========================================================================== DIALS Installation version: dev-9 machine type: intel-linux-2.6 OS version: 2.6.32-49-generic-pae user shell: /bin/tcsh destination: /scratch/builder/dials_tmp # of processors: 8 ========================================================================= No binary bundles found for intel-linux-2.6 Okay, this must be the source-only installer. DIALS installation target directory set to: /scratch/builder/dials_tmp/dials-dev-9 DIALS installation source directory set to: /scratch/builder/dials_tmp/dials-installer-dev-9 DIALS installation build directory set to: /scratch/builder/dials_tmp/dials-dev-9/build/intel-linux-2.6 DIALS temporary build directory set to: /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1 **************************************************************************** Automated CCTBX dependencies build script report problems to cctbx-dev@cci.lbl.gov **************************************************************************** Setting up directories... creating /scratch/builder/dials_tmp/dials-dev-9/build/intel-linux-2.6/base *** Building dependencies first *** -------------------------------------------------------------------------------- Installing Python... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/Python_install_log getting package Python-2.7.6_cci.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/Python-2.7.6_cci.tar.gz verifying Python installation... OK -------------------------------------------------------------------------------- Installing numpy... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/numpy_install_log getting package numpy-1.8.1.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/numpy-1.8.1.tar.gz verifying numpy installation... OK -------------------------------------------------------------------------------- Installing BioPython... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/BioPython_install_log getting package biopython-1.64.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/biopython-1.64.tar.gz verifying BioPython installation... OK -------------------------------------------------------------------------------- Installing Freetype... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/Freetype_install_log getting package freetype-2.4.2.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/freetype-2.4.2.tar.gz -------------------------------------------------------------------------------- Installing Imaging... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/Imaging_install_log getting package Imaging-1.1.7.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/Imaging-1.1.7.tar.gz verifying Imaging installation... OK -------------------------------------------------------------------------------- Installing reportlab... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/reportlab_install_log getting package reportlab-2.6.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/reportlab-2.6.tar.gz verifying reportlab installation... OK -------------------------------------------------------------------------------- Installing HDF5... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/HDF5_install_log getting package hdf5-1.8.8.tar.bz2... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/hdf5-1.8.8.tar.bz2 getting package h5py-2.0.1-edit.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/h5py-2.0.1-edit.tar.gz verifying h5py installation... OK -------------------------------------------------------------------------------- Installing libpng... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/libpng_install_log getting package libpng-1.2.32.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/libpng-1.2.32.tar.gz -------------------------------------------------------------------------------- Installing gettext... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/gettext_install_log getting package gettext-0.18.2.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/gettext-0.18.2.tar.gz -------------------------------------------------------------------------------- Installing glib... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/glib_install_log getting package glib-2.12.11.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/glib-2.12.11.tar.gz -------------------------------------------------------------------------------- Installing expat... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/expat_install_log getting package expat-1.95.8.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/expat-1.95.8.tar.gz -------------------------------------------------------------------------------- Installing fontconfig... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/fontconfig_install_log getting package fontconfig-2.3.95.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/fontconfig-2.3.95.tar.gz -------------------------------------------------------------------------------- Installing render... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/render_install_log getting package render-0.8.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/render-0.8.tar.gz -------------------------------------------------------------------------------- Installing Xrender... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/Xrender_install_log getting package xrender-0.8.3.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/xrender-0.8.3.tar.gz -------------------------------------------------------------------------------- Installing Xft... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/Xft_install_log getting package xft-2.1.2.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/xft-2.1.2.tar.gz -------------------------------------------------------------------------------- Installing pixman... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/pixman_install_log getting package pixman-0.19.2.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/pixman-0.19.2.tar.gz -------------------------------------------------------------------------------- Installing cairo... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/cairo_install_log getting package cairo-1.8.10.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/cairo-1.8.10.tar.gz -------------------------------------------------------------------------------- Installing pango... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/pango_install_log getting package pango-1.16.1.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/pango-1.16.1.tar.gz -------------------------------------------------------------------------------- Installing atk... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/atk_install_log getting package atk-1.9.1.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/atk-1.9.1.tar.gz -------------------------------------------------------------------------------- Installing tiff... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/tiff_install_log getting package tiff-v3.6.1.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/tiff-v3.6.1.tar.gz -------------------------------------------------------------------------------- Installing gtk+... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/gtk+_install_log getting package gtk+-2.10.11.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/gtk+-2.10.11.tar.gz -------------------------------------------------------------------------------- Installing gtk-engine... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/gtk-engine_install_log getting package clearlooks-0.5.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/clearlooks-0.5.tar.gz -------------------------------------------------------------------------------- Installing fonts... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/fonts_install_log getting package fonts.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/fonts.tar.gz -------------------------------------------------------------------------------- Installing wxPython... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/wxPython_install_log getting package wxPython-src-2.8.12.1.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/wxPython-src-2.8.12.1.tar.gz building wxWidgets with options: --disable-mediactrl --with-opengl --prefix="/scratch/builder/dials_tmp/dials-dev-9/build/intel-linux-2.6/base" --enable-optimize --disable-debugreport --with-gtk --with-gtk-prefix="/scratch/builder/dials_tmp/dials-dev-9/build/intel-linux-2.6/base" --with-gtk-exec-prefix="/scratch/builder/dials_tmp/dials-dev-9/build/intel-linux-2.6/base/lib" --enable-graphics_ctx building wxPython with options: BUILD_GLCANVAS=1 BUILD_STC=0 BUILD_GIZMOS=0 BUILD_DLLWIDGET=0 BUILD_OGL=0 UNICODE=0 verifying wxPython installation... OK -------------------------------------------------------------------------------- Installing PyRTF... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/PyRTF_install_log getting package PyRTF-0.45.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/PyRTF-0.45.tar.gz verifying PyRTF installation... OK -------------------------------------------------------------------------------- Installing Matplotlib... log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/Matplotlib_install_log getting package matplotlib-1.3.1.tar.gz... using /scratch/builder/dials_tmp/dials-installer-dev-9/dependencies/matplotlib-1.3.1.tar.gz verifying Matplotlib installation... OK -------------------------------------------------------------------------------- Dependencies finished building. ****************************** * BASE INSTALLATION COMPLETE * ****************************** -------------------------------------------------------------------------------- Building core DIALS components unwrapping cctbx_bundle.tar.gz... unwrapping dials.tar.gz... unwrapping cbflib.tar.gz... unwrapping annlib.tar.gz... unwrapping annlib_adaptbx.tar.gz... configuring DIALS components with optimization... ok compiling DIALS components - this might take an hour... done ******************************* * DIALS INSTALLATION COMPLETE * ******************************* ************************************************************************ FINALIZING DIALS INSTALLATION log file is /scratch/builder/dials_tmp/dials-installer-dev-9/install_tmp/intel-linux-2.6/cci-vm-1/install_finalize.log generating pangorc file generating pango.modules file generating gtk.immodules file generating gdk-pixbuf.loaders file updating fonts/local.conf file running mkfontdir Couldn't determine weight for Vera.pfa Couldn't determine weight for VeraMono.pfa rebuilding font cache /scratch/builder/dials_tmp/dials-dev-9/build/intel-linux-2.6/base/bin/fc-cache: "/scratch/builder/dials_tmp/dials-dev-9/build/intel-linux-2.6/base/share/fonts": caching, 12 fonts, 0 dirs /scratch/builder/dials_tmp/dials-dev-9/build/intel-linux-2.6/base/bin/fc-cache: succeeded generating index.theme file generating DIALS environment additions for dispatchers generating DIALS environment setup scripts: csh: /scratch/builder/dials_tmp/dials-dev-9/dials_env.csh sh: /scratch/builder/dials_tmp/dials-dev-9/dials_env.sh configuring DIALS components... precompiling .py files... ok Updating build directory... ok /scratch/builder/dials_tmp/dials-installer-dev-9/lib Setting rpath in shared libraries... Copying dependencies... Copying base modules... copying annlib_adaptbx... copying boost... copying ccp4io_adaptbx... copying annlib... copying dials... copying cctbx_project... copying opt_resources... copying scons... copying gui_resources... copying lapack_fem... copying ccp4io... copying cbflib... copying clipper... copying tntbx... created base bundle /scratch/builder/dials_tmp/dials-installer-dev-9/bundles/base-dev-9-intel-linux-2.6.tar.gz created bundle /scratch/builder/dials_tmp/dials-installer-dev-9/bundles/bundle-dev-9-intel-linux-2.6.tar.gz