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  1. $ make PREFIX=bin
  2.  
  3. Compilation options (you can change them of course)
  4.  
  5. PREFIX = bin
  6. MAXKMERLENGTH = 96
  7. FORCE_PACKING = n
  8. ASSERT = n
  9. HAVE_LIBZ = y
  10. HAVE_LIBBZ2 = y
  11. INTEL_COMPILER = n
  12. MPICXX = mpicxx
  13. GPROF = n
  14. OPTIMIZE = y
  15. DEBUG = n
  16.  
  17. Compilation and linking flags (generated automatically)
  18.  
  19. CXXFLAGS = -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\"
  20. LDFLAGS = -lz -lbz2
  21.  
  22. make[1]: Entering directory `/home/bma/software/Ray-v2.1.0/RayPlatform'
  23. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o memory/ReusableMemoryStore.o memory/ReusableMemoryStore.cpp
  24. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o memory/MyAllocator.o memory/MyAllocator.cpp
  25. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o memory/RingAllocator.o memory/RingAllocator.cpp
  26. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o memory/allocator.o memory/allocator.cpp
  27. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o memory/DefragmentationGroup.o memory/DefragmentationGroup.cpp
  28. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o memory/ChunkAllocatorWithDefragmentation.o memory/ChunkAllocatorWithDefragmentation.cpp
  29. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o memory/DefragmentationLane.o memory/DefragmentationLane.cpp
  30. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o routing/GraphImplementation.o routing/GraphImplementation.cpp
  31. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o routing/GraphImplementationRandom.o routing/GraphImplementationRandom.cpp
  32. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o routing/GraphImplementationComplete.o routing/GraphImplementationComplete.cpp
  33. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o routing/GraphImplementationDeBruijn.o routing/GraphImplementationDeBruijn.cpp
  34. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o routing/GraphImplementationKautz.o routing/GraphImplementationKautz.cpp
  35. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o routing/GraphImplementationExperimental.o routing/GraphImplementationExperimental.cpp
  36. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o routing/GraphImplementationGroup.o routing/GraphImplementationGroup.cpp
  37. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o routing/Hypercube.o routing/Hypercube.cpp
  38. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o routing/ConnectionGraph.o routing/ConnectionGraph.cpp
  39. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o communication/mpi_tags.o communication/mpi_tags.cpp
  40. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o communication/VirtualCommunicator.o communication/VirtualCommunicator.cpp
  41. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o communication/BufferedData.o communication/BufferedData.cpp
  42. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o communication/Message.o communication/Message.cpp
  43. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o communication/MessagesHandler.o communication/MessagesHandler.cpp
  44. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o communication/MessageRouter.o communication/MessageRouter.cpp
  45. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o scheduling/VirtualProcessor.o scheduling/VirtualProcessor.cpp
  46. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o scheduling/TaskCreator.o scheduling/TaskCreator.cpp
  47. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o scheduling/SwitchMan.o scheduling/SwitchMan.cpp
  48. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o core/slave_modes.o core/slave_modes.cpp
  49. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o core/OperatingSystem.o core/OperatingSystem.cpp
  50. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o core/master_modes.o core/master_modes.cpp
  51. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o core/ComputeCore.o core/ComputeCore.cpp
  52. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o core/statistics.o core/statistics.cpp
  53. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o plugins/CorePlugin.o plugins/CorePlugin.cpp
  54. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o plugins/RegisteredPlugin.o plugins/RegisteredPlugin.cpp
  55. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o structures/StaticVector.o structures/StaticVector.cpp
  56. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o profiling/Profiler.o profiling/Profiler.cpp
  57. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o profiling/Derivative.o profiling/Derivative.cpp
  58. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o profiling/TickLogger.o profiling/TickLogger.cpp
  59. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o profiling/TimePrinter.o profiling/TimePrinter.cpp
  60. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o handlers/MasterModeExecutor.o handlers/MasterModeExecutor.cpp
  61. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o handlers/SlaveModeExecutor.o handlers/SlaveModeExecutor.cpp
  62. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o handlers/MessageTagExecutor.o handlers/MessageTagExecutor.cpp
  63. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o cryptography/crypto.o cryptography/crypto.cpp
  64. ar rcs libRayPlatform.a memory/ReusableMemoryStore.o memory/MyAllocator.o memory/RingAllocator.o memory/allocator.o memory/DefragmentationGroup.o memory/ChunkAllocatorWithDefragmentation.o memory/DefragmentationLane.o routing/GraphImplementation.o routing/GraphImplementationRandom.o routing/GraphImplementationComplete.o routing/GraphImplementationDeBruijn.o routing/GraphImplementationKautz.o routing/GraphImplementationExperimental.o routing/GraphImplementationGroup.o routing/Hypercube.o routing/ConnectionGraph.o communication/mpi_tags.o communication/VirtualCommunicator.o communication/BufferedData.o communication/Message.o communication/MessagesHandler.o communication/MessageRouter.o scheduling/VirtualProcessor.o scheduling/TaskCreator.o scheduling/SwitchMan.o core/slave_modes.o core/OperatingSystem.o core/master_modes.o core/ComputeCore.o core/statistics.o plugins/CorePlugin.o plugins/RegisteredPlugin.o structures/StaticVector.o profiling/Profiler.o profiling/Derivative.o profiling/TickLogger.o profiling/TimePrinter.o handlers/MasterModeExecutor.o handlers/SlaveModeExecutor.o handlers/MessageTagExecutor.o cryptography/crypto.o
  65. make[1]: Leaving directory `/home/bma/software/Ray-v2.1.0/RayPlatform'
  66. make[1]: Entering directory `/home/bma/software/Ray-v2.1.0/code'
  67. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o application_core/ray_main.o application_core/ray_main.cpp
  68. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o application_core/Machine.o application_core/Machine.cpp
  69. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o application_core/Parameters.o application_core/Parameters.cpp
  70. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o application_core/common_functions.o application_core/common_functions.cpp
  71. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_Amos/Amos.o plugin_Amos/Amos.cpp
  72. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_CoverageGatherer/CoverageGatherer.o plugin_CoverageGatherer/CoverageGatherer.cpp
  73. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_CoverageGatherer/CoverageDistribution.o plugin_CoverageGatherer/CoverageDistribution.cpp
  74. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_EdgePurger/EdgePurger.o plugin_EdgePurger/EdgePurger.cpp
  75. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_EdgePurger/EdgePurgerWorker.o plugin_EdgePurger/EdgePurgerWorker.cpp
  76. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_FusionData/FusionData.o plugin_FusionData/FusionData.cpp
  77. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_FusionTaskCreator/FusionWorker.o plugin_FusionTaskCreator/FusionWorker.cpp
  78. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_FusionTaskCreator/FusionTaskCreator.o plugin_FusionTaskCreator/FusionTaskCreator.cpp
  79. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_GeneOntology/KeyEncoder.o plugin_GeneOntology/KeyEncoder.cpp
  80. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_GeneOntology/GeneOntology.o plugin_GeneOntology/GeneOntology.cpp
  81. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_GenomeNeighbourhood/GenomeNeighbourhood.o plugin_GenomeNeighbourhood/GenomeNeighbourhood.cpp
  82. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_GenomeNeighbourhood/Neighbour.o plugin_GenomeNeighbourhood/Neighbour.cpp
  83. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_GenomeNeighbourhood/NeighbourPair.o plugin_GenomeNeighbourhood/NeighbourPair.cpp
  84. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_JoinerTaskCreator/JoinerWorker.o plugin_JoinerTaskCreator/JoinerWorker.cpp
  85. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_JoinerTaskCreator/JoinerTaskCreator.o plugin_JoinerTaskCreator/JoinerTaskCreator.cpp
  86. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_KmerAcademyBuilder/KmerAcademyBuilder.o plugin_KmerAcademyBuilder/KmerAcademyBuilder.cpp
  87. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_KmerAcademyBuilder/BloomFilter.o plugin_KmerAcademyBuilder/BloomFilter.cpp
  88. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_KmerAcademyBuilder/Kmer.o plugin_KmerAcademyBuilder/Kmer.cpp
  89. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_Library/LibraryPeakFinder.o plugin_Library/LibraryPeakFinder.cpp
  90. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_Library/LibraryWorker.o plugin_Library/LibraryWorker.cpp
  91. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_Library/Library.o plugin_Library/Library.cpp
  92. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_MachineHelper/MachineHelper.o plugin_MachineHelper/MachineHelper.cpp
  93. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_MessageProcessor/MessageProcessor.o plugin_MessageProcessor/MessageProcessor.cpp
  94. plugin_MessageProcessor/MessageProcessor.cpp: In member function 'void MessageProcessor::call_RAY_MPI_TAG_REQUEST_VERTEX_READS(Message*)':
  95. plugin_MessageProcessor/MessageProcessor.cpp:331: warning: dereferencing type-punned pointer will break strict-aliasing rules
  96. plugin_MessageProcessor/MessageProcessor.cpp:392: warning: dereferencing type-punned pointer will break strict-aliasing rules
  97. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_NetworkTest/NetworkTest.o plugin_NetworkTest/NetworkTest.cpp
  98. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_Partitioner/Partitioner.o plugin_Partitioner/Partitioner.cpp
  99. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_PhylogenyViewer/PhylogenyViewer.o plugin_PhylogenyViewer/PhylogenyViewer.cpp
  100. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_PhylogenyViewer/GenomeToTaxonLoader.o plugin_PhylogenyViewer/GenomeToTaxonLoader.cpp
  101. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_PhylogenyViewer/PhylogeneticTreeLoader.o plugin_PhylogenyViewer/PhylogeneticTreeLoader.cpp
  102. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_PhylogenyViewer/TaxonNameLoader.o plugin_PhylogenyViewer/TaxonNameLoader.cpp
  103. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_Scaffolder/Scaffolder.o plugin_Scaffolder/Scaffolder.cpp
  104. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_Scaffolder/ScaffoldingLink.o plugin_Scaffolder/ScaffoldingLink.cpp
  105. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_Scaffolder/SummarizedLink.o plugin_Scaffolder/SummarizedLink.cpp
  106. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_Scaffolder/ScaffoldingAlgorithm.o plugin_Scaffolder/ScaffoldingAlgorithm.cpp
  107. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_Scaffolder/ScaffoldingVertex.o plugin_Scaffolder/ScaffoldingVertex.cpp
  108. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_Scaffolder/ScaffoldingEdge.o plugin_Scaffolder/ScaffoldingEdge.cpp
  109. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_Searcher/Searcher.o plugin_Searcher/Searcher.cpp
  110. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_Searcher/SearchDirectory.o plugin_Searcher/SearchDirectory.cpp
  111. plugin_Searcher/Searcher.cpp: In member function 'void Searcher::call_RAY_SLAVE_MODE_SEQUENCE_BIOLOGICAL_ABUNDANCES()':
  112. plugin_Searcher/Searcher.cpp:1987: warning: converting to 'long unsigned int' from 'double'
  113. plugin_Searcher/Searcher.cpp:1988: warning: converting to 'long unsigned int' from 'double'
  114. plugin_Searcher/Searcher.cpp:1989: warning: converting to 'long unsigned int' from 'double'
  115. plugin_Searcher/Searcher.cpp: In member function 'void Searcher::generateSummaryOfColoredDeBruijnGraph()':
  116. plugin_Searcher/Searcher.cpp:4015: warning: unused variable 'numberOfPhysicalColors'
  117. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_Searcher/ContigSearchEntry.o plugin_Searcher/ContigSearchEntry.cpp
  118. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_Searcher/ContigHit.o plugin_Searcher/ContigHit.cpp
  119. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_Searcher/ColorSet.o plugin_Searcher/ColorSet.cpp
  120. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_Searcher/VirtualKmerColor.o plugin_Searcher/VirtualKmerColor.cpp
  121. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_Searcher/QualityCaller.o plugin_Searcher/QualityCaller.cpp
  122. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_Searcher/DistributionWriter.o plugin_Searcher/DistributionWriter.cpp
  123. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_Searcher/ColoredPeakFinder.o plugin_Searcher/ColoredPeakFinder.cpp
  124. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/SeedExtender.o plugin_SeedExtender/SeedExtender.cpp
  125. plugin_SeedExtender/SeedExtender.cpp: In member function 'void SeedExtender::markCurrentVertexAsAssembled(Kmer*, RingAllocator*, int*, StaticVector*, int, int, ExtensionData*, bool*, bool*, int*, bool*, std::vector<Kmer, std::allocator<Kmer> >*, Chooser*, BubbleData*, int, OpenAssemblerChooser*, int, std::vector<AssemblySeed, std::allocator<AssemblySeed> >*)':
  126. plugin_SeedExtender/SeedExtender.cpp:1598: warning: converting to 'CoverageDepth' from 'double'
  127. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/Direction.o plugin_SeedExtender/Direction.cpp
  128. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/VertexMessenger.o plugin_SeedExtender/VertexMessenger.cpp
  129. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/ReadFetcher.o plugin_SeedExtender/ReadFetcher.cpp
  130. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/BubbleTool.o plugin_SeedExtender/BubbleTool.cpp
  131. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/Chooser.o plugin_SeedExtender/Chooser.cpp
  132. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/OpenAssemblerChooser.o plugin_SeedExtender/OpenAssemblerChooser.cpp
  133. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/TipWatchdog.o plugin_SeedExtender/TipWatchdog.cpp
  134. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/NovaEngine.o plugin_SeedExtender/NovaEngine.cpp
  135. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/ExtensionElement.o plugin_SeedExtender/ExtensionElement.cpp
  136. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/DepthFirstSearchData.o plugin_SeedExtender/DepthFirstSearchData.cpp
  137. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/ExtensionData.o plugin_SeedExtender/ExtensionData.cpp
  138. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SeedingData/AssemblySeed.o plugin_SeedingData/AssemblySeed.cpp
  139. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SeedingData/SeedWorker.o plugin_SeedingData/SeedWorker.cpp
  140. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SeedingData/SeedingData.o plugin_SeedingData/SeedingData.cpp
  141. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SequencesIndexer/SequencesIndexer.o plugin_SequencesIndexer/SequencesIndexer.cpp
  142. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SequencesIndexer/IndexerWorker.o plugin_SequencesIndexer/IndexerWorker.cpp
  143. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SequencesIndexer/PairedRead.o plugin_SequencesIndexer/PairedRead.cpp
  144. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SequencesIndexer/ReadAnnotation.o plugin_SequencesIndexer/ReadAnnotation.cpp
  145. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/SequencesLoader.o plugin_SequencesLoader/SequencesLoader.cpp
  146. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/Read.o plugin_SequencesLoader/Read.cpp
  147. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/ArrayOfReads.o plugin_SequencesLoader/ArrayOfReads.cpp
  148. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/ColorSpaceDecoder.o plugin_SequencesLoader/ColorSpaceDecoder.cpp
  149. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/ColorSpaceLoader.o plugin_SequencesLoader/ColorSpaceLoader.cpp
  150. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/FastaLoader.o plugin_SequencesLoader/FastaLoader.cpp
  151. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/FastqLoader.o plugin_SequencesLoader/FastqLoader.cpp
  152. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/SffLoader.o plugin_SequencesLoader/SffLoader.cpp
  153. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/Loader.o plugin_SequencesLoader/Loader.cpp
  154. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_VerticesExtractor/VerticesExtractor.o plugin_VerticesExtractor/VerticesExtractor.cpp
  155. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_VerticesExtractor/GridTable.o plugin_VerticesExtractor/GridTable.cpp
  156. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_VerticesExtractor/GridTableIterator.o plugin_VerticesExtractor/GridTableIterator.cpp
  157. mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=96 -DHAVE_LIBZ -DHAVE_LIBBZ2 -D RAY_VERSION=\"2.1.0\" -I ../RayPlatform -I. -c -o plugin_VerticesExtractor/Vertex.o plugin_VerticesExtractor/Vertex.cpp
  158. ar rcs TheRayGenomeAssembler.a application_core/ray_main.o application_core/Machine.o application_core/Parameters.o application_core/common_functions.o plugin_Amos/Amos.o plugin_CoverageGatherer/CoverageGatherer.o plugin_CoverageGatherer/CoverageDistribution.o plugin_EdgePurger/EdgePurger.o plugin_EdgePurger/EdgePurgerWorker.o plugin_FusionData/FusionData.o plugin_FusionTaskCreator/FusionWorker.o plugin_FusionTaskCreator/FusionTaskCreator.o plugin_GeneOntology/KeyEncoder.o plugin_GeneOntology/GeneOntology.o plugin_GenomeNeighbourhood/GenomeNeighbourhood.o plugin_GenomeNeighbourhood/Neighbour.o plugin_GenomeNeighbourhood/NeighbourPair.o plugin_JoinerTaskCreator/JoinerWorker.o plugin_JoinerTaskCreator/JoinerTaskCreator.o plugin_KmerAcademyBuilder/KmerAcademyBuilder.o plugin_KmerAcademyBuilder/BloomFilter.o plugin_KmerAcademyBuilder/Kmer.o plugin_Library/LibraryPeakFinder.o plugin_Library/LibraryWorker.o plugin_Library/Library.o plugin_MachineHelper/MachineHelper.o plugin_MessageProcessor/MessageProcessor.o plugin_NetworkTest/NetworkTest.o plugin_Partitioner/Partitioner.o plugin_PhylogenyViewer/PhylogenyViewer.o plugin_PhylogenyViewer/GenomeToTaxonLoader.o plugin_PhylogenyViewer/PhylogeneticTreeLoader.o plugin_PhylogenyViewer/TaxonNameLoader.o plugin_Scaffolder/Scaffolder.o plugin_Scaffolder/ScaffoldingLink.o plugin_Scaffolder/SummarizedLink.o plugin_Scaffolder/ScaffoldingAlgorithm.o plugin_Scaffolder/ScaffoldingVertex.o plugin_Scaffolder/ScaffoldingEdge.o plugin_Searcher/Searcher.o plugin_Searcher/SearchDirectory.o plugin_Searcher/ContigSearchEntry.o plugin_Searcher/ContigHit.o plugin_Searcher/ColorSet.o plugin_Searcher/VirtualKmerColor.o plugin_Searcher/QualityCaller.o plugin_Searcher/DistributionWriter.o plugin_Searcher/ColoredPeakFinder.o plugin_SeedExtender/SeedExtender.o plugin_SeedExtender/Direction.o plugin_SeedExtender/VertexMessenger.o plugin_SeedExtender/ReadFetcher.o plugin_SeedExtender/BubbleTool.o plugin_SeedExtender/Chooser.o plugin_SeedExtender/OpenAssemblerChooser.o plugin_SeedExtender/TipWatchdog.o plugin_SeedExtender/NovaEngine.o plugin_SeedExtender/ExtensionElement.o plugin_SeedExtender/DepthFirstSearchData.o plugin_SeedExtender/ExtensionData.o plugin_SeedingData/AssemblySeed.o plugin_SeedingData/SeedWorker.o plugin_SeedingData/SeedingData.o plugin_SequencesIndexer/SequencesIndexer.o plugin_SequencesIndexer/IndexerWorker.o plugin_SequencesIndexer/PairedRead.o plugin_SequencesIndexer/ReadAnnotation.o plugin_SequencesLoader/SequencesLoader.o plugin_SequencesLoader/Read.o plugin_SequencesLoader/ArrayOfReads.o plugin_SequencesLoader/ColorSpaceDecoder.o plugin_SequencesLoader/ColorSpaceLoader.o plugin_SequencesLoader/FastaLoader.o plugin_SequencesLoader/FastqLoader.o plugin_SequencesLoader/SffLoader.o plugin_SequencesLoader/Loader.o plugin_VerticesExtractor/VerticesExtractor.o plugin_VerticesExtractor/GridTable.o plugin_VerticesExtractor/GridTableIterator.o plugin_VerticesExtractor/Vertex.o
  159. make[1]: Leaving directory `/home/bma/software/Ray-v2.1.0/code'
  160. mpicxx -lz -lbz2 code/TheRayGenomeAssembler.a RayPlatform/libRayPlatform.a -o Ray
  161. code/TheRayGenomeAssembler.a(Loader.o): In function `Loader::load(std::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool)':
  162. Loader.cpp:(.text+0x8a3): undefined reference to `FastqBz2Loader::open(std::basic_string<char, std::char_traits<char>, std::allocator<char> >, int)'
  163. Loader.cpp:(.text+0x8c3): undefined reference to `FastqBz2Loader::getSize()'
  164. Loader.cpp:(.text+0xb3b): undefined reference to `FastqGzLoader::open(std::basic_string<char, std::char_traits<char>, std::allocator<char> >, int)'
  165. Loader.cpp:(.text+0xb5b): undefined reference to `FastqGzLoader::getSize()'
  166. Loader.cpp:(.text+0xc5e): undefined reference to `FastqGzLoader::open(std::basic_string<char, std::char_traits<char>, std::allocator<char> >, int)'
  167. Loader.cpp:(.text+0xd0c): undefined reference to `FastqBz2Loader::open(std::basic_string<char, std::char_traits<char>, std::allocator<char> >, int)'
  168. code/TheRayGenomeAssembler.a(Loader.o): In function `Loader::loadSequences()':
  169. Loader.cpp:(.text+0x1ac): undefined reference to `FastqGzLoader::load(int, ArrayOfReads*, MyAllocator*, int)'
  170. Loader.cpp:(.text+0x20c): undefined reference to `FastqBz2Loader::load(int, ArrayOfReads*, MyAllocator*, int)'
  171. collect2: ld returned 1 exit status
  172. make: *** [Ray] Error 1
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