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  1. biascorrection.h(18): catastrophic error: cannot open source file "boost/tr1/unordered_map.hpp"
  2. #include <boost/tr1/unordered_map.hpp>
  3. ^
  4.  
  5. In file included from abundances.h(26),
  6. from genes.h(18),
  7. from filters.h(18),
  8. from filters.cpp(10):
  9. biascorrection.h(18): catastrophic error: cannot open source file "boost/tr1/unordered_map.hpp"
  10. #include <boost/tr1/unordered_map.hpp>
  11. ^
  12.  
  13. In file included from abundances.h(26),
  14. from bundles.cpp(20):
  15. biascorrection.h(18): catastrophic error: cannot open source file "boost/tr1/unordered_map.hpp"
  16. #include <boost/tr1/unordered_map.hpp>
  17. ^
  18.  
  19. compilation aborted for hits.cpp (code 4)
  20. make[2]: *** [hits.o] Error 1
  21. compilation aborted for filters.cpp (code 4)
  22. make[2]: *** [filters.o] Error 1
  23. compilation aborted for bundles.cpp (code 4)
  24. make[2]: *** [bundles.o] Error 1
  25. In file included from bundles.h(20),
  26. from graph_optimize.h(17),
  27. from graph_optimize.cpp(13):
  28. hits.h(396): warning #869: parameter "keep_seqs" was never referenced
  29. RefSequenceTable(bool keep_names, bool keep_seqs = false) :
  30. ^
  31.  
  32. In file included from abundances.h(25),
  33. from clustering.h(38),
  34. from clustering.cpp(10):
  35. bundles.h(52): warning #869: parameter "rhs" was never referenced
  36. HitBundle(const HitBundle& rhs) {}
  37. ^
  38.  
  39. In file included from abundances.h(26),
  40. from clustering.h(38),
  41. from clustering.cpp(10):
  42. biascorrection.h(18): catastrophic error: cannot open source file "boost/tr1/unordered_map.hpp"
  43. #include <boost/tr1/unordered_map.hpp>
  44. ^
  45.  
  46. compilation aborted for clustering.cpp (code 4)
  47. make[2]: *** [clustering.o] Error 1
  48. In file included from graph_optimize.h(17),
  49. from graph_optimize.cpp(13):
  50. bundles.h(52): warning #869: parameter "rhs" was never referenced
  51. HitBundle(const HitBundle& rhs) {}
  52. ^
  53.  
  54. In file included from abundances.h(26),
  55. from clustering.h(38),
  56. from assemble.cpp(54):
  57. biascorrection.h(18): catastrophic error: cannot open source file "boost/tr1/unordered_map.hpp"
  58. #include <boost/tr1/unordered_map.hpp>
  59. ^
  60.  
  61. compilation aborted for assemble.cpp (code 4)
  62. make[2]: *** [assemble.o] Error 1
  63. In file included from ./lemon/bits/base_extender.h(23),
  64. from ./lemon/list_graph.h(26),
  65. from ./lemon/dfs.h(26),
  66. from ./lemon/topology.h(22),
  67. from graph_optimize.cpp(16):
  68. ./lemon/error.h(108): warning #1478: class "std::auto_ptr<std::ostringstream>" (declared at line 87 of "/gpfs0/users/rescomp/adamh/.local/easybuild/software/GCCcore/6.4.0/bin/../include/c++/6.4.0/backward/auto_ptr.h") was declared deprecated
  69. std::auto_ptr<std::ostringstream> buf;
  70. ^
  71.  
  72. In file included from ./lemon/bits/base_extender.h(23),
  73. from ./lemon/list_graph.h(26),
  74. from ./lemon/dfs.h(26),
  75. from ./lemon/topology.h(22),
  76. from graph_optimize.cpp(16):
  77. ./lemon/error.h(93): warning #1478: class "std::auto_ptr<std::__cxx11::string>" (declared at line 87 of "/gpfs0/users/rescomp/adamh/.local/easybuild/software/GCCcore/6.4.0/bin/../include/c++/6.4.0/backward/auto_ptr.h") was declared deprecated
  78. std::auto_ptr<_Type> ptr;
  79. ^
  80. detected during instantiation of class "lemon::ExceptionMember<_Type> [with _Type=std::__cxx11::string]" at line 248
  81.  
  82. In file included from abundances.h(26),
  83. from genes.h(18),
  84. from filters.h(18),
  85. from graph_optimize.cpp(22):
  86. biascorrection.h(18): catastrophic error: cannot open source file "boost/tr1/unordered_map.hpp"
  87. #include <boost/tr1/unordered_map.hpp>
  88. ^
  89.  
  90. compilation aborted for graph_optimize.cpp (code 4)
  91. make[2]: *** [graph_optimize.o] Error 1
  92. make[2]: Leaving directory `/dev/shm/Cufflinks/2.2.1/intel-2017b/cufflinks-2.2.1/src'
  93. make[1]: *** [all-recursive] Error 1
  94. make[1]: Leaving directory `/dev/shm/Cufflinks/2.2.1/intel-2017b/cufflinks-2.2.1'
  95. make: *** [all] Error 2
  96.  
  97. == 2017-11-17 10:28:56,476 build_log.py:158 ERROR EasyBuild crashed with an error (at easybuild/software/EasyBuild/3.4.1/lib/python2.7/site-packages/vsc_base-2.5.8-py2.7.egg/vsc/utils/exceptions.py:124 in __init__): cmd " make -j 16 " exited with exitcode 2 and output:
  98. make all-recursive
  99. make[1]: Entering directory `/dev/shm/Cufflinks/2.2.1/intel-2017b/cufflinks-2.2.1'
  100. Making all in src
  101. make[2]: Entering directory `/dev/shm/Cufflinks/2.2.1/intel-2017b/cufflinks-2.2.1/src'
  102. if icpc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/well/rescomp/eb/software/Eigen/3.3.4/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -march=nocona -O3 -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNDEBUG -pthread -I/well/rescomp/eb/software/Boost/1.65.1-intel-2017b/include -MT clustering.o -MD -MP -MF ".deps/clustering.Tpo" -c -o clustering.o clustering.cpp; \
  103. then mv -f ".deps/clustering.Tpo" ".deps/clustering.Po"; else rm -f ".deps/clustering.Tpo"; exit 1; fi
  104. if icpc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/well/rescomp/eb/software/Eigen/3.3.4/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -march=nocona -O3 -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNDEBUG -pthread -I/well/rescomp/eb/software/Boost/1.65.1-intel-2017b/include -MT differential.o -MD -MP -MF ".deps/differential.Tpo" -c -o differential.o differential.cpp; \
  105. then mv -f ".deps/differential.Tpo" ".deps/differential.Po"; else rm -f ".deps/differential.Tpo"; exit 1; fi
  106. if icpc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/well/rescomp/eb/software/Eigen/3.3.4/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -march=nocona -O3 -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNDEBUG -pthread -I/well/rescomp/eb/software/Boost/1.65.1-intel-2017b/include -MT common.o -MD -MP -MF ".deps/common.Tpo" -c -o common.o common.cpp; \
  107. then mv -f ".deps/common.Tpo" ".deps/common.Po"; else rm -f ".deps/common.Tpo"; exit 1; fi
  108. if icpc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/well/rescomp/eb/software/Eigen/3.3.4/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -march=nocona -O3 -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNDEBUG -pthread -I/well/rescomp/eb/software/Boost/1.65.1-intel-2017b/include -MT assemble.o -MD -MP -MF ".deps/assemble.Tpo" -c -o assemble.o assemble.cpp; \
  109. then mv -f ".deps/assemble.Tpo" ".deps/assemble.Po"; else rm -f ".deps/assemble.Tpo"; exit 1; fi
  110. if icpc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/well/rescomp/eb/software/Eigen/3.3.4/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -march=nocona -O3 -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNDEBUG -pthread -I/well/rescomp/eb/software/Boost/1.65.1-intel-2017b/include -MT tokenize.o -MD -MP -MF ".deps/tokenize.Tpo" -c -o tokenize.o tokenize.cpp; \
  111. then mv -f ".deps/tokenize.Tpo" ".deps/tokenize.Po"; else rm -f ".deps/tokenize.Tpo"; exit 1; fi
  112. if icpc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/well/rescomp/eb/software/Eigen/3.3.4/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -march=nocona -O3 -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNDEBUG -pthread -I/well/rescomp/eb/software/Boost/1.65.1-intel-2017b/include -MT abundances.o -MD -MP -MF ".deps/abundances.Tpo" -c -o abundances.o abundances.cpp; \
  113. then mv -f ".deps/abundances.Tpo" ".deps/abundances.Po"; else rm -f ".deps/abundances.Tpo"; exit 1; fi
  114. if icpc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/well/rescomp/eb/software/Eigen/3.3.4/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -march=nocona -O3 -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNDEBUG -pthread -I/well/rescomp/eb/software/Boost/1.65.1-intel-2017b/include -MT scaffolds.o -MD -MP -MF ".deps/scaffolds.Tpo" -c -o scaffolds.o scaffolds.cpp; \
  115. then mv -f ".deps/scaffolds.Tpo" ".deps/scaffolds.Po"; else rm -f ".deps/scaffolds.Tpo"; exit 1; fi
  116. if icpc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/well/rescomp/eb/software/Eigen/3.3.4/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -march=nocona -O3 -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNDEBUG -pthread -I/well/rescomp/eb/software/Boost/1.65.1-intel-2017b/include -MT hits.o -MD -MP -MF ".deps/hits.Tpo" -c -o hits.o hits.cpp; \
  117. then mv -f ".deps/hits.Tpo" ".deps/hits.Po"; else rm -f ".deps/hits.Tpo"; exit 1; fi
  118. if icpc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/well/rescomp/eb/software/Eigen/3.3.4/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -march=nocona -O3 -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNDEBUG -pthread -I/well/rescomp/eb/software/Boost/1.65.1-intel-2017b/include -MT genes.o -MD -MP -MF ".deps/genes.Tpo" -c -o genes.o genes.cpp; \
  119. then mv -f ".deps/genes.Tpo" ".deps/genes.Po"; else rm -f ".deps/genes.Tpo"; exit 1; fi
  120. if icpc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/well/rescomp/eb/software/Eigen/3.3.4/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -march=nocona -O3 -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNDEBUG -pthread -I/well/rescomp/eb/software/Boost/1.65.1-intel-2017b/include -MT bundles.o -MD -MP -MF ".deps/bundles.Tpo" -c -o bundles.o bundles.cpp; \
  121. then mv -f ".deps/bundles.Tpo" ".deps/bundles.Po"; else rm -f ".deps/bundles.Tpo"; exit 1; fi
  122. if icpc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/well/rescomp/eb/software/Eigen/3.3.4/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -march=nocona -O3 -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNDEBUG -pthread -I/well/rescomp/eb/software/Boost/1.65.1-intel-2017b/include -MT filters.o -MD -MP -MF ".deps/filters.Tpo" -c -o filters.o filters.cpp; \
  123. then mv -f ".deps/filters.Tpo" ".deps/filters.Po"; else rm -f ".deps/filters.Tpo"; exit 1; fi
  124. if icpc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/well/rescomp/eb/software/Eigen/3.3.4/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -march=nocona -O3 -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNDEBUG -pthread -I/well/rescomp/eb/software/Boost/1.65.1-intel-2017b/include -MT scaffold_graph.o -MD -MP -MF ".deps/scaffold_graph.Tpo" -c -o scaffold_graph.o scaffold_graph.cpp; \
  125. then mv -f ".deps/scaffold_graph.Tpo" ".deps/scaffold_graph.Po"; else rm -f ".deps/scaffold_graph.Tpo"; exit 1; fi
  126. if icpc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/well/rescomp/eb/software/Eigen/3.3.4/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -march=nocona -O3 -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNDEBUG -pthread -I/well/rescomp/eb/software/Boost/1.65.1-intel-2017b/include -MT matching_merge.o -MD -MP -MF ".deps/matching_merge.Tpo" -c -o matching_merge.o matching_merge.cpp; \
  127. then mv -f ".deps/matching_merge.Tpo" ".deps/matching_merge.Po"; else rm -f ".deps/matching_merge.Tpo"; exit 1; fi
  128. if icpc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/well/rescomp/eb/software/Eigen/3.3.4/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -march=nocona -O3 -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNDEBUG -pthread -I/well/rescomp/eb/software/Boost/1.65.1-intel-2017b/include -MT graph_optimize.o -MD -MP -MF ".deps/graph_optimize.Tpo" -c -o graph_optimize.o graph_optimize.cpp; \
  129. then mv -f ".deps/graph_optimize.Tpo" ".deps/graph_optimize.Po"; else rm -f ".deps/graph_optimize.Tpo"; exit 1; fi
  130. if icpc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/well/rescomp/eb/software/Eigen/3.3.4/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -march=nocona -O3 -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNDEBUG -pthread -I/well/rescomp/eb/software/Boost/1.65.1-intel-2017b/include -MT biascorrection.o -MD -MP -MF ".deps/biascorrection.Tpo" -c -o biascorrection.o biascorrection.cpp; \
  131. then mv -f ".deps/biascorrection.Tpo" ".deps/biascorrection.Po"; else rm -f ".deps/biascorrection.Tpo"; exit 1; fi
  132. if icpc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/well/rescomp/eb/software/Eigen/3.3.4/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -march=nocona -O3 -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNDEBUG -pthread -I/well/rescomp/eb/software/Boost/1.65.1-intel-2017b/include -MT sampling.o -MD -MP -MF ".deps/sampling.Tpo" -c -o sampling.o sampling.cpp; \
  133. then mv -f ".deps/sampling.Tpo" ".deps/sampling.Po"; else rm -f ".deps/sampling.Tpo"; exit 1; fi
  134. icpc: command line warning #10121: overriding '-march=nocona' with '-xHost'
  135. icpc: command line warning #10121: overriding '-march=nocona' with '-xHost'
  136. icpc: command line warning #10121: overriding '-march=nocona' with '-xHost'
  137. icpc: command line warning #10121: overriding '-march=nocona' with '-xHost'
  138. icpc: command line warning #10121: overriding '-march=nocona' with '-xHost'
  139. icpc: command line warning #10121: overriding '-march=nocona' with '-xHost'
  140. icpc: command line warning #10121: overriding '-march=nocona' with '-xHost'
  141. icpc: command line warning #10121: overriding '-march=nocona' with '-xHost'
  142. icpc: command line warning #10121: overriding '-march=nocona' with '-xHost'
  143. icpc: command line warning #10121: overriding '-march=nocona' with '-xHost'
  144. icpc: command line warning #10121: overriding '-march=nocona' with '-xHost'
  145. icpc: command line warning #10121: overriding '-march=nocona' with '-xHost'
  146. icpc: command line warning #10121: overriding '-march=nocona' with '-xHost'
  147. icpc: command line warning #10121: overriding '-march=nocona' with '-xHost'
  148. icpc: command line warning #10121: overriding '-march=nocona' with '-xHost'
  149. icpc: command line warning #10121: overriding '-march=nocona' with '-xHost'
  150. In file included from ./lemon/bits/base_extender.h(23),
  151. from ./lemon/smart_graph.h(30),
  152. from matching_merge.h(16),
  153. from matching_merge.cpp(10):
  154. ./lemon/error.h(108): warning #1478: class "std::auto_ptr<std::ostringstream>" (declared at line 87 of "/gpfs0/users/rescomp/adamh/.local/easybuild/software/GCCcore/6.4.0/bin/../include/c++/6.4.0/backward/auto_ptr.h") was declared deprecated
  155. std::auto_ptr<std::ostringstream> buf;
  156. ^
  157.  
  158. In file included from ./lemon/bits/base_extender.h(23),
  159. from ./lemon/smart_graph.h(30),
  160. from matching_merge.h(16),
  161. from matching_merge.cpp(10):
  162. ./lemon/error.h(93): warning #1478: class "std::auto_ptr<std::__cxx11::string>" (declared at line 87 of "/gpfs0/users/rescomp/adamh/.local/easybuild/software/GCCcore/6.4.0/bin/../include/c++/6.4.0/backward/auto_ptr.h") was declared deprecated
  163. std::auto_ptr<_Type> ptr;
  164. ^
  165. detected during instantiation of class "lemon::ExceptionMember<_Type> [with _Type=std::__cxx11::string]" at line 248
  166.  
  167. In file included from ./lemon/bits/base_extender.h(23),
  168. from ./lemon/list_graph.h(26),
  169. from ./lemon/dfs.h(26),
  170. from ./lemon/topology.h(22),
  171. from assemble.cpp(19):
  172. ./lemon/error.h(108): warning #1478: class "std::auto_ptr<std::ostringstream>" (declared at line 87 of "/gpfs0/users/rescomp/adamh/.local/easybuild/software/GCCcore/6.4.0/bin/../include/c++/6.4.0/backward/auto_ptr.h") was declared deprecated
  173. std::auto_ptr<std::ostringstream> buf;
  174. ^
  175.  
  176. In file included from ./lemon/bits/base_extender.h(23),
  177. from ./lemon/list_graph.h(26),
  178. from ./lemon/dfs.h(26),
  179. from ./lemon/topology.h(22),
  180. from assemble.cpp(19):
  181. ./lemon/error.h(93): warning #1478: class "std::auto_ptr<std::__cxx11::string>" (declared at line 87 of "/gpfs0/users/rescomp/adamh/.local/easybuild/software/GCCcore/6.4.0/bin/../include/c++/6.4.0/backward/auto_ptr.h") was declared deprecated
  182. std::auto_ptr<_Type> ptr;
  183. ^
  184. detected during instantiation of class "lemon::ExceptionMember<_Type> [with _Type=std::__cxx11::string]" at line 248
  185.  
  186. if icc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/well/rescomp/eb/software/Eigen/3.3.4/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -march=nocona -O3 -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNDEBUG -MT adap.o -MD -MP -MF ".deps/adap.Tpo" -c -o adap.o `test -f 'locfit/adap.c' || echo './'`locfit/adap.c; \
  187. then mv -f ".deps/adap.Tpo" ".deps/adap.Po"; else rm -f ".deps/adap.Tpo"; exit 1; fi
  188. icc: command line warning #10121: overriding '-march=nocona' with '-xHost'
  189. locfit/adap.c(29): warning #593: variable "p" was set but never used
  190. { int i, ii, j, p, p1;
  191. ^
  192.  
  193. locfit/adap.c(157): warning #593: variable "d" was set but never used
  194. INT i, i0, d, n;
  195. ^
  196.  
  197. locfit/adap.c(157): warning #593: variable "n" was set but never used
  198. INT i, i0, d, n;
  199. ^
  200.  
  201. if icc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/well/rescomp/eb/software/Eigen/3.3.4/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -march=nocona -O3 -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNDEBUG -MT ar_funs.o -MD -MP -MF ".deps/ar_funs.Tpo" -c -o ar_funs.o `test -f 'locfit/ar_funs.c' || echo './'`locfit/ar_funs.c; \
  202. then mv -f ".deps/ar_funs.Tpo" ".deps/ar_funs.Po"; else rm -f ".deps/ar_funs.Tpo"; exit 1; fi
  203. icc: command line warning #10121: overriding '-march=nocona' with '-xHost'
  204. if icc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/well/rescomp/eb/software/Eigen/3.3.4/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -march=nocona -O3 -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNDEBUG -MT arith.o -MD -MP -MF ".deps/arith.Tpo" -c -o arith.o `test -f 'locfit/arith.c' || echo './'`locfit/arith.c; \
  205. then mv -f ".deps/arith.Tpo" ".deps/arith.Po"; else rm -f ".deps/arith.Tpo"; exit 1; fi
  206. icc: command line warning #10121: overriding '-march=nocona' with '-xHost'
  207. locfit/arith.c(544): warning #180: argument is incompatible with formal parameter
  208. va = arbuild(z,0,strlen(z)-1,NULL,1,0);
  209. ^
  210.  
  211. locfit/arith.c(582): warning #180: argument is incompatible with formal parameter
  212. va = arbuild(z,0,strlen(z)-1,NULL,1,0);
  213. ^
  214.  
  215. if icc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/well/rescomp/eb/software/Eigen/3.3.4/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -march=nocona -O3 -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNDEBUG -MT band.o -MD -MP -MF ".deps/band.Tpo" -c -o band.o `test -f 'locfit/band.c' || echo './'`locfit/band.c; \
  216. then mv -f ".deps/band.Tpo" ".deps/band.Po"; else rm -f ".deps/band.Tpo"; exit 1; fi
  217. In file included from biascorrection.cpp(10):
  218. biascorrection.h(18): catastrophic error: cannot open source file "boost/tr1/unordered_map.hpp"
  219. #include <boost/tr1/unordered_map.hpp>
  220. ^
  221.  
  222. compilation aborted for biascorrection.cpp (code 4)
  223. make[2]: *** [biascorrection.o] Error 1
  224. make[2]: *** Waiting for unfinished jobs....
  225. icc: command line warning #10121: overriding '-march=nocona' with '-xHost'
  226. In file included from scaffolds.h(20),
  227. from genes.h(17),
  228. from genes.cpp(10):
  229. hits.h(396): warning #869: parameter "keep_seqs" was never referenced
  230. RefSequenceTable(bool keep_names, bool keep_seqs = false) :
  231. ^
  232.  
  233. In file included from scaffolds.h(20),
  234. from matching_merge.h(20),
  235. from matching_merge.cpp(10):
  236. hits.h(396): warning #869: parameter "keep_seqs" was never referenced
  237. RefSequenceTable(bool keep_names, bool keep_seqs = false) :
  238. ^
  239.  
  240. In file included from scaffolds.h(20),
  241. from scaffold_graph.cpp(12):
  242. hits.h(396): warning #869: parameter "keep_seqs" was never referenced
  243. RefSequenceTable(bool keep_names, bool keep_seqs = false) :
  244. ^
  245.  
  246. In file included from hits.cpp(22):
  247. hits.h(396): warning #869: parameter "keep_seqs" was never referenced
  248. RefSequenceTable(bool keep_names, bool keep_seqs = false) :
  249. ^
  250.  
  251. In file included from abundances.h(23),
  252. from abundances.cpp(16):
  253. hits.h(396): warning #869: parameter "keep_seqs" was never referenced
  254. RefSequenceTable(bool keep_names, bool keep_seqs = false) :
  255. ^
  256.  
  257. In file included from scaffolds.h(20),
  258. from filters.h(17),
  259. from filters.cpp(10):
  260. hits.h(396): warning #869: parameter "keep_seqs" was never referenced
  261. RefSequenceTable(bool keep_names, bool keep_seqs = false) :
  262. ^
  263.  
  264. In file included from scaffolds.h(20),
  265. from scaffolds.cpp(14):
  266. hits.h(396): warning #869: parameter "keep_seqs" was never referenced
  267. RefSequenceTable(bool keep_names, bool keep_seqs = false) :
  268. ^
  269.  
  270. In file included from abundances.h(23),
  271. from differential.cpp(20):
  272. hits.h(396): warning #869: parameter "keep_seqs" was never referenced
  273. RefSequenceTable(bool keep_names, bool keep_seqs = false) :
  274. ^
  275.  
  276. In file included from bundles.h(20),
  277. from bundles.cpp(17):
  278. hits.h(396): warning #869: parameter "keep_seqs" was never referenced
  279. RefSequenceTable(bool keep_names, bool keep_seqs = false) :
  280. ^
  281.  
  282. In file included from bundles.h(20),
  283. from replicates.h(10),
  284. from common.cpp(28):
  285. hits.h(396): warning #869: parameter "keep_seqs" was never referenced
  286. RefSequenceTable(bool keep_names, bool keep_seqs = false) :
  287. ^
  288.  
  289. scaffolds.cpp(1115): warning #869: parameter "op" was never referenced
  290. double Scaffold::score_overlap(const AugmentedCuffOp& op,
  291. ^
  292.  
  293. scaffolds.cpp(1116): warning #869: parameter "inner_left_edge" was never referenced
  294. int inner_left_edge,
  295. ^
  296.  
  297. scaffolds.cpp(1117): warning #869: parameter "inner_right_edge" was never referenced
  298. int inner_right_edge)
  299. ^
  300.  
  301. In file included from abundances.h(25),
  302. from abundances.cpp(16):
  303. bundles.h(52): warning #869: parameter "rhs" was never referenced
  304. HitBundle(const HitBundle& rhs) {}
  305. ^
  306.  
  307. In file included from bundles.cpp(17):
  308. bundles.h(52): warning #869: parameter "rhs" was never referenced
  309. HitBundle(const HitBundle& rhs) {}
  310. ^
  311.  
  312. In file included from replicates.h(10),
  313. from common.cpp(28):
  314. bundles.h(52): warning #869: parameter "rhs" was never referenced
  315. HitBundle(const HitBundle& rhs) {}
  316. ^
  317.  
  318. In file included from abundances.h(26),
  319. from abundances.cpp(16):
  320. biascorrection.h(18): catastrophic error: cannot open source file "boost/tr1/unordered_map.hpp"
  321. #include <boost/tr1/unordered_map.hpp>
  322. ^
  323.  
  324. In file included from abundances.h(25),
  325. from differential.cpp(20):
  326. bundles.h(52): warning #869: parameter "rhs" was never referenced
  327. HitBundle(const HitBundle& rhs) {}
  328. ^
  329.  
  330. compilation aborted for abundances.cpp (code 4)
  331. make[2]: *** [abundances.o] Error 1
  332. In file included from abundances.h(25),
  333. from genes.h(18),
  334. from genes.cpp(10):
  335. bundles.h(52): warning #869: parameter "rhs" was never referenced
  336. HitBundle(const HitBundle& rhs) {}
  337. ^
  338.  
  339. In file included from abundances.h(26),
  340. from differential.cpp(20):
  341. biascorrection.h(18): catastrophic error: cannot open source file "boost/tr1/unordered_map.hpp"
  342. #include <boost/tr1/unordered_map.hpp>
  343. ^
  344.  
  345. In file included from common.cpp(28):
  346. replicates.h(224): warning #177: variable "s2" was declared but never referenced
  347. const vector<boost::shared_ptr<Scaffold> >& s2 = bundles[i-1]->ref_scaffolds();
  348. ^
  349.  
  350. compilation aborted for differential.cpp (code 4)
  351. make[2]: *** [differential.o] Error 1
  352. In file included from bundles.h(20),
  353. from assemble.h(21),
  354. from assemble.cpp(48):
  355. hits.h(396): warning #869: parameter "keep_seqs" was never referenced
  356. RefSequenceTable(bool keep_names, bool keep_seqs = false) :
  357. ^
  358.  
  359. In file included from abundances.h(26),
  360. from genes.h(18),
  361. from genes.cpp(10):
  362. biascorrection.h(18): catastrophic error: cannot open source file "boost/tr1/unordered_map.hpp"
  363. #include <boost/tr1/unordered_map.hpp>
  364. ^
  365.  
  366. compilation aborted for genes.cpp (code 4)
  367. make[2]: *** [genes.o] Error 1
  368. In file included from abundances.h(23),
  369. from clustering.h(38),
  370. from clustering.cpp(10):
  371. hits.h(396): warning #869: parameter "keep_seqs" was never referenced
  372. RefSequenceTable(bool keep_names, bool keep_seqs = false) :
  373. ^
  374.  
  375. In file included from assemble.h(21),
  376. from assemble.cpp(48):
  377. bundles.h(52): warning #869: parameter "rhs" was never referenced
  378. HitBundle(const HitBundle& rhs) {}
  379. ^
  380.  
  381. In file included from abundances.h(25),
  382. from hits.cpp(25):
  383. bundles.h(52): warning #869: parameter "rhs" was never referenced
  384. HitBundle(const HitBundle& rhs) {}
  385. ^
  386.  
  387. In file included from abundances.h(25),
  388. from genes.h(18),
  389. from filters.h(18),
  390. from filters.cpp(10):
  391. bundles.h(52): warning #869: parameter "rhs" was never referenced
  392. HitBundle(const HitBundle& rhs) {}
  393. ^
  394.  
  395. In file included from abundances.h(26),
  396. from hits.cpp(25):
  397. biascorrection.h(18): catastrophic error: cannot open source file "boost/tr1/unordered_map.hpp"
  398. #include <boost/tr1/unordered_map.hpp>
  399. ^
  400.  
  401. In file included from abundances.h(26),
  402. from genes.h(18),
  403. from filters.h(18),
  404. from filters.cpp(10):
  405. biascorrection.h(18): catastrophic error: cannot open source file "boost/tr1/unordered_map.hpp"
  406. #include <boost/tr1/unordered_map.hpp>
  407. ^
  408.  
  409. In file included from abundances.h(26),
  410. from bundles.cpp(20):
  411. biascorrection.h(18): catastrophic error: cannot open source file "boost/tr1/unordered_map.hpp"
  412. #include <boost/tr1/unordered_map.hpp>
  413. ^
  414.  
  415. compilation aborted for hits.cpp (code 4)
  416. make[2]: *** [hits.o] Error 1
  417. compilation aborted for filters.cpp (code 4)
  418. make[2]: *** [filters.o] Error 1
  419. compilation aborted for bundles.cpp (code 4)
  420. make[2]: *** [bundles.o] Error 1
  421. In file included from bundles.h(20),
  422. from graph_optimize.h(17),
  423. from graph_optimize.cpp(13):
  424. hits.h(396): warning #869: parameter "keep_seqs" was never referenced
  425. RefSequenceTable(bool keep_names, bool keep_seqs = false) :
  426. ^
  427.  
  428. In file included from abundances.h(25),
  429. from clustering.h(38),
  430. from clustering.cpp(10):
  431. bundles.h(52): warning #869: parameter "rhs" was never referenced
  432. HitBundle(const HitBundle& rhs) {}
  433. ^
  434.  
  435. In file included from abundances.h(26),
  436. from clustering.h(38),
  437. from clustering.cpp(10):
  438. biascorrection.h(18): catastrophic error: cannot open source file "boost/tr1/unordered_map.hpp"
  439. #include <boost/tr1/unordered_map.hpp>
  440. ^
  441.  
  442. compilation aborted for clustering.cpp (code 4)
  443. make[2]: *** [clustering.o] Error 1
  444. In file included from graph_optimize.h(17),
  445. from graph_optimize.cpp(13):
  446. bundles.h(52): warning #869: parameter "rhs" was never referenced
  447. HitBundle(const HitBundle& rhs) {}
  448. ^
  449.  
  450. In file included from abundances.h(26),
  451. from clustering.h(38),
  452. from assemble.cpp(54):
  453. biascorrection.h(18): catastrophic error: cannot open source file "boost/tr1/unordered_map.hpp"
  454. #include <boost/tr1/unordered_map.hpp>
  455. ^
  456.  
  457. compilation aborted for assemble.cpp (code 4)
  458. make[2]: *** [assemble.o] Error 1
  459. In file included from ./lemon/bits/base_extender.h(23),
  460. from ./lemon/list_graph.h(26),
  461. from ./lemon/dfs.h(26),
  462. from ./lemon/topology.h(22),
  463. from graph_optimize.cpp(16):
  464. ./lemon/error.h(108): warning #1478: class "std::auto_ptr<std::ostringstream>" (declared at line 87 of "/gpfs0/users/rescomp/adamh/.local/easybuild/software/GCCcore/6.4.0/bin/../include/c++/6.4.0/backward/auto_ptr.h") was declared deprecated
  465. std::auto_ptr<std::ostringstream> buf;
  466. ^
  467.  
  468. In file included from ./lemon/bits/base_extender.h(23),
  469. from ./lemon/list_graph.h(26),
  470. from ./lemon/dfs.h(26),
  471. from ./lemon/topology.h(22),
  472. from graph_optimize.cpp(16):
  473. ./lemon/error.h(93): warning #1478: class "std::auto_ptr<std::__cxx11::string>" (declared at line 87 of "/gpfs0/users/rescomp/adamh/.local/easybuild/software/GCCcore/6.4.0/bin/../include/c++/6.4.0/backward/auto_ptr.h") was declared deprecated
  474. std::auto_ptr<_Type> ptr;
  475. ^
  476. detected during instantiation of class "lemon::ExceptionMember<_Type> [with _Type=std::__cxx11::string]" at line 248
  477.  
  478. In file included from abundances.h(26),
  479. from genes.h(18),
  480. from filters.h(18),
  481. from graph_optimize.cpp(22):
  482. biascorrection.h(18): catastrophic error: cannot open source file "boost/tr1/unordered_map.hpp"
  483. #include <boost/tr1/unordered_map.hpp>
  484. ^
  485.  
  486. compilation aborted for graph_optimize.cpp (code 4)
  487. make[2]: *** [graph_optimize.o] Error 1
  488. make[2]: Leaving directory `/dev/shm/Cufflinks/2.2.1/intel-2017b/cufflinks-2.2.1/src'
  489. make[1]: *** [all-recursive] Error 1
  490. make[1]: Leaving directory `/dev/shm/Cufflinks/2.2.1/intel-2017b/cufflinks-2.2.1'
  491. make: *** [all] Error 2
  492. (at easybuild/software/EasyBuild/3.4.1/lib/python2.7/site-packages/easybuild_framework-3.4.1-py2.7.egg/easybuild/tools/run.py:483 in parse_cmd_output)
  493. == 2017-11-17 10:28:56,476 easyblock.py:2669 WARNING build failed (first 300 chars): cmd " make -j 16 " exited with exitcode 2 and output:
  494. make all-recursive
  495. make[1]: Entering directory `/dev/shm/Cufflinks/2.2.1/intel-2017b/cufflinks-2.2.1'
  496. Making all in src
  497. make[2]: Entering directory `/dev/shm/Cufflinks/2.2.1/intel-2017b/cufflinks-2.2.1/src'
  498. if icpc -DHAVE_CONFIG_H -I. -I. -I..
  499. == 2017-11-17 10:28:56,476 easyblock.py:288 INFO Closing log for application name Cufflinks version 2.2.1
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