<div dir="ltr">Hi Markus,<div><br></div><div>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?</div><div><br></div><div>Also, I copied an email below that I sent to phenixdev about the update</div><div><br></div><div><div>Hi all,</div><div><br></div><div>I just checked in some updated packages and Linux packages specific to the GUI. Here is the list of changes.</div><div><br></div><div>- zlib 1.2.7 -> 1.2.8</div><div>- biopython 1.64 -> 1.66</div><div>- sphinx 1.2.2 -> 1.3.5</div><div>- ipython 2.1.0 -> 3.2.1</div><div>- pip 6.0.7 -> 8.0.2</div><div>- py2app 0.7.3 -> 0.9 (Mac)</div><div>- libpng 1.2.52 -> 1.5.26</div><div>- freetype 2.4.2 -> 2.6.3</div><div>- gettext 0.18.2 -> 0.19.7</div><div>- glib 2.12.11 -> 2.46.2</div><div>- expat 1.95.8 -> 2.1.0</div><div>- fontconfig 2.3.95 -> 2.11.1</div><div>- render 0.8 -> 0.11.1</div><div>- xrender 0.8.3 -> 0.9.7</div><div>- xft 2.1.2 -> 2.3.2</div><div>- pixman 0.19.2 -> 0.34.0</div><div>- cairo 1.8.10 -> 1.14.4</div><div>- pango 1.16.1 -> 1.38.1</div><div>- atk 1.9.1 -> 2.18.0</div><div>- libtiff 3.6.1 -> 4.0.6</div><div>- gtk+ 2.10.11 -> 2.24.29</div><div><br></div><div>To use the new dependencies in your Linux builds, you will have to delete your base and base_tmp directories before running bootstrap.py.</div><div><br></div><div>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.</div><div><br></div><div>Let me know if there are any issues. Thanks!</div></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Fri, Jun 10, 2016 at 1:25 AM, <span dir="ltr"><<a href="mailto:markus.gerstel@diamond.ac.uk" target="_blank">markus.gerstel@diamond.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div lang="EN-GB" link="blue" vlink="purple">
<div>
<p class="MsoNormal">Following the latest package updates we are now observing installer failures.<u></u><u></u></p>
<p class="MsoNormal">In particular the configure step appears to fail with a missing
<b><span style="font-size:10.0pt;font-family:"Courier New"">libffi.so.6</span></b><u></u><u></u></p>
<p class="MsoNormal">Any ideas how to rectify this, or if this error can be ignored safely?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">-Markus<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Running with --verbose:<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> ==========================================================================<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> DIALS Installation<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> version: dev20160610<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> machine type: intel-linux-2.6-x86_64<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> OS version: 2.6.32-573.18.1.el6.x86_64<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> destination: /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> # of processors: 24<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> =========================================================================<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">Configuring DIALS components...<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">['/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']<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Python: 2.7.8 "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base/bin/python"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Compiler: default<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Build mode: release<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Warning level: 0<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Precompiled Headers: False<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Static libraries: False<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Static exe: False<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Scan Boost headers: False<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Write full flex_fwd.h files: False<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Build Boost.Python extensions: True<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Define BOOST_PYTHON_NO_PY_SIGNATURES: False<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Define BOOST_PYTHON_BOOL_INT_STRICT: True<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Enable OpenMP if possible: False<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Boost threads enabled: False<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Enable CUDA: False<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Use opt_resources if available: False<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Use environment flags: False<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Enable C++11: False<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Force true division: True<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: command_version_suffix: None<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Relocatable paths anchored at: /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Top-down list of all modules involved:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: prime "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/prime"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: iota "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/iota"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: xia2 "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/xia2"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: mmtbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/mmtbx"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: dials "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/dials"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: xfel "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/xfel"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: cma_es "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cma_es"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: gltbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/gltbx"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: crys3d "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/crys3d"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: rstbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/rstbx"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: spotfinder "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/spotfinder"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: annlib+adaptbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/annlib"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/annlib_adaptbx"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: dxtbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/dxtbx"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: iotbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/iotbx"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: cbflib+adaptbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cbflib"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cbflib_adaptbx"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: ccp4io+adaptbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/ccp4io"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/ccp4io_adaptbx"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: smtbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/smtbx"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: ucif "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/ucif"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: cctbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cctbx"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: chiltbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/chiltbx"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: scitbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/scitbx"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: fable "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/fable"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: omptbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/omptbx"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: boost+adaptbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/boost"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/boost_adaptbx"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: tbxx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/tbxx"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: libtbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Creating files in build directory: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: dispatcher_include_template.sh<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: dispatcher_head.sh<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: setpaths.sh<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: setpaths.csh<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: setpaths_all.sh<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: setpaths_all.csh<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: setpaths_debug.sh<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: unsetpaths.sh<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: setpaths_debug.csh<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: unsetpaths.csh<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: SConstruct<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Makefile<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: run_tests.csh<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/command_line"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/boost_adaptbx/command_line"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/fable/command_line"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/scitbx/command_line"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cctbx/command_line"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/smtbx/command_line"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cbflib_adaptbx/command_line"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/iotbx/command_line"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/dxtbx/command_line"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/spotfinder/command_line"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/rstbx/command_line"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/crys3d/command_line"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/gltbx/command_line"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/xfel/command_line"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/xfel/ui/command_line"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/dials/command_line"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/mmtbx/command_line"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/xia2/command_line"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/iota/command_line"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/prime/command_line"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/scitbx/libtbx_refresh.py"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Generating C++ header files in:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/include/scitbx/array_family"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Generating C++ files in:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/include/scitbx/array_family/boost_python"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Using fable to convert scitbx/lbfgs.f<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cctbx/libtbx_refresh.py"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Generating C++ files in:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/cctbx/eltbx"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Generating C++ files in:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/include/cctbx/boost_python"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/smtbx/libtbx_refresh.py"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Generating C++ files in:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/include/smtbx/boost_python"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cbflib_adaptbx/libtbx_refresh.py"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Copying to lib: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cbflib/pycbf/pycbf.py"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/iotbx/libtbx_refresh.py"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Using fable to convert iotbx/pdb/hybrid_36_f.f<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Writing: iotbx/pdb/hybrid_36_fem.cpp<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/annlib_adaptbx/libtbx_refresh.py"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Generating C++ files for self-inclusive approximate nearest neighbor<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/crys3d/libtbx_refresh.py"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/gltbx/libtbx_refresh.py"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Generating C++ files in:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/gltbx"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Info: Re-using existing font cpp files.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Hint: Remove gltbx/FONTS_UCS_DONE_FLAG_FILE<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: to force generation of new font files.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/xfel/libtbx_refresh.py"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Creating cxi_user directory<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Creating cxi_user/__init__.py<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/dials/libtbx_refresh.py"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: DIALS 1.dev.360-ge6510c8<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: 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<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Installing autocompletion script into: setpaths_all.sh setpaths_debug.sh setpaths.sh<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/mmtbx/libtbx_refresh.py"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/xia2/libtbx_refresh.py"<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: XIA2 0.4.0.381-g9b3a992<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/exe_dev"<u></u><u></u></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Courier New"">: Regenerating module files in /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base<u></u><u></u></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Courier New"">: /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base/etc/pango not present, could not regenerate pango files<u></u><u></u></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Courier New"">: generating gtk.immodules file<u></u><u></u></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Courier New"">: /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<u></u><u></u></span></b></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: Traceback (most recent call last):<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/configure.py", line 22, in <module><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: if not run():<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/configure.py", line 17, in run<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: libtbx.env_config.cold_start(sys.argv)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/env_config.py", line 2264, in cold_start<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: env.refresh()<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/env_config.py", line 1537, in refresh<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: regenerate_module_files.run(libtbx.env.under_base('.'), only_if_needed=True)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/auto_build/regenerate_module_files.py", line 154, in
run<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: fix_gtk(base_dir, out)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: 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<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: log=out)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/auto_build/installer_utils.py", line 81, in call<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc))<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">: 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<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">Traceback (most recent call last):<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> File "./bin/install.py", line 97, in <module><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> installer(sys.argv[1:]).install()<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> File "/scratch/jenkins_slave/workspace/dials_install_dls_module/dials-installer-dev/lib/libtbx/auto_build/install_distribution.py", line 197, in install<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> self.install_from_binary()<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> 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<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> self.reconfigure(log=log)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> File "/scratch/jenkins_slave/workspace/dials_install_dls_module/dials-installer-dev/lib/libtbx/auto_build/install_distribution.py", line 484, in reconfigure<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> call(args=args, log=log, verbose=self.options.verbose)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> File "/scratch/jenkins_slave/workspace/dials_install_dls_module/dials-installer-dev/lib/libtbx/auto_build/installer_utils.py", line 81, in call<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc))<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">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<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span>Markus Gerstel MBCS<u></u><u></u></span></p>
<p class="MsoNormal"><span>Postdoctoral Research Associate<u></u><u></u></span></p>
<p class="MsoNormal"><span>Tel: <a href="tel:%2B44%201235%20778698" value="+441235778698" target="_blank">+44 1235 778698</a><u></u><u></u></span></p>
<p class="MsoNormal"><span><u></u> <u></u></span></p>
<p class="MsoNormal"><span>Diamond Light Source Ltd.<u></u><u></u></span></p>
<p class="MsoNormal"><span>Diamond House<u></u><u></u></span></p>
<p class="MsoNormal"><span>Harwell Science & Innovation Campus<u></u><u></u></span></p>
<p class="MsoNormal"><span>Didcot<u></u><u></u></span></p>
<p class="MsoNormal"><span>Oxfordshire<u></u><u></u></span></p>
<p class="MsoNormal"><span>OX11 0DE<span class="HOEnZb"><font color="#888888"><u></u><u></u></font></span></span></p><span class="HOEnZb"><font color="#888888">
<p class="MsoNormal"><u></u> <u></u></p>
</font></span></div><span class="HOEnZb"><font color="#888888">
<p align="justify"> </p>
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