- cctbxbb - phenix-online.org

rpath problem on Mac system
by Haiguang Liu 21 Sep '16

21 Sep '16

Dear CCTBX developing team, Is there already a solution for the run path problem in the new Mac OS? The System Integrity Protection <https://support.apple.com/en-us/HT204899> does not allow relative run path. I temporarily disabled this feature to run the programs that requires boost (for example). If there is already a solution, please let me know. Thanks, Haiguang

3 4

Python 2.4 compatibility
by richard.gildea＠diamond.ac.uk 16 Sep '16

16 Sep '16

This commit uses the "with" statement, which was introduced in Python 2.5, to libtbx/__init__.py, preventing installation of DIALS from sources on systems with Python 2.4: https://sourceforge.net/p/cctbx/code/25101/ Could this code be changed to remove the use of the "with" statement? Cheers, Richard Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078 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

3 5

failing test with CCP4 7.0.18
by markus.gerstel＠diamond.ac.uk 16 Sep '16

16 Sep '16

Hi, The test libtbx.python $(libtbx.find_in_repositories cctbx/development/run_shelx.py) P31 works with CCP4 7.0.17, but fails when run with SHELXL from CCP4 7.0.18. The test apparently involves creating a small random crystal structure, calculating the structure factors and solving the structure using SHELXL. The updated SHELXL version creates deterministic, but slightly different anisotropic temperature factors. I am not sure if this is a problem with the test or with the SHELXL update. Could anybody have a look into that? -Markus -- 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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Re: [cctbxbb] [Cctbx-cvs] SF.net SVN: cctbx:[25333] trunk/libtbx/env_config.py
by markus.gerstel＠diamond.ac.uk 09 Sep '16

09 Sep '16

Hi, I just spent some time tracking software crashes to this change. Is setting the default to en_US really appropriate and what we want? In particular it affects the output of downstream, external software we run from within python. What is the unicode issue you hint at in the commit message? -Markus Dr Markus Gerstel MBCS Postdoctoral Research Associate Tel: +44 1235 778698 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE -----Original Message----- From: bkpoon(a)users.sourceforge.net [mailto:[email protected]] Sent: 07 September 2016 00:54 To: cctbx-cvs(a)lists.sourceforge.net Subject: [Cctbx-cvs] SF.net SVN: cctbx:[25333] trunk/libtbx/env_config.py Revision: 25333 http://sourceforge.net/p/cctbx/code/25333 Author: bkpoon Date: 2016-09-06 23:54:29 +0000 (Tue, 06 Sep 2016) Log Message: ----------- Unicode support: set LC_ALL in dispatchers to the one in the user's environment (if available, and supports UTF-8), otherwise use the default setting of en_US.UTF-8; fixes unicode issue with python in Linux (e.g. os.path functions do not work correctly with unicode if LC_ALL=C Modified Paths: -------------- trunk/libtbx/env_config.py Modified: trunk/libtbx/env_config.py =================================================================== --- trunk/libtbx/env_config.py 2016-09-06 21:15:34 UTC (rev 25332) +++ trunk/libtbx/env_config.py 2016-09-06 23:54:29 UTC (rev 25333) @@ -945,6 +945,15 @@ def write_bin_sh_dispatcher(self, source_file, target_file, source_is_python_exe=False): + + # determine LC_ALL from environment (Python UTF-8 compatibility in Linux) + LC_ALL = os.environ.get('LC_ALL') # user setting + if (LC_ALL is not None): + if ( ('UTF-8' not in LC_ALL) and ('utf8' not in LC_ALL) ): + LC_ALL = None + if (LC_ALL is None): + LC_ALL = 'en_US.UTF-8' # default + f = target_file.open("w") if (source_file is not None): print >> f, '#! /bin/sh' @@ -975,7 +984,7 @@ print >> f, '#' print >> f, _SHELLREALPATH_CODE print >> f, 'unset PYTHONHOME' - print >> f, 'LC_ALL=C' + print >> f, 'LC_ALL=' + LC_ALL print >> f, 'export LC_ALL' print >> f, 'LIBTBX_BUILD="$(shellrealpath "$0" && cd "$(dirname "$RESULT")/.." && pwd)"' print >> f, 'export LIBTBX_BUILD' This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. ------------------------------------------------------------------------------ _______________________________________________ Cctbx-cvs mailing list Cctbx-cvs(a)lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cctbx-cvs -- 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

2 3

Inserting F000 into reflection (mtg) file
by Nicholas Pearce 22 Aug '16

22 Aug '16

Hi Everyone, I’ve been looking through the cctbx/phenix scripts and although there’s a script for estimating F000 (phenix.f000), I can’t find any way of inserting it into an mtz file to make it accessible for easy map generation. Is this implemented anywhere/what do people use as the best way of doing this? If the insertion of F000 into an mtz file has been purposefully avoided, I presume it's done because we don't want the possibility of someone refining a model where F000 is used in refinement. Unless there’s another reason? Thanks, Nick

2 1

Git
by Graeme.Winter＠diamond.ac.uk 01 Aug '16

01 Aug '16

Folks, Can we revisit the idea of moving to git for cctbx? Thanks Graeme -- 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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Structure Factor for 000
by Gareth.Nisbet＠diamond.ac.uk 28 Jul '16

28 Jul '16

Is it possible to get the structure_factors function to give the structure factor for the 000 reflection? I appreciate this might be a slightly odd question. Gareth -- 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

3 3

Berkeley Server Downtime (24 hours, 7/22 - 7/23)
by Billy Poon 20 Jul '16

20 Jul '16

Dear all, On Friday, July 22, our servers will be shut down starting at 5:00 pm Pacific for scheduled maintenance in our building. We expect that the servers will be available the next day (7/23) by 5:00 pm Pacific at the latest. This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- 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

1 0

Re: [cctbxbb] Git
by R. D. Oeffner 02 Jul '16

02 Jul '16

How often is this git repo of cctbx copied from the svn repo of cctbx? Rob -----Original Message----- From: cctbxbb-request(a)phenix-online.org Sent: Friday, July 1, 2016 8:00 PM To: cctbxbb(a)phenix-online.org Subject: cctbxbb Digest, Vol 88, Issue 1 Send cctbxbb mailing list submissions to cctbxbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit http://phenix-online.org/mailman/listinfo/cctbxbb or, via email, send a message with subject or body 'help' to cctbxbb-request(a)phenix-online.org You can reach the person managing the list at cctbxbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of cctbxbb digest..." Today's Topics: 1. Re: Git (markus.gerstel(a)diamond.ac.uk) ---------------------------------------------------------------------- Message: 1 Date: Fri, 1 Jul 2016 12:34:56 +0000 From: <markus.gerstel(a)diamond.ac.uk> To: <cctbxbb(a)phenix-online.org> Subject: Re: [cctbxbb] Git Message-ID: <415F7F573406BB498256C68158D45674666211BB@exchmbx01> Content-Type: text/plain; charset="utf-8" Hello everyone, Following up the earlier discussion, do have we reached a consensus? Also, I think timeframe has not been discussed, but I assume this will boil down to ?after phenix release? anyway. In the meantime I have contacted (nearly) all cctbx developers and obtained their github user-IDs - alongside some enthusiastic* feedback. I will mass-invite you all soonishly to a cctbx organisation with a preliminary git copy of the svn history to play with. 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 * The best comment I received was ?What?s CCTBX?? ? and that was talking to the correct person :) (name withheld) -- 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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Installation failure after package updates
by markus.gerstel＠diamond.ac.uk 27 Jun '16

27 Jun '16

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. 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