murpholinox

phenix in manjaro round 2.2

Feb 6th, 2017
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  1. [fmp@eva03 ~]$ su
  2. Contraseña:
  3. [eva03 fmp]# rm -rf /usr/local/phenix-dev-2666/
  4. [eva03 fmp]# cd Descargas/
  5. [eva03 Descargas]# cd phenix-installer-dev-2666-intel-linux-2.6-x86_64-centos6
  6. [eva03 phenix-installer-dev-2666-intel-linux-2.6-x86_64-centos6]# ./install
  7.  
  8. ==========================================================================
  9. Phenix Installation
  10.  
  11. version: dev-2666
  12. machine type: intel-linux-2.6-x86_64
  13. OS version: 4.4.33-1-MANJARO
  14. destination: /usr/local/phenix-dev-2666
  15. # of processors: 4
  16. =========================================================================
  17.  
  18. Configuring Phenix components...
  19. Traceback (most recent call last):
  20. File "./bin/install.py", line 275, in <module>
  21. installer(sys.argv[1:]).install()
  22. File "/home/fmp/Descargas/phenix-installer-dev-2666-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 197, in install
  23. self.install_from_binary()
  24. File "/home/fmp/Descargas/phenix-installer-dev-2666-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 319, in install_from_binary
  25. self.reconfigure(log=log)
  26. File "/home/fmp/Descargas/phenix-installer-dev-2666-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 485, in reconfigure
  27. call(args=args, log=log, verbose=self.options.verbose)
  28. File "/home/fmp/Descargas/phenix-installer-dev-2666-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/installer_utils.py", line 81, in call
  29. raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc))
  30. RuntimeError: Call to '/usr/local/phenix-dev-2666/base/bin/python /usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/configure.py --current_working_directory /usr/local/phenix-dev-2666/build --command_version_suffix dev-2666 phenix phaser solve_resolve labelit dials xia2 iota prime' failed with exit code 1
  31. [eva03 phenix-installer-dev-2666-intel-linux-2.6-x86_64-centos6]# cd /usr/local/phenix-dev-2666/
  32. [eva03 phenix-dev-2666]# cd build/
  33. [eva03 build]# /usr/local/phenix-dev-2666/base/bin/python /usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/configure.py --current_working_directory /usr/local/phenix-dev-2666/build --command_version_suffix dev-2666 phenix phaser solve_resolve labelit dials xia2 iota prime
  34. Python: 2.7.8 "/usr/local/phenix-dev-2666/base/bin/python"
  35. Compiler: default
  36. Build mode: release
  37. Warning level: 0
  38. Precompiled Headers: False
  39. Static libraries: False
  40. Static exe: False
  41. Scan Boost headers: False
  42. Write full flex_fwd.h files: False
  43. Build Boost.Python extensions: True
  44. Define BOOST_PYTHON_NO_PY_SIGNATURES: False
  45. Define BOOST_PYTHON_BOOL_INT_STRICT: True
  46. Enable OpenMP if possible: False
  47. Boost threads enabled: False
  48. Enable CUDA: False
  49. Use opt_resources if available: False
  50. Use environment flags: False
  51. Enable C++11: False
  52. Force true division: True
  53. command_version_suffix: dev-2666
  54. Relocatable paths anchored at: /usr/local/phenix-dev-2666/build
  55. Top-down list of all modules involved:
  56. prime "/usr/local/phenix-dev-2666/modules/cctbx_project/prime"
  57. iota "/usr/local/phenix-dev-2666/modules/cctbx_project/iota"
  58. xia2 "/usr/local/phenix-dev-2666/modules/xia2"
  59. dials "/usr/local/phenix-dev-2666/modules/dials"
  60. xfel "/usr/local/phenix-dev-2666/modules/cctbx_project/xfel"
  61. cma_es "/usr/local/phenix-dev-2666/modules/cctbx_project/cma_es"
  62. labelit "/usr/local/phenix-dev-2666/modules/labelit"
  63. rstbx "/usr/local/phenix-dev-2666/modules/cctbx_project/rstbx"
  64. spotfinder "/usr/local/phenix-dev-2666/modules/cctbx_project/spotfinder"
  65. annlib+adaptbx "/usr/local/phenix-dev-2666/modules/annlib"
  66. "/usr/local/phenix-dev-2666/modules/annlib_adaptbx"
  67. phenix "/usr/local/phenix-dev-2666/modules/phenix"
  68. reel "/usr/local/phenix-dev-2666/modules/reel"
  69. wxtbx "/usr/local/phenix-dev-2666/modules/cctbx_project/wxtbx"
  70. phaser "/usr/local/phenix-dev-2666/modules/phaser"
  71. phaser_regression "/usr/local/phenix-dev-2666/modules/phaser_regression"
  72. tntbx "/usr/local/phenix-dev-2666/modules/tntbx"
  73. solve_resolve "/usr/local/phenix-dev-2666/modules/solve_resolve"
  74. muscle "/usr/local/phenix-dev-2666/modules/muscle"
  75. ksdssp "/usr/local/phenix-dev-2666/modules/ksdssp"
  76. pulchra "/usr/local/phenix-dev-2666/modules/pulchra"
  77. phenix_html "/usr/local/phenix-dev-2666/modules/phenix_html"
  78. phenix_regression "/usr/local/phenix-dev-2666/modules/phenix_regression"
  79. elbow "/usr/local/phenix-dev-2666/modules/elbow"
  80. Plex "/usr/local/phenix-dev-2666/modules/Plex"
  81. PyQuante "/usr/local/phenix-dev-2666/modules/PyQuante"
  82. crys3d "/usr/local/phenix-dev-2666/modules/cctbx_project/crys3d"
  83. gltbx "/usr/local/phenix-dev-2666/modules/cctbx_project/gltbx"
  84. mmtbx "/usr/local/phenix-dev-2666/modules/cctbx_project/mmtbx"
  85. suitename "/usr/local/phenix-dev-2666/modules/suitename"
  86. king "/usr/local/phenix-dev-2666/modules/king"
  87. probe "/usr/local/phenix-dev-2666/modules/probe"
  88. reduce "/usr/local/phenix-dev-2666/modules/reduce"
  89. iotbx "/usr/local/phenix-dev-2666/modules/cctbx_project/iotbx"
  90. cbflib+adaptbx "/usr/local/phenix-dev-2666/modules/cbflib"
  91. "/usr/local/phenix-dev-2666/modules/cctbx_project/cbflib_adaptbx"
  92. ccp4io+adaptbx "/usr/local/phenix-dev-2666/modules/ccp4io"
  93. "/usr/local/phenix-dev-2666/modules/ccp4io_adaptbx"
  94. dxtbx "/usr/local/phenix-dev-2666/modules/cctbx_project/dxtbx"
  95. smtbx "/usr/local/phenix-dev-2666/modules/cctbx_project/smtbx"
  96. ucif "/usr/local/phenix-dev-2666/modules/cctbx_project/ucif"
  97. cctbx "/usr/local/phenix-dev-2666/modules/cctbx_project/cctbx"
  98. scitbx "/usr/local/phenix-dev-2666/modules/cctbx_project/scitbx"
  99. fable "/usr/local/phenix-dev-2666/modules/cctbx_project/fable"
  100. omptbx "/usr/local/phenix-dev-2666/modules/cctbx_project/omptbx"
  101. boost+adaptbx "/usr/local/phenix-dev-2666/modules/boost"
  102. "/usr/local/phenix-dev-2666/modules/cctbx_project/boost_adaptbx"
  103. tbxx "/usr/local/phenix-dev-2666/modules/cctbx_project/tbxx"
  104. chiltbx "/usr/local/phenix-dev-2666/modules/cctbx_project/chiltbx"
  105. libtbx "/usr/local/phenix-dev-2666/modules/cctbx_project/libtbx"
  106. Creating files in build directory: "/usr/local/phenix-dev-2666/build"
  107. dispatcher_include_template.sh
  108. dispatcher_head.sh
  109. setpaths.sh
  110. setpaths.csh
  111. setpaths_all.sh
  112. setpaths_all.csh
  113. setpaths_debug.sh
  114. unsetpaths.sh
  115. setpaths_debug.csh
  116. unsetpaths.csh
  117. SConstruct
  118. Makefile
  119. run_tests.csh
  120. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/command_line"
  121. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/boost_adaptbx/command_line"
  122. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/fable/command_line"
  123. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/scitbx/command_line"
  124. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/cctbx/command_line"
  125. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/smtbx/command_line"
  126. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/dxtbx/command_line"
  127. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/cbflib_adaptbx/command_line"
  128. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/iotbx/command_line"
  129. Processing: "/usr/local/phenix-dev-2666/modules/reduce/command_line"
  130. Processing: "/usr/local/phenix-dev-2666/modules/probe/command_line"
  131. Processing: "/usr/local/phenix-dev-2666/modules/king/command_line"
  132. Processing: "/usr/local/phenix-dev-2666/modules/suitename/command_line"
  133. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/mmtbx/command_line"
  134. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/gltbx/command_line"
  135. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/crys3d/command_line"
  136. Processing: "/usr/local/phenix-dev-2666/modules/elbow/elbow/command_line"
  137. *****************************************************************************************************************************************************************************
  138. WARNING: Ignoring file "relocatable_path(anchor="/usr/local/phenix-dev-2666/build", relocatable="../modules/elbow/elbow/command_line/carbo_load.py.eli")" due to missing "#!"
  139. *****************************************************************************************************************************************************************************
  140. Processing: "/usr/local/phenix-dev-2666/modules/phenix_regression/command_line"
  141. Processing: "/usr/local/phenix-dev-2666/modules/phenix_html/command_line"
  142. Processing: "/usr/local/phenix-dev-2666/modules/ksdssp/command_line"
  143. Processing: "/usr/local/phenix-dev-2666/modules/muscle/command_line"
  144. Processing: "/usr/local/phenix-dev-2666/modules/solve_resolve/command_line"
  145. Processing: "/usr/local/phenix-dev-2666/modules/phaser_regression/command_line"
  146. Processing: "/usr/local/phenix-dev-2666/modules/phaser/phaser/command_line"
  147. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/wxtbx/command_line"
  148. Processing: "/usr/local/phenix-dev-2666/modules/reel/reel/command_line"
  149. Processing: "/usr/local/phenix-dev-2666/modules/phenix/phenix/command_line"
  150. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/spotfinder/command_line"
  151. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/rstbx/command_line"
  152. Processing: "/usr/local/phenix-dev-2666/modules/labelit/command_line"
  153. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/xfel/command_line"
  154. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/xfel/ui/command_line"
  155. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/xfel/cxi/command_line"
  156. Processing: "/usr/local/phenix-dev-2666/modules/dials/command_line"
  157. Processing: "/usr/local/phenix-dev-2666/modules/xia2/command_line"
  158. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/iota/command_line"
  159. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/prime/command_line"
  160. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py"
  161. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/scitbx/libtbx_refresh.py"
  162. Generating C++ header files in:
  163. "/usr/local/phenix-dev-2666/build/include/scitbx/array_family"
  164. Generating C++ files in:
  165. "/usr/local/phenix-dev-2666/build/include/scitbx/array_family/boost_python"
  166. Using fable to convert scitbx/lbfgs.f
  167. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/cctbx/libtbx_refresh.py"
  168. Generating C++ files in:
  169. "/usr/local/phenix-dev-2666/build/cctbx/eltbx"
  170. Generating C++ files in:
  171. "/usr/local/phenix-dev-2666/build/include/cctbx/boost_python"
  172. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/smtbx/libtbx_refresh.py"
  173. Generating C++ files in:
  174. "/usr/local/phenix-dev-2666/build/include/smtbx/boost_python"
  175. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/cbflib_adaptbx/libtbx_refresh.py"
  176. Copying to lib: "/usr/local/phenix-dev-2666/modules/cbflib/pycbf/pycbf.py"
  177. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/iotbx/libtbx_refresh.py"
  178. Using fable to convert iotbx/pdb/hybrid_36_f.f
  179. Writing: iotbx/pdb/hybrid_36_fem.cpp
  180. Processing: "/usr/local/phenix-dev-2666/modules/reduce/libtbx_refresh.py"
  181. Processing: "/usr/local/phenix-dev-2666/modules/probe/libtbx_refresh.py"
  182. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/mmtbx/libtbx_refresh.py"
  183. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/gltbx/libtbx_refresh.py"
  184. Generating C++ files in:
  185. "/usr/local/phenix-dev-2666/build/gltbx"
  186. Info: Re-using existing font cpp files.
  187. Hint: Remove gltbx/FONTS_UCS_DONE_FLAG_FILE
  188. to force generation of new font files.
  189. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/crys3d/libtbx_refresh.py"
  190. Processing: "/usr/local/phenix-dev-2666/modules/phenix_regression/libtbx_refresh.py"
  191. Processing: "/usr/local/phenix-dev-2666/modules/solve_resolve/libtbx_refresh.py"
  192. Number of hpp files generated from resolve cpp files: 720
  193. Processing: "/usr/local/phenix-dev-2666/modules/phenix/libtbx_refresh.py"
  194. Processing: "/usr/local/phenix-dev-2666/modules/annlib_adaptbx/libtbx_refresh.py"
  195. Generating C++ files for self-inclusive approximate nearest neighbor
  196. Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/xfel/libtbx_refresh.py"
  197. Processing: "/usr/local/phenix-dev-2666/modules/dials/libtbx_refresh.py"
  198. Cleaning up 'dials/extensions':
  199. Deleting /usr/local/phenix-dev-2666/modules/dials/extensions/median_background_ext.pyc
  200. Deleting /usr/local/phenix-dev-2666/modules/dials/extensions/null_background_ext.pyc
  201. Deleting /usr/local/phenix-dev-2666/modules/dials/extensions/gmodel_background_ext.pyc
  202. Deleting /usr/local/phenix-dev-2666/modules/dials/extensions/simple_background_ext.pyc
  203. Deleting /usr/local/phenix-dev-2666/modules/dials/extensions/kabsch_spotfinder_threshold_ext.pyc
  204. Deleting /usr/local/phenix-dev-2666/modules/dials/extensions/simple_centroid_ext.pyc
  205. Deleting /usr/local/phenix-dev-2666/modules/dials/extensions/gaussian_rs_profile_model_ext.pyc
  206. Deleting /usr/local/phenix-dev-2666/modules/dials/extensions/glm_background_ext.pyc
  207. Deleting /usr/local/phenix-dev-2666/modules/dials/extensions/__init__.pyc
  208. Deleting /usr/local/phenix-dev-2666/modules/dials/extensions/helen_spotfinder_threshold_ext.pyc
  209. Violación de segmento (`core' generado)
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