacm1t64:amd64 (56.0-3ubuntu1) ... 1526s Selecting previously unselected package libfabric1:amd64. 1526s Preparing to unpack .../032-libfabric1_1.17.0-3.1_amd64.deb ... 1526s Unpacking libfabric1:amd64 (1.17.0-3.1) ... 1526s Selecting previously unselected package libhwloc15:amd64. 1526s Preparing to unpack .../033-libhwloc15_2.12.0-1_amd64.deb ... 1526s Unpacking libhwloc15:amd64 (2.12.0-1) ... 1526s Selecting previously unselected package libmunge2:amd64. 1526s Preparing to unpack .../034-libmunge2_0.5.16-1_amd64.deb ... 1526s Unpacking libmunge2:amd64 (0.5.16-1) ... 1526s Selecting previously unselected package libpciaccess0:amd64. 1526s Preparing to unpack .../035-libpciaccess0_0.17-3build1_amd64.deb ... 1526s Unpacking libpciaccess0:amd64 (0.17-3build1) ... 1526s Selecting previously unselected package libxnvctrl0:amd64. 1526s Preparing to unpack .../036-libxnvctrl0_510.47.03-0ubuntu4_amd64.deb ... 1526s Unpacking libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 1526s Selecting previously unselected package ocl-icd-libopencl1:amd64. 1526s Preparing to unpack .../037-ocl-icd-libopencl1_2.3.2-1build1_amd64.deb ... 1526s Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 1526s Selecting previously unselected package libhwloc-plugins:amd64. 1526s Preparing to unpack .../038-libhwloc-plugins_2.12.0-1_amd64.deb ... 1526s Unpacking libhwloc-plugins:amd64 (2.12.0-1) ... 1526s Selecting previously unselected package libpmix2t64:amd64. 1526s Preparing to unpack .../039-libpmix2t64_5.0.6-5_amd64.deb ... 1526s Unpacking libpmix2t64:amd64 (5.0.6-5) ... 1526s Selecting previously unselected package libllvm17t64:amd64. 1526s Preparing to unpack .../040-libllvm17t64_1%3a17.0.6-21_amd64.deb ... 1526s Unpacking libllvm17t64:amd64 (1:17.0.6-21) ... 1527s Selecting previously unselected package libamd-comgr2:amd64. 1527s Preparing to unpack .../041-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_amd64.deb ... 1527s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 1527s Selecting previously unselected package libhsakmt1:amd64. 1527s Preparing to unpack .../042-libhsakmt1_5.7.0-1build1_amd64.deb ... 1527s Unpacking libhsakmt1:amd64 (5.7.0-1build1) ... 1527s Selecting previously unselected package libhsa-runtime64-1. 1527s Preparing to unpack .../043-libhsa-runtime64-1_5.7.1-2build1_amd64.deb ... 1527s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 1527s Selecting previously unselected package libamdhip64-5. 1527s Preparing to unpack .../044-libamdhip64-5_5.7.1-5build1_amd64.deb ... 1527s Unpacking libamdhip64-5 (5.7.1-5build1) ... 1527s Selecting previously unselected package libibumad3:amd64. 1527s Preparing to unpack .../045-libibumad3_56.0-3ubuntu1_amd64.deb ... 1527s Unpacking libibumad3:amd64 (56.0-3ubuntu1) ... 1527s Selecting previously unselected package libibmad5:amd64. 1527s Preparing to unpack .../046-libibmad5_56.0-3ubuntu1_amd64.deb ... 1527s Unpacking libibmad5:amd64 (56.0-3ubuntu1) ... 1527s Selecting previously unselected package libucx0:amd64. 1527s Preparing to unpack .../047-libucx0_1.18.1+ds-2_amd64.deb ... 1527s Unpacking libucx0:amd64 (1.18.1+ds-2) ... 1527s Selecting previously unselected package libopenmpi40:amd64. 1527s Preparing to unpack .../048-libopenmpi40_5.0.7-1_amd64.deb ... 1527s Unpacking libopenmpi40:amd64 (5.0.7-1) ... 1527s Selecting previously unselected package libhdf5-openmpi-310:amd64. 1527s Preparing to unpack .../049-libhdf5-openmpi-310_1.14.5+repack-3_amd64.deb ... 1527s Unpacking libhdf5-openmpi-310:amd64 (1.14.5+repack-3) ... 1527s Selecting previously unselected package bitshuffle. 1527s Preparing to unpack .../050-bitshuffle_0.5.2-1build2_amd64.deb ... 1527s Unpacking bitshuffle (0.5.2-1build2) ... 1527s Selecting previously unselected package libtcl8.6:amd64. 1527s Preparing to unpack .../051-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 1527s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 1527s Selecting previously unselected package fonts-dejavu-mono. 1527s Preparing to unpack .../052-fonts-dejavu-mono_2.37-8_all.deb ... 1527s Unpacking fonts-dejavu-mono (2.37-8) ... 1527s Selecting previously unselected package fonts-dejavu-core. 1527s Preparing to unpack .../053-fonts-dejavu-core_2.37-8_all.deb ... 1527s Unpacking fonts-dejavu-core (2.37-8) ... 1528s Selecting previously unselected package fontconfig-config. 1528s Preparing to unpack .../054-fontconfig-config_2.15.0-2.1ubuntu1_amd64.deb ... 1528s Unpacking fontconfig-config (2.15.0-2.1ubuntu1) ... 1528s Selecting previously unselected package libfontconfig1:amd64. 1528s Preparing to unpack .../055-libfontconfig1_2.15.0-2.1ubuntu1_amd64.deb ... 1528s Unpacking libfontconfig1:amd64 (2.15.0-2.1ubuntu1) ... 1528s Selecting previously unselected package libxrender1:amd64. 1528s Preparing to unpack .../056-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 1528s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 1528s Selecting previously unselected package libxft2:amd64. 1528s Preparing to unpack .../057-libxft2_2.3.6-1build1_amd64.deb ... 1528s Unpacking libxft2:amd64 (2.3.6-1build1) ... 1528s Selecting previously unselected package x11-common. 1528s Preparing to unpack .../058-x11-common_1%3a7.7+23ubuntu3_all.deb ... 1528s Unpacking x11-common (1:7.7+23ubuntu3) ... 1528s Selecting previously unselected package libxss1:amd64. 1528s Preparing to unpack .../059-libxss1_1%3a1.2.3-1build3_amd64.deb ... 1528s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 1528s Selecting previously unselected package libtk8.6:amd64. 1528s Preparing to unpack .../060-libtk8.6_8.6.16-1_amd64.deb ... 1528s Unpacking libtk8.6:amd64 (8.6.16-1) ... 1528s Selecting previously unselected package tk8.6-blt2.5. 1528s Preparing to unpack .../061-tk8.6-blt2.5_2.5.3+dfsg-8_amd64.deb ... 1528s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 1528s Selecting previously unselected package blt. 1528s Preparing to unpack .../062-blt_2.5.3+dfsg-8_amd64.deb ... 1528s Unpacking blt (2.5.3+dfsg-8) ... 1528s Selecting previously unselected package libdconf1:amd64. 1528s Preparing to unpack .../063-libdconf1_0.40.0-5_amd64.deb ... 1528s Unpacking libdconf1:amd64 (0.40.0-5) ... 1528s Selecting previously unselected package dconf-service. 1528s Preparing to unpack .../064-dconf-service_0.40.0-5_amd64.deb ... 1528s Unpacking dconf-service (0.40.0-5) ... 1528s Selecting previously unselected package dconf-gsettings-backend:amd64. 1528s Preparing to unpack .../065-dconf-gsettings-backend_0.40.0-5_amd64.deb ... 1528s Unpacking dconf-gsettings-backend:amd64 (0.40.0-5) ... 1528s Selecting previously unselected package fontconfig. 1528s Preparing to unpack .../066-fontconfig_2.15.0-2.1ubuntu1_amd64.deb ... 1528s Unpacking fontconfig (2.15.0-2.1ubuntu1) ... 1528s Selecting previously unselected package fonts-font-awesome. 1528s Preparing to unpack .../067-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 1528s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 1528s Selecting previously unselected package fonts-lyx. 1528s Preparing to unpack .../068-fonts-lyx_2.4.3-1_all.deb ... 1528s Unpacking fonts-lyx (2.4.3-1) ... 1528s Selecting previously unselected package libann-cctbx0. 1528s Preparing to unpack .../069-libann-cctbx0_1.1.2+doc-9build1_amd64.deb ... 1528s Unpacking libann-cctbx0 (1.1.2+doc-9build1) ... 1528s Selecting previously unselected package libann-cctbx-dev. 1528s Preparing to unpack .../070-libann-cctbx-dev_1.1.2+doc-9build1_amd64.deb ... 1528s Unpacking libann-cctbx-dev (1.1.2+doc-9build1) ... 1528s Selecting previously unselected package libantlr3c-3.4-0:amd64. 1528s Preparing to unpack .../071-libantlr3c-3.4-0_3.4+dfsg-4build2_amd64.deb ... 1528s Unpacking libantlr3c-3.4-0:amd64 (3.4+dfsg-4build2) ... 1528s Selecting previously unselected package libasan8:amd64. 1528s Preparing to unpack .../072-libasan8_15-20250315-1ubuntu1_amd64.deb ... 1528s Unpacking libasan8:amd64 (15-20250315-1ubuntu1) ... 1528s Selecting previously unselected package libatk1.0-0t64:amd64. 1528s Preparing to unpack .../073-libatk1.0-0t64_2.56.0-2_amd64.deb ... 1528s Unpacking libatk1.0-0t64:amd64 (2.56.0-2) ... 1528s Selecting previously unselected package libxi6:amd64. 1528s Preparing to unpack .../074-libxi6_2%3a1.8.2-1_amd64.deb ... 1528s Unpacking libxi6:amd64 (2:1.8.2-1) ... 1529s Selecting previously unselected package libatspi2.0-0t64:amd64. 1529s Preparing to unpack .../075-libatspi2.0-0t64_2.56.0-2_amd64.deb ... 1529s Unpacking libatspi2.0-0t64:amd64 (2.56.0-2) ... 1529s Selecting previously unselected package libatk-bridge2.0-0t64:amd64. 1529s Preparing to unpack .../076-libatk-bridge2.0-0t64_2.56.0-2_amd64.deb ... 1529s Unpacking libatk-bridge2.0-0t64:amd64 (2.56.0-2) ... 1529s Selecting previously unselected package libavahi-common-data:amd64. 1529s Preparing to unpack .../077-libavahi-common-data_0.8-16ubuntu2_amd64.deb ... 1529s Unpacking libavahi-common-data:amd64 (0.8-16ubuntu2) ... 1529s Selecting previously unselected package libavahi-common3:amd64. 1529s Preparing to unpack .../078-libavahi-common3_0.8-16ubuntu2_amd64.deb ... 1529s Unpacking libavahi-common3:amd64 (0.8-16ubuntu2) ... 1529s Selecting previously unselected package libavahi-client3:amd64. 1529s Preparing to unpack .../079-libavahi-client3_0.8-16ubuntu2_amd64.deb ... 1529s Unpacking libavahi-client3:amd64 (0.8-16ubuntu2) ... 1529s Selecting previously unselected package libboost-python1.83.0. 1529s Preparing to unpack .../080-libboost-python1.83.0_1.83.0-4.1ubuntu2_amd64.deb ... 1529s Unpacking libboost-python1.83.0 (1.83.0-4.1ubuntu2) ... 1529s Selecting previously unselected package libboost-numpy1.83.0. 1529s Preparing to unpack .../081-libboost-numpy1.83.0_1.83.0-4.1ubuntu2_amd64.deb ... 1529s Unpacking libboost-numpy1.83.0 (1.83.0-4.1ubuntu2) ... 1529s Selecting previously unselected package libitm1:amd64. 1529s Preparing to unpack .../082-libitm1_15-20250315-1ubuntu1_amd64.deb ... 1529s Unpacking libitm1:amd64 (15-20250315-1ubuntu1) ... 1529s Selecting previously unselected package liblsan0:amd64. 1529s Preparing to unpack .../083-liblsan0_15-20250315-1ubuntu1_amd64.deb ... 1529s Unpacking liblsan0:amd64 (15-20250315-1ubuntu1) ... 1529s Selecting previously unselected package libtsan2:amd64. 1529s Preparing to unpack .../084-libtsan2_15-20250315-1ubuntu1_amd64.deb ... 1529s Unpacking libtsan2:amd64 (15-20250315-1ubuntu1) ... 1529s Selecting previously unselected package libubsan1:amd64. 1529s Preparing to unpack .../085-libubsan1_15-20250315-1ubuntu1_amd64.deb ... 1529s Unpacking libubsan1:amd64 (15-20250315-1ubuntu1) ... 1529s Selecting previously unselected package libhwasan0:amd64. 1529s Preparing to unpack .../086-libhwasan0_15-20250315-1ubuntu1_amd64.deb ... 1529s Unpacking libhwasan0:amd64 (15-20250315-1ubuntu1) ... 1529s Selecting previously unselected package libquadmath0:amd64. 1529s Preparing to unpack .../087-libquadmath0_15-20250315-1ubuntu1_amd64.deb ... 1529s Unpacking libquadmath0:amd64 (15-20250315-1ubuntu1) ... 1529s Selecting previously unselected package libgcc-14-dev:amd64. 1529s Preparing to unpack .../088-libgcc-14-dev_14.2.0-19ubuntu1_amd64.deb ... 1529s Unpacking libgcc-14-dev:amd64 (14.2.0-19ubuntu1) ... 1529s Selecting previously unselected package libstdc++-14-dev:amd64. 1529s Preparing to unpack .../089-libstdc++-14-dev_14.2.0-19ubuntu1_amd64.deb ... 1529s Unpacking libstdc++-14-dev:amd64 (14.2.0-19ubuntu1) ... 1529s Selecting previously unselected package libboost1.83-dev:amd64. 1530s Preparing to unpack .../090-libboost1.83-dev_1.83.0-4.1ubuntu2_amd64.deb ... 1530s Unpacking libboost1.83-dev:amd64 (1.83.0-4.1ubuntu2) ... 1531s Selecting previously unselected package libexpat1-dev:amd64. 1531s Preparing to unpack .../091-libexpat1-dev_2.6.4-1_amd64.deb ... 1531s Unpacking libexpat1-dev:amd64 (2.6.4-1) ... 1531s Selecting previously unselected package zlib1g-dev:amd64. 1531s Preparing to unpack .../092-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ... 1531s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 1531s Selecting previously unselected package libpython3.13-dev:amd64. 1531s Preparing to unpack .../093-libpython3.13-dev_3.13.2-2_amd64.deb ... 1531s Unpacking libpython3.13-dev:amd64 (3.13.2-2) ... 1532s Selecting previously unselected package libpython3-dev:amd64. 1532s Preparing to unpack .../094-libpython3-dev_3.13.2-2_amd64.deb ... 1532s Unpacking libpython3-dev:amd64 (3.13.2-2) ... 1532s Selecting previously unselected package python3.13-dev. 1532s Preparing to unpack .../095-python3.13-dev_3.13.2-2_amd64.deb ... 1532s Unpacking python3.13-dev (3.13.2-2) ... 1532s Selecting previously unselected package libjs-jquery. 1532s Preparing to unpack .../096-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 1532s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 1532s Selecting previously unselected package libjs-underscore. 1532s Preparing to unpack .../097-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 1532s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 1532s Selecting previously unselected package libjs-sphinxdoc. 1532s Preparing to unpack .../098-libjs-sphinxdoc_8.1.3-5_all.deb ... 1532s Unpacking libjs-sphinxdoc (8.1.3-5) ... 1532s Selecting previously unselected package python3-dev. 1532s Preparing to unpack .../099-python3-dev_3.13.2-2_amd64.deb ... 1532s Unpacking python3-dev (3.13.2-2) ... 1532s Selecting previously unselected package libboost-python1.83-dev. 1532s Preparing to unpack .../100-libboost-python1.83-dev_1.83.0-4.1ubuntu2_amd64.deb ... 1532s Unpacking libboost-python1.83-dev (1.83.0-4.1ubuntu2) ... 1532s Selecting previously unselected package libboost-python-dev. 1532s Preparing to unpack .../101-libboost-python-dev_1.83.0.2ubuntu1_amd64.deb ... 1532s Unpacking libboost-python-dev (1.83.0.2ubuntu1) ... 1532s Selecting previously unselected package libboost-thread1.83.0:amd64. 1532s Preparing to unpack .../102-libboost-thread1.83.0_1.83.0-4.1ubuntu2_amd64.deb ... 1532s Unpacking libboost-thread1.83.0:amd64 (1.83.0-4.1ubuntu2) ... 1532s Selecting previously unselected package libboost-timer1.83.0:amd64. 1532s Preparing to unpack .../103-libboost-timer1.83.0_1.83.0-4.1ubuntu2_amd64.deb ... 1532s Unpacking libboost-timer1.83.0:amd64 (1.83.0-4.1ubuntu2) ... 1532s Selecting previously unselected package libpixman-1-0:amd64. 1532s Preparing to unpack .../104-libpixman-1-0_0.44.0-3_amd64.deb ... 1532s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 1532s Selecting previously unselected package libxcb-render0:amd64. 1532s Preparing to unpack .../105-libxcb-render0_1.17.0-2_amd64.deb ... 1532s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 1532s Selecting previously unselected package libxcb-shm0:amd64. 1532s Preparing to unpack .../106-libxcb-shm0_1.17.0-2_amd64.deb ... 1532s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 1532s Selecting previously unselected package libcairo2:amd64. 1532s Preparing to unpack .../107-libcairo2_1.18.4-1_amd64.deb ... 1532s Unpacking libcairo2:amd64 (1.18.4-1) ... 1532s Selecting previously unselected package libcairo-gobject2:amd64. 1532s Preparing to unpack .../108-libcairo-gobject2_1.18.4-1_amd64.deb ... 1532s Unpacking libcairo-gobject2:amd64 (1.18.4-1) ... 1532s Selecting previously unselected package libcbf1t64:amd64. 1532s Preparing to unpack .../109-libcbf1t64_0.9.7+dfsg1-5build1_amd64.deb ... 1532s Unpacking libcbf1t64:amd64 (0.9.7+dfsg1-5build1) ... 1532s Selecting previously unselected package libccp4-data. 1532s Preparing to unpack .../110-libccp4-data_8.0.0-4_all.deb ... 1532s Unpacking libccp4-data (8.0.0-4) ... 1532s Selecting previously unselected package libccp4c0t64:amd64. 1532s Preparing to unpack .../111-libccp4c0t64_8.0.0-4_amd64.deb ... 1532s Unpacking libccp4c0t64:amd64 (8.0.0-4) ... 1532s Selecting previously unselected package libmmdb2-0:amd64. 1532s Preparing to unpack .../112-libmmdb2-0_2.0.22-1_amd64.deb ... 1532s Unpacking libmmdb2-0:amd64 (2.0.22-1) ... 1532s Selecting previously unselected package libccp4f0t64:amd64. 1532s Preparing to unpack .../113-libccp4f0t64_8.0.0-4_amd64.deb ... 1532s Unpacking libccp4f0t64:amd64 (8.0.0-4) ... 1532s Selecting previously unselected package libccp4-dev:amd64. 1532s Preparing to unpack .../114-libccp4-dev_8.0.0-4_amd64.deb ... 1532s Unpacking libccp4-dev:amd64 (8.0.0-4) ... 1532s Selecting previously unselected package libcctbx0. 1532s Preparing to unpack .../115-libcctbx0_2024.10+ds2+~3.22.1+ds1-4build2_amd64.deb ... 1532s Unpacking libcctbx0 (2024.10+ds2+~3.22.1+ds1-4build2) ... 1533s Selecting previously unselected package libcctbx-dev. 1533s Preparing to unpack .../116-libcctbx-dev_2024.10+ds2+~3.22.1+ds1-4build2_amd64.deb ... 1533s Unpacking libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4build2) ... 1533s Selecting previously unselected package liblcms2-2:amd64. 1533s Preparing to unpack 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previously unselected package libglvnd0:amd64. 1534s Preparing to unpack .../138-libglvnd0_1.7.0-1build1_amd64.deb ... 1534s Unpacking libglvnd0:amd64 (1.7.0-1build1) ... 1534s Selecting previously unselected package libxcb-glx0:amd64. 1534s Preparing to unpack .../139-libxcb-glx0_1.17.0-2_amd64.deb ... 1534s Unpacking libxcb-glx0:amd64 (1.17.0-2) ... 1534s Selecting previously unselected package libxxf86vm1:amd64. 1534s Preparing to unpack .../140-libxxf86vm1_1%3a1.1.4-1build4_amd64.deb ... 1534s Unpacking libxxf86vm1:amd64 (1:1.1.4-1build4) ... 1534s Selecting previously unselected package libglx-mesa0:amd64. 1534s Preparing to unpack .../141-libglx-mesa0_25.0.1-2ubuntu2_amd64.deb ... 1534s Unpacking libglx-mesa0:amd64 (25.0.1-2ubuntu2) ... 1534s Selecting previously unselected package libglx0:amd64. 1534s Preparing to unpack .../142-libglx0_1.7.0-1build1_amd64.deb ... 1534s Unpacking libglx0:amd64 (1.7.0-1build1) ... 1534s Selecting previously unselected package libgl1:amd64. 1534s 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unpack .../184-libxcb-util1_0.4.1-1_amd64.deb ... 1536s Unpacking libxcb-util1:amd64 (0.4.1-1) ... 1536s Selecting previously unselected package libxcb-image0:amd64. 1536s Preparing to unpack .../185-libxcb-image0_0.4.0-2build1_amd64.deb ... 1536s Unpacking libxcb-image0:amd64 (0.4.0-2build1) ... 1536s Selecting previously unselected package libxcb-keysyms1:amd64. 1536s Preparing to unpack .../186-libxcb-keysyms1_0.4.1-1_amd64.deb ... 1536s Unpacking libxcb-keysyms1:amd64 (0.4.1-1) ... 1536s Selecting previously unselected package libxcb-render-util0:amd64. 1536s Preparing to unpack .../187-libxcb-render-util0_0.3.10-1_amd64.deb ... 1536s Unpacking libxcb-render-util0:amd64 (0.3.10-1) ... 1536s Selecting previously unselected package libxcb-shape0:amd64. 1536s Preparing to unpack .../188-libxcb-shape0_1.17.0-2_amd64.deb ... 1536s Unpacking libxcb-shape0:amd64 (1.17.0-2) ... 1536s Selecting previously unselected package libxcb-xinerama0:amd64. 1536s Preparing to unpack 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unselected package libqt5opengl5t64:amd64. 1536s Preparing to unpack .../199-libqt5opengl5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 1536s Unpacking libqt5opengl5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1536s Selecting previously unselected package libqt5printsupport5t64:amd64. 1536s Preparing to unpack .../200-libqt5printsupport5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 1536s Unpacking libqt5printsupport5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1536s Selecting previously unselected package libqt5test5t64:amd64. 1536s Preparing to unpack .../201-libqt5test5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 1536s Unpacking libqt5test5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1536s Selecting previously unselected package libraqm0:amd64. 1536s Preparing to unpack .../202-libraqm0_0.10.2-1_amd64.deb ... 1536s Unpacking libraqm0:amd64 (0.10.2-1) ... 1536s Selecting previously unselected package libssm2:amd64. 1536s Preparing to unpack .../203-libssm2_1.4.0-2build1_amd64.deb ... 1536s Unpacking libssm2:amd64 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(3.2.6+dfsg-2ubuntu1) ... 1537s Selecting previously unselected package libwxgtk-gl3.2-1t64:amd64. 1537s Preparing to unpack .../209-libwxgtk-gl3.2-1t64_3.2.6+dfsg-2ubuntu1_amd64.deb ... 1537s Unpacking libwxgtk-gl3.2-1t64:amd64 (3.2.6+dfsg-2ubuntu1) ... 1537s Selecting previously unselected package libxslt1.1:amd64. 1537s Preparing to unpack .../210-libxslt1.1_1.1.39-0exp1ubuntu4_amd64.deb ... 1537s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu4) ... 1537s Selecting previously unselected package pymol-data. 1537s Preparing to unpack .../211-pymol-data_3.1.0+dfsg-1_all.deb ... 1537s Unpacking pymol-data (3.1.0+dfsg-1) ... 1537s Selecting previously unselected package python-matplotlib-data. 1537s Preparing to unpack .../212-python-matplotlib-data_3.8.3-7build1_all.deb ... 1537s Unpacking python-matplotlib-data (3.8.3-7build1) ... 1537s Selecting previously unselected package python3-all. 1537s Preparing to unpack .../213-python3-all_3.13.2-2_amd64.deb ... 1537s Unpacking python3-all 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package libopenjp2-7:amd64. 1537s Preparing to unpack .../219-libopenjp2-7_2.5.3-2_amd64.deb ... 1537s Unpacking libopenjp2-7:amd64 (2.5.3-2) ... 1537s Selecting previously unselected package python3-pil:amd64. 1537s Preparing to unpack .../220-python3-pil_11.1.0-5build1_amd64.deb ... 1537s Unpacking python3-pil:amd64 (11.1.0-5build1) ... 1537s Selecting previously unselected package python3.13-tk. 1537s Preparing to unpack .../221-python3.13-tk_3.13.2-2_amd64.deb ... 1537s Unpacking python3.13-tk (3.13.2-2) ... 1537s Selecting previously unselected package python3-tk:amd64. 1537s Preparing to unpack .../222-python3-tk_3.13.2-1_amd64.deb ... 1537s Unpacking python3-tk:amd64 (3.13.2-1) ... 1537s Selecting previously unselected package python3-pil.imagetk:amd64. 1537s Preparing to unpack .../223-python3-pil.imagetk_11.1.0-5build1_amd64.deb ... 1537s Unpacking python3-pil.imagetk:amd64 (11.1.0-5build1) ... 1537s Selecting previously unselected package python3-contourpy. 1537s Preparing to unpack .../224-python3-contourpy_1.3.1-1build1_amd64.deb ... 1537s Unpacking python3-contourpy (1.3.1-1build1) ... 1537s Selecting previously unselected package python3-cycler. 1537s Preparing to unpack .../225-python3-cycler_0.12.1-1_all.deb ... 1537s Unpacking python3-cycler (0.12.1-1) ... 1537s Selecting previously unselected package python3-platformdirs. 1537s Preparing to unpack .../226-python3-platformdirs_4.3.6-1_all.deb ... 1537s Unpacking python3-platformdirs (4.3.6-1) ... 1537s Selecting previously unselected package python3-fs. 1537s Preparing to unpack .../227-python3-fs_2.4.16-7_all.deb ... 1537s Unpacking python3-fs (2.4.16-7) ... 1537s Selecting previously unselected package python3-lxml:amd64. 1537s Preparing to unpack .../228-python3-lxml_5.3.1-1build1_amd64.deb ... 1537s Unpacking python3-lxml:amd64 (5.3.1-1build1) ... 1538s Selecting previously unselected package python3-lz4. 1538s Preparing to unpack .../229-python3-lz4_4.4.0+dfsg-1build1_amd64.deb ... 1538s 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unselected package unicode-data. 1538s Preparing to unpack .../235-unicode-data_15.1.0-1_all.deb ... 1538s Unpacking unicode-data (15.1.0-1) ... 1539s Selecting previously unselected package python3-fonttools. 1539s Preparing to unpack .../236-python3-fonttools_4.55.3-2build1_amd64.deb ... 1539s Unpacking python3-fonttools (4.55.3-2build1) ... 1539s Selecting previously unselected package python3-importlib-resources. 1539s Preparing to unpack .../237-python3-importlib-resources_6.5.2-1_all.deb ... 1539s Unpacking python3-importlib-resources (6.5.2-1) ... 1539s Selecting previously unselected package python3-kiwisolver. 1539s Preparing to unpack .../238-python3-kiwisolver_1.4.7-3build1_amd64.deb ... 1539s Unpacking python3-kiwisolver (1.4.7-3build1) ... 1539s Selecting previously unselected package python3-packaging. 1539s Preparing to unpack .../239-python3-packaging_24.2-1_all.deb ... 1539s Unpacking python3-packaging (24.2-1) ... 1539s Selecting previously unselected package python3-matplotlib. 1539s Preparing to unpack .../240-python3-matplotlib_3.8.3-7build1_amd64.deb ... 1539s Unpacking python3-matplotlib (3.8.3-7build1) ... 1539s Selecting previously unselected package sphinx-rtd-theme-common. 1539s Preparing to unpack .../241-sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb ... 1539s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 1539s Selecting previously unselected package python3-mrcfile. 1539s Preparing to unpack .../242-python3-mrcfile_1.5.4-2_all.deb ... 1539s Unpacking python3-mrcfile (1.5.4-2) ... 1539s Selecting previously unselected package python3-natsort. 1539s Preparing to unpack .../243-python3-natsort_8.0.2-2_all.deb ... 1539s Unpacking python3-natsort (8.0.2-2) ... 1539s Selecting previously unselected package python3-flexcache. 1539s Preparing to unpack .../244-python3-flexcache_0.3-2_all.deb ... 1539s Unpacking python3-flexcache (0.3-2) ... 1539s Selecting previously unselected package python3-flexparser. 1539s Preparing to unpack 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libpcre2-16-0:amd64 (10.45-1) ... 1543s Setting up libaec0:amd64 (1.1.3-1) ... 1543s Setting up libcolord2:amd64 (1.4.7-3) ... 1543s Setting up python3-platformdirs (4.3.6-1) ... 1543s Setting up libopengl0:amd64 (1.7.0-1build1) ... 1543s Setting up python3-natsort (8.0.2-2) ... 1543s Setting up libxcb-util1:amd64 (0.4.1-1) ... 1543s Setting up libxxf86vm1:amd64 (1:1.1.4-1build4) ... 1543s Setting up libxcb-xkb1:amd64 (1.17.0-2) ... 1543s Setting up libxcb-image0:amd64 (0.4.0-2build1) ... 1543s Setting up python3-fs (2.4.16-7) ... 1544s Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 1544s Setting up libxcb-present0:amd64 (1.17.0-2) ... 1544s Setting up libdconf1:amd64 (0.40.0-5) ... 1544s Setting up unicode-data (15.1.0-1) ... 1544s Setting up python3-six (1.17.0-1) ... 1544s Setting up libqt5core5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1544s Setting up python3-decorator (5.1.1-5) ... 1544s Setting up libboost-numpy1.83.0 (1.83.0-4.1ubuntu2) ... 1544s Setting up libpcre2-32-0:amd64 (10.45-1) ... 1544s Setting up libblas3:amd64 (3.12.1-2) ... 1544s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 1544s Setting up python3-packaging (24.2-1) ... 1544s Setting up libxcb-xinerama0:amd64 (1.17.0-2) ... 1544s Setting up python3-flexparser (0.4-1) ... 1544s Setting up libmunge2:amd64 (0.5.16-1) ... 1544s Setting up libllvm17t64:amd64 (1:17.0.6-21) ... 1544s Setting up libexpat1-dev:amd64 (2.6.4-1) ... 1544s Setting up libann-cctbx0 (1.1.2+doc-9build1) ... 1544s Setting up libepoxy0:amd64 (1.5.10-2) ... 1544s Setting up libxfixes3:amd64 (1:6.0.0-2build1) ... 1544s Setting up libxcb-sync1:amd64 (1.17.0-2) ... 1544s Setting up python3-brotli (1.1.0-2build4) ... 1544s Setting up libavahi-common-data:amd64 (0.8-16ubuntu2) ... 1544s Setting up libatspi2.0-0t64:amd64 (2.56.0-2) ... 1544s Setting up liblzf1:amd64 (3.6-4) ... 1544s Setting up libquadmath0:amd64 (15-20250315-1ubuntu1) ... 1544s Setting up python3-cycler (0.12.1-1) ... 1544s Setting up libxinerama1:amd64 (2:1.1.4-3build1) ... 1544s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 1544s Setting up pymol-data (3.1.0+dfsg-1) ... 1544s Setting up libxkbcommon-x11-0:amd64 (1.7.0-2) ... 1544s Setting up fonts-dejavu-mono (2.37-8) ... 1544s Setting up python3-kiwisolver (1.4.7-3build1) ... 1545s Setting up libhwloc15:amd64 (2.12.0-1) ... 1545s Setting up python3-numpy-dev:amd64 (1:2.2.3+ds-5) ... 1545s Setting up libxrandr2:amd64 (2:1.5.4-1) ... 1545s Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... 1545s Setting up fonts-dejavu-core (2.37-8) ... 1545s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 1545s Setting up libgfortran5:amd64 (15-20250315-1ubuntu1) ... 1545s Setting up libvulkan1:amd64 (1.4.304.0-1) ... 1545s Setting up python3-pluggy (1.5.0-1) ... 1545s Setting up libwebp7:amd64 (1.5.0-0.1) ... 1545s Setting up libubsan1:amd64 (15-20250315-1ubuntu1) ... 1545s Setting up python3-legacy-cgi (2.6.2-1) ... 1545s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 1545s Setting up python3-pyqt5.sip (12.17.0-1build1) ... 1545s Setting up libmtdev1t64:amd64 (1.1.7-1) ... 1545s Setting up ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 1545s Setting up libxshmfence1:amd64 (1.3-1build5) ... 1545s Setting up libhwasan0:amd64 (15-20250315-1ubuntu1) ... 1545s Setting up at-spi2-common (2.56.0-2) ... 1545s Setting up libccp4c0t64:amd64 (8.0.0-4) ... 1545s Setting up libxcb-randr0:amd64 (1.17.0-2) ... 1545s Setting up libasan8:amd64 (15-20250315-1ubuntu1) ... 1545s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu4) ... 1545s Setting up libpsm2-2 (11.2.185-2.1) ... 1545s Setting up libqt5sql5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1545s Setting up libmd4c0:amd64 (0.5.2-2) ... 1545s Setting up librdmacm1t64:amd64 (56.0-3ubuntu1) ... 1545s Setting up libopenjp2-7:amd64 (2.5.3-2) ... 1545s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 1545s Setting up libthai-data (0.1.29-2build1) ... 1545s Setting up python3-dateutil (2.9.0-4) ... 1545s Setting up python3-flexcache (0.3-2) ... 1545s Setting up libglu1-mesa:amd64 (9.0.2-1.1build1) ... 1545s Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 1545s Setting up libwayland-egl1:amd64 (1.23.1-3) ... 1545s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 1545s Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 1545s update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode 1545s Setting up libtsan2:amd64 (15-20250315-1ubuntu1) ... 1545s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 1545s Setting up libwxbase3.2-1t64:amd64 (3.2.6+dfsg-2ubuntu1) ... 1545s Setting up python3-mpmath (1.3.0-1) ... 1545s Setting up python-matplotlib-data (3.8.3-7build1) ... 1545s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 1545s Setting up libxcomposite1:amd64 (1:0.4.6-1) ... 1545s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 1545s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 1545s Setting up python3-procrunner (2.3.3-2) ... 1546s Setting up liblsan0:amd64 (15-20250315-1ubuntu1) ... 1546s Setting up libhsakmt1:amd64 (5.7.0-1build1) ... 1546s Setting up libsz2:amd64 (1.1.3-1) ... 1546s Setting up libitm1:amd64 (15-20250315-1ubuntu1) ... 1546s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 1546s Setting up libann-cctbx-dev (1.1.2+doc-9build1) ... 1546s Setting up libwacom-common (2.14.0-1) ... 1546s Setting up libwayland-client0:amd64 (1.23.1-3) ... 1546s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 1546s Setting up libfabric1:amd64 (1.17.0-3.1) ... 1546s Setting up python3-sympy (1.13.3-5) ... 1550s Setting up libice6:amd64 (2:1.1.1-1) ... 1550s Setting up mesa-libgallium:amd64 (25.0.1-2ubuntu2) ... 1550s Setting up liblapack3:amd64 (3.12.1-2) ... 1550s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 1550s Setting up libqt5dbus5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1550s Setting up libssm2:amd64 (1.4.0-2build1) ... 1550s Setting up libatk1.0-0t64:amd64 (2.56.0-2) ... 1550s Setting up libgbm1:amd64 (25.0.1-2ubuntu2) ... 1550s Setting up libwacom9:amd64 (2.14.0-1) ... 1550s Setting up fontconfig-config (2.15.0-2.1ubuntu1) ... 1551s Setting up python3-pytest (8.3.5-1) ... 1551s Setting up libxtst6:amd64 (2:1.2.5-1) ... 1551s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 1551s Setting up python3-pytest-datadir (1.4.1+ds-1) ... 1551s Setting up libxcursor1:amd64 (1:1.2.3-1) ... 1551s Setting up libgl1-mesa-dri:amd64 (25.0.1-2ubuntu2) ... 1551s Setting up libqt5network5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1551s Setting up libavahi-common3:amd64 (0.8-16ubuntu2) ... 1551s Setting up libqt5xml5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1551s Setting up dconf-service (0.40.0-5) ... 1551s Setting up libqt5test5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1551s Setting up libhwloc-plugins:amd64 (2.12.0-1) ... 1551s Setting up libccp4f0t64:amd64 (8.0.0-4) ... 1551s Setting up libinput-bin (1.27.1-1) ... 1551s Setting up python3-pint (0.24.4-1) ... 1551s Setting up libthai0:amd64 (0.1.29-2build1) ... 1551s Setting up libegl-mesa0:amd64 (25.0.1-2ubuntu2) ... 1551s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 1551s Setting up libraqm0:amd64 (0.10.2-1) ... 1551s Setting up libpython3.13-dev:amd64 (3.13.2-2) ... 1551s Setting up libpmix2t64:amd64 (5.0.6-5) ... 1551s Setting up python3-numpy (1:2.2.3+ds-5) ... 1553s Setting up libjs-sphinxdoc (8.1.3-5) ... 1553s Setting up libhdf5-310:amd64 (1.14.5+repack-3) ... 1553s Setting up python3-pytest-mock (3.14.0-2) ... 1553s Setting up python3-lxml:amd64 (5.3.1-1build1) ... 1553s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 1553s Setting up libwayland-cursor0:amd64 (1.23.1-3) ... 1553s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 1553s Setting up libegl1:amd64 (1.7.0-1build1) ... 1553s Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... 1553s Setting up python3-contourpy (1.3.1-1build1) ... 1553s Setting up libfontconfig1:amd64 (2.15.0-2.1ubuntu1) ... 1553s Setting up libgcc-14-dev:amd64 (14.2.0-19ubuntu1) ... 1553s Setting up python3-dials-data (2.4.0-2) ... 1553s Setting up libstdc++-14-dev:amd64 (14.2.0-19ubuntu1) ... 1553s Setting up libsm6:amd64 (2:1.2.4-1) ... 1553s Setting up libavahi-client3:amd64 (0.8-16ubuntu2) ... 1553s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 1553s Setting up python3-mrcfile (1.5.4-2) ... 1553s Setting up libatk-bridge2.0-0t64:amd64 (2.56.0-2) ... 1553s Setting up libinput10:amd64 (1.27.1-1) ... 1553s Setting up gtk-update-icon-cache (4.18.2+ds-1) ... 1553s Setting up libhdf5-hl-310:amd64 (1.14.5+repack-3) ... 1553s Setting up fontconfig (2.15.0-2.1ubuntu1) ... 1555s Regenerating fonts cache... done. 1555s Setting up libxft2:amd64 (2.3.6-1build1) ... 1555s Setting up libboost1.83-dev:amd64 (1.83.0-4.1ubuntu2) ... 1555s Setting up libglx-mesa0:amd64 (25.0.1-2ubuntu2) ... 1555s Setting up python3-scipy (1.14.1-4ubuntu2) ... 1558s Setting up libpython3-dev:amd64 (3.13.2-2) ... 1558s Setting up libcbf1t64:amd64 (0.9.7+dfsg1-5build1) ... 1558s Setting up libglx0:amd64 (1.7.0-1build1) ... 1558s Setting up dconf-gsettings-backend:amd64 (0.40.0-5) ... 1558s Setting up libccp4-dev:amd64 (8.0.0-4) ... 1558s Setting up python3.13-dev (3.13.2-2) ... 1558s Setting up libtk8.6:amd64 (8.6.16-1) ... 1558s Setting up libpango-1.0-0:amd64 (1.56.3-1) ... 1558s Setting up libnetcdf22:amd64 (1:4.9.3-1) ... 1558s Setting up python3-h5py-serial (3.13.0-1) ... 1558s Setting up libcairo2:amd64 (1.18.4-1) ... 1558s Setting up python3.13-tk (3.13.2-2) ... 1558s Setting up python3-pil:amd64 (11.1.0-5build1) ... 1559s Setting up libgl1:amd64 (1.7.0-1build1) ... 1559s Setting up libamdhip64-5 (5.7.1-5build1) ... 1559s Setting up python3-pytest-regressions (2.5.0+ds-2) ... 1559s Setting up adwaita-icon-theme (48.0-1) ... 1559s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 1559s Setting up libglut3.12:amd64 (3.4.0-4) ... 1559s Setting up libnotify4:amd64 (0.8.4-1) ... 1559s Setting up python3-dev (3.13.2-2) ... 1559s Setting up libboost-python1.83-dev (1.83.0-4.1ubuntu2) ... 1559s Setting up python3-pycbf (0.9.7+dfsg1-5build1) ... 1559s Setting up python3-h5py (3.13.0-1) ... 1559s Setting up libglew2.2:amd64 (2.2.0-4build1) ... 1559s Setting up python3-hdf5plugin (5.0.0-1) ... 1559s Setting up libcairo-gobject2:amd64 (1.18.4-1) ... 1559s Setting up libpangoft2-1.0-0:amd64 (1.56.3-1) ... 1559s Setting up python3-nxmx (0.0.4-1) ... 1560s Setting up libcups2t64:amd64 (2.4.11-0ubuntu2) ... 1560s Setting up libgtk-3-common (3.24.49-2ubuntu1) ... 1560s Setting up libpangocairo-1.0-0:amd64 (1.56.3-1) ... 1560s Setting up libcctbx0 (2024.10+ds2+~3.22.1+ds1-4build2) ... 1560s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 1560s Setting up libucx0:amd64 (1.18.1+ds-2) ... 1560s Setting up blt (2.5.3+dfsg-8) ... 1560s Setting up python3-tk:amd64 (3.13.2-1) ... 1560s Setting up python3-opengl (3.1.9+dfsg-1syncable1) ... 1560s /usr/lib/python3/dist-packages/OpenGL/GL/AMD/vertex_shader_tessellator.py:30: SyntaxWarning: invalid escape sequence '\ ' 1560s |\ |\ 1561s Setting up libboost-python-dev (1.83.0.2ubuntu1) ... 1561s Setting up libqt5gui5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1561s Setting up python3-pil.imagetk:amd64 (11.1.0-5build1) ... 1561s Setting up libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4build2) ... 1561s Setting up libopenmpi40:amd64 (5.0.7-1) ... 1561s Setting up libqt5widgets5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1561s Setting up libhdf5-openmpi-310:amd64 (1.14.5+repack-3) ... 1561s Setting up libqt5help5:amd64 (5.15.15-6build1) ... 1561s Setting up libqt5opengl5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1561s Setting up libqt5printsupport5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 1561s Setting up bitshuffle (0.5.2-1build2) ... 1561s Setting up libqt5designer5:amd64 (5.15.15-6build1) ... 1561s Setting up python3-pyqt5 (5.15.11+dfsg-2) ... 1561s Setting up python3-pyqt5.qtopengl (5.15.11+dfsg-2) ... 1561s Setting up python3-pymol (3.1.0+dfsg-1) ... 1562s Setting up python3-fonttools (4.55.3-2build1) ... 1563s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 1563s Setting up python3-matplotlib (3.8.3-7build1) ... 1564s Processing triggers for libc-bin (2.41-1ubuntu2) ... 1564s Processing triggers for man-db (2.13.0-1) ... 1565s Processing triggers for libglib2.0-0t64:amd64 (2.84.0-1) ... 1565s Setting up libgtk-3-0t64:amd64 (3.24.49-2ubuntu1) ... 1565s Processing triggers for udev (257.4-1ubuntu1) ... 1566s Setting up libwxgtk3.2-1t64:amd64 (3.2.6+dfsg-2ubuntu1) ... 1566s Setting up libwxgtk-gl3.2-1t64:amd64 (3.2.6+dfsg-2ubuntu1) ... 1566s Setting up python3-wxgtk4.0 (4.2.2+dfsg-3build1) ... 1567s Setting up python3-cctbx (2024.10+ds2+~3.22.1+ds1-4build2) ... 1569s /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:18: SyntaxWarning: invalid escape sequence '\{' 1569s []_,.;:"&<>()/\{}'`~!@#$%*|+- 1569s /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:46: SyntaxWarning: invalid escape sequence '\/' 1569s special_characters = """[]_,.;:"&<>()\/\{}'`~!@#$%*|+-""" 1578s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:724: SyntaxWarning: invalid escape sequence '\o' 1578s width=pairwise_differences_db, label='$\omega_{hkl}$' 1578s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:739: SyntaxWarning: invalid escape sequence '\o' 1578s axes[0].set_ylabel('Distribution of $\omega_{hbk}$') 1578s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:740: SyntaxWarning: invalid escape sequence '\o' 1578s axes[0].set_xlabel('Normalized PD ($\omega_{hbk}$)') 1578s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:759: SyntaxWarning: invalid escape sequence '\o' 1578s axes[1].set_xlabel('Sorted Normalized PD ($\omega_{hbk}$)') 1578s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:778: SyntaxWarning: invalid escape sequence '\s' 1578s axes[2].set_ylabel('Standard Deviation of $I_{hbk}/\sigma_{hbk}$') 1578s /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:807: SyntaxWarning: invalid escape sequence '\m' 1578s axes_sadd.set_ylabel('$s_{\mathrm{fac}}^2 \\times s_{\mathrm{add}}^2$') 1578s Processing triggers for libc-bin (2.41-1ubuntu2) ... 1595s autopkgtest [13:32:37]: test dxtbx: [----------------------- 1595s Testing dxtbx with python3.13: 1598s Fatal Python error: Segmentation fault 1598s 1598s Current thread 0x00007be92d1f9100 (most recent call first): 1598s File "/usr/lib/python3/dist-packages/cctbx/sgtbx/__init__.py", line 102 in __init__ 1598s File "/usr/lib/python3/dist-packages/cctbx/crystal/__init__.py", line 75 in __init__ 1598s File "/tmp/autopkgtest.gw2uST/autopkgtest_tmp/tests/test_crystal_model_equivalence.py", line 28 in 1598s File "/usr/lib/python3/dist-packages/_pytest/assertion/rewrite.py", line 185 in exec_module 1598s File "", line 935 in _load_unlocked 1598s File "", line 1331 in _find_and_load_unlocked 1598s File "", line 1360 in _find_and_load 1598s File "", line 1387 in _gcd_import 1598s File "/usr/lib/python3.13/importlib/__init__.py", line 88 in import_module 1598s File "/usr/lib/python3/dist-packages/_pytest/pathlib.py", line 587 in import_path 1598s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 493 in importtestmodule 1598s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 546 in _getobj 1598s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 284 in obj 1598s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 562 in _register_setup_module_fixture 1598s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 549 in collect 1598s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389 in collect 1598s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341 in from_call 1598s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 391 in pytest_make_collect_report 1598s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall 1598s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec 1598s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ 1598s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 567 in collect_one_node 1598s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 835 in _collect_one_node 1598s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 970 in genitems 1598s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 975 in genitems 1598s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 975 in genitems 1598s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 809 in perform_collect 1598s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 347 in pytest_collection 1598s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall 1598s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec 1598s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ 1598s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 336 in _main 1598s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 283 in wrap_session 1598s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 330 in pytest_cmdline_main 1598s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall 1598s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec 1598s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ 1598s File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 175 in main 1598s File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 201 in console_main 1598s File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 9 in 1598s File "", line 88 in _run_code 1598s File "", line 198 in _run_module_as_main 1598s 1598s 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) 1601s Segmentation fault (core dumped) 1602s autopkgtest [13:32:44]: test dxtbx: -----------------------] 1602s autopkgtest [13:32:44]: test dxtbx: - - - - - - - - - - results - - - - - - - - - - 1602s dxtbx FAIL non-zero exit status 139 1602s autopkgtest [13:32:44]: @@@@@@@@@@@@@@@@@@@@ summary 1602s cctbx FAIL non-zero exit status 1 1602s dxtbx FAIL non-zero exit status 139 1617s nova [W] Skipping flock for amd64 1617s Creating nova instance adt-plucky-amd64-cctbx-20250322-130601-juju-7f2275-prod-proposed-migration-environment-2-58a8511e-b12f-41e9-8c33-dcebd5980839 from image adt/ubuntu-plucky-amd64-server-20250306.img (UUID 60d877d7-b74c-4f24-920d-f4570db0a338)... 1617s nova [W] Timed out waiting for 17b5ffec-f3fb-4e98-8f34-93609e98cf9f to get deleted. 1617s nova [W] Skipping flock for amd64 1617s Creating nova instance adt-plucky-amd64-cctbx-20250322-130601-juju-7f2275-prod-proposed-migration-environment-2-58a8511e-b12f-41e9-8c33-dcebd5980839 from image adt/ubuntu-plucky-amd64-server-20250306.img (UUID 60d877d7-b74c-4f24-920d-f4570db0a338)... 1617s nova [W] Timed out waiting for 8a145f23-dc85-4d95-aa57-07b6f49f73fc to get deleted.