[cctbxbb] Installation failure after package updates
markus.gerstel at diamond.ac.uk
markus.gerstel at diamond.ac.uk
Fri Jun 10 01:25:03 PDT 2016
Following the latest package updates we are now observing installer failures.
In particular the configure step appears to fail with a missing libffi.so.6
Any ideas how to rectify this, or if this error can be ignored safely?
-Markus
Running with --verbose:
==========================================================================
DIALS Installation
version: dev20160610
machine type: intel-linux-2.6-x86_64
OS version: 2.6.32-573.18.1.el6.x86_64
destination: /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610
# of processors: 24
=========================================================================
Configuring DIALS components...
/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build
['/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base/bin/python', '/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/configure.py', '--current_working_directory', '/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build', 'dials', 'xia2', 'iota', 'prime']
: Python: 2.7.8 "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base/bin/python"
: Compiler: default
: Build mode: release
: Warning level: 0
: Precompiled Headers: False
: Static libraries: False
: Static exe: False
: Scan Boost headers: False
: Write full flex_fwd.h files: False
: Build Boost.Python extensions: True
: Define BOOST_PYTHON_NO_PY_SIGNATURES: False
: Define BOOST_PYTHON_BOOL_INT_STRICT: True
: Enable OpenMP if possible: False
: Boost threads enabled: False
: Enable CUDA: False
: Use opt_resources if available: False
: Use environment flags: False
: Enable C++11: False
: Force true division: True
: command_version_suffix: None
: Relocatable paths anchored at: /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build
: Top-down list of all modules involved:
: prime "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/prime"
: iota "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/iota"
: xia2 "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/xia2"
: mmtbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/mmtbx"
: dials "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/dials"
: xfel "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/xfel"
: cma_es "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cma_es"
: gltbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/gltbx"
: crys3d "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/crys3d"
: rstbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/rstbx"
: spotfinder "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/spotfinder"
: annlib+adaptbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/annlib"
: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/annlib_adaptbx"
: dxtbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/dxtbx"
: iotbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/iotbx"
: cbflib+adaptbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cbflib"
: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cbflib_adaptbx"
: ccp4io+adaptbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/ccp4io"
: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/ccp4io_adaptbx"
: smtbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/smtbx"
: ucif "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/ucif"
: cctbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cctbx"
: chiltbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/chiltbx"
: scitbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/scitbx"
: fable "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/fable"
: omptbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/omptbx"
: boost+adaptbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/boost"
: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/boost_adaptbx"
: tbxx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/tbxx"
: libtbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx"
: Creating files in build directory: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build"
: dispatcher_include_template.sh
: dispatcher_head.sh
: setpaths.sh
: setpaths.csh
: setpaths_all.sh
: setpaths_all.csh
: setpaths_debug.sh
: unsetpaths.sh
: setpaths_debug.csh
: unsetpaths.csh
: SConstruct
: Makefile
: run_tests.csh
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/command_line"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/boost_adaptbx/command_line"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/fable/command_line"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/scitbx/command_line"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cctbx/command_line"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/smtbx/command_line"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cbflib_adaptbx/command_line"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/iotbx/command_line"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/dxtbx/command_line"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/spotfinder/command_line"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/rstbx/command_line"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/crys3d/command_line"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/gltbx/command_line"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/xfel/command_line"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/xfel/ui/command_line"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/dials/command_line"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/mmtbx/command_line"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/xia2/command_line"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/iota/command_line"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/prime/command_line"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/scitbx/libtbx_refresh.py"
: Generating C++ header files in:
: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/include/scitbx/array_family"
: Generating C++ files in:
: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/include/scitbx/array_family/boost_python"
: Using fable to convert scitbx/lbfgs.f
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cctbx/libtbx_refresh.py"
: Generating C++ files in:
: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/cctbx/eltbx"
: Generating C++ files in:
: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/include/cctbx/boost_python"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/smtbx/libtbx_refresh.py"
: Generating C++ files in:
: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/include/smtbx/boost_python"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cbflib_adaptbx/libtbx_refresh.py"
: Copying to lib: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cbflib/pycbf/pycbf.py"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/iotbx/libtbx_refresh.py"
: Using fable to convert iotbx/pdb/hybrid_36_f.f
: Writing: iotbx/pdb/hybrid_36_fem.cpp
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/annlib_adaptbx/libtbx_refresh.py"
: Generating C++ files for self-inclusive approximate nearest neighbor
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/crys3d/libtbx_refresh.py"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/gltbx/libtbx_refresh.py"
: Generating C++ files in:
: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/gltbx"
: Info: Re-using existing font cpp files.
: Hint: Remove gltbx/FONTS_UCS_DONE_FLAG_FILE
: to force generation of new font files.
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/xfel/libtbx_refresh.py"
: Creating cxi_user directory
: Creating cxi_user/__init__.py
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/dials/libtbx_refresh.py"
: DIALS 1.dev.360-ge6510c8
: Identifying autocompletable commands: dials.analyse_background dials.combine_found_spots dials.find_spots dials.index dials.integrate dials.reciprocal_lattice_viewer dials.refine dials.reindex dials.rl_png
: Installing autocompletion script into: setpaths_all.sh setpaths_debug.sh setpaths.sh
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/mmtbx/libtbx_refresh.py"
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/xia2/libtbx_refresh.py"
: XIA2 0.4.0.381-g9b3a992
: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/exe_dev"
: Regenerating module files in /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base
: /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base/etc/pango not present, could not regenerate pango files
: generating gtk.immodules file
: /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base/bin/gtk-query-immodules-2.0: error while loading shared libraries: libffi.so.6: cannot open shared object file: No such file or directory
: Traceback (most recent call last):
: File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/configure.py", line 22, in <module>
: if not run():
: File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/configure.py", line 17, in run
: libtbx.env_config.cold_start(sys.argv)
: File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/env_config.py", line 2264, in cold_start
: env.refresh()
: File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/env_config.py", line 1537, in refresh
: regenerate_module_files.run(libtbx.env.under_base('.'), only_if_needed=True)
: File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/auto_build/regenerate_module_files.py", line 154, in run
: fix_gtk(base_dir, out)
: File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/auto_build/regenerate_module_files.py", line 72, in fix_gtk
: log=out)
: File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/auto_build/installer_utils.py", line 81, in call
: raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc))
: RuntimeError: Call to '/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base/bin/gtk-query-immodules-2.0 /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base/lib/gtk-2.0/2.10.0/immodules/*.so> /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base/etc/gtk-2.0/gtk.immodules' failed with exit code 127
Traceback (most recent call last):
File "./bin/install.py", line 97, in <module>
installer(sys.argv[1:]).install()
File "/scratch/jenkins_slave/workspace/dials_install_dls_module/dials-installer-dev/lib/libtbx/auto_build/install_distribution.py", line 197, in install
self.install_from_binary()
File "/scratch/jenkins_slave/workspace/dials_install_dls_module/dials-installer-dev/lib/libtbx/auto_build/install_distribution.py", line 318, in install_from_binary
self.reconfigure(log=log)
File "/scratch/jenkins_slave/workspace/dials_install_dls_module/dials-installer-dev/lib/libtbx/auto_build/install_distribution.py", line 484, in reconfigure
call(args=args, log=log, verbose=self.options.verbose)
File "/scratch/jenkins_slave/workspace/dials_install_dls_module/dials-installer-dev/lib/libtbx/auto_build/installer_utils.py", line 81, in call
raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc))
RuntimeError: Call to '/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base/bin/python /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/configure.py --current_working_directory /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build dials xia2 iota prime' failed with exit code 1
Markus Gerstel MBCS
Postdoctoral Research Associate
Tel: +44 1235 778698
Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE
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