[cctbxbb] Installation failure after package updates

Billy Poon bkpoon at lbl.gov
Fri Jun 10 09:10:22 PDT 2016 

Hi Markus,

The libffi dependency is built with glib (build_glib function in
install_base_packages.py). Did you delete your base and base_tmp
directories before rebuilding?

Also, I copied an email below that I sent to phenixdev about the update

Hi all,

I just checked in some updated packages and Linux packages specific to the
GUI. Here is the list of changes.

- zlib 1.2.7 -> 1.2.8
- biopython 1.64 -> 1.66
- sphinx 1.2.2 -> 1.3.5
- ipython 2.1.0 -> 3.2.1
- pip 6.0.7 -> 8.0.2
- py2app 0.7.3 -> 0.9 (Mac)
- libpng 1.2.52 -> 1.5.26
- freetype 2.4.2 -> 2.6.3
- gettext 0.18.2 -> 0.19.7
- glib 2.12.11 -> 2.46.2
- expat 1.95.8 -> 2.1.0
- fontconfig 2.3.95 -> 2.11.1
- render 0.8 -> 0.11.1
- xrender 0.8.3 -> 0.9.7
- xft 2.1.2 -> 2.3.2
- pixman 0.19.2 -> 0.34.0
- cairo 1.8.10 -> 1.14.4
- pango 1.16.1 -> 1.38.1
- atk 1.9.1 -> 2.18.0
- libtiff 3.6.1 -> 4.0.6
- gtk+ 2.10.11 -> 2.24.29

To use the new dependencies in your Linux builds, you will have to delete
your base and base_tmp directories before running bootstrap.py.

I have tested the build from bootstrap.py on CentOS 5.11 (32-bit and
64-bit), 6.8, 7.2, Ubuntu 12.04.5, 14.04.4, 16.04, and OS X 10.10.5.

Let me know if there are any issues. Thanks!

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org

On Fri, Jun 10, 2016 at 1:25 AM, <markus.gerstel at diamond.ac.uk> wrote:

> 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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