Hi Billy, Yes, this is from a completely clean working directory. So far all I could find out is that the installer works as expected when it is being run on the same machine as the build. As part of our build pipeline we also pass the installer on to another machine and that is when the installer crashes. Since all our machines have completely identical operating systems I suspect that absolute paths are involved somehow. -Markus Markus Gerstel MBCS Postdoctoral Research Associate Tel: +44 1235 778698 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE From: [email protected] [mailto:[email protected]] On Behalf Of Billy Poon Sent: 10 June 2016 17:10 To: cctbx mailing list Subject: Re: [cctbxbb] Installation failure after package updates 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, mailto:[email protected]> 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 778698tel:%2B44%201235%20778698 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom _______________________________________________ cctbxbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

Hi Markus, I just checked in a fix. I updated the LD_LIBRARY_PATH to include base/lib64 so that libffi is found. I also updated the path for the gdk-pixbuf loaders. Also, pango should not need to rebuild its modules anymore. Let me know if you have any other 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 9:44 AM, Billy Poon wrote:

Hi Markus,

It looks like libffi installed in base/lib64 and the installer is having issues with that. I'll get that fixed today. 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 9:17 AM, wrote:

...

Hi Billy,

Yes, this is from a completely clean working directory.

So far all I could find out is that the installer works as expected when it is being run on the same machine as the build. As part of our build pipeline we also pass the installer on to another machine and that is when the installer crashes. Since all our machines have completely identical operating systems I suspect that absolute paths are involved somehow.

-Markus

Markus Gerstel MBCS

Postdoctoral Research Associate

Tel: +44 1235 778698

Diamond Light Source Ltd.

Diamond House

Harwell Science & Innovation Campus

Didcot

Oxfordshire

OX11 0DE

*From:* [email protected] [mailto: [email protected]] *On Behalf Of *Billy Poon *Sent:* 10 June 2016 17:10 *To:* cctbx mailing list *Subject:* Re: [cctbxbb] Installation failure after package updates

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, 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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This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

Hi Markus, I just checked in the update for Sphinx to 1.4.4. -- 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 Mon, Jun 27, 2016 at 3:30 AM, wrote:

Hi Billy,

We just identified another dependency issue, which was masked by us not checking exit codes…

The DIALS documentation does no longer build with sphinx 1.3.5.

It does with the previous version 1.2.2 and with the current stable release 1.4.4.

Can we revert to the old version or skip to the current version?

Best wishes

-Markus

Markus Gerstel MBCS

Postdoctoral Research Associate

Tel: +44 1235 778698

Diamond Light Source Ltd.

Diamond House

Harwell Science & Innovation Campus

Didcot

Oxfordshire

OX11 0DE

*From:* [email protected] [mailto: [email protected]] *On Behalf Of *Billy Poon *Sent:* 10 June 2016 22:01 *To:* cctbx mailing list *Subject:* Re: [cctbxbb] Installation failure after package updates

Hi Markus,

(..)

Let me know if you have any other 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

--

This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb