Hi, I am having problems installing Ray v2.2.0 on our assembly rig under CentOS5.9. Ray v2.1 installs and runs without any problems using the exact same make instructions.
I have listed the output of the make command below. Any help would be appreciated. Cheers, Anthony $make HAVE_LIBZ=y HAVE_LIBBZ2=y MAXKMERLENGTH=64 MPICXX=/usr/lib64/openmpi/1.4-gcc/bin/mpicxx Compilation options (you can change them of course) PREFIX = install-prefix MPICXX = /usr/lib64/openmpi/1.4-gcc/bin/mpicxx MAXKMERLENGTH = 64 FORCE_PACKING = n ASSERT = n HAVE_LIBZ = y HAVE_LIBBZ2 = y Compilation and linking flags (generated automatically) CXXFLAGS = -O3 -std=c++98 -Wall -g CONFIG_FLAGS = -D CONFIG_MAXKMERLENGTH=64 -D CONFIG_HAVE_LIBZ -D CONFIG_HAVE_LIBBZ2 -D CONFIG_RAY_VERSION="2.2.0" LDFLAGS = -lz -lbz2 make[1]: Entering directory `/scratch/aborneman/bin/Ray-v2.2.0/RayPlatform' CXX RayPlatform/memory/ReusableMemoryStore.o CXX RayPlatform/memory/MyAllocator.o CXX RayPlatform/memory/RingAllocator.o CXX RayPlatform/memory/allocator.o CXX RayPlatform/memory/DefragmentationGroup.o CXX RayPlatform/memory/ChunkAllocatorWithDefragmentation.o CXX RayPlatform/memory/DefragmentationLane.o CXX RayPlatform/routing/ConnectionGraph.o CXX RayPlatform/routing/GraphImplementation.o CXX RayPlatform/routing/GraphImplementationRandom.o CXX RayPlatform/routing/GraphImplementationComplete.o CXX RayPlatform/routing/GraphImplementationDeBruijn.o CXX RayPlatform/routing/GraphImplementationKautz.o CXX RayPlatform/routing/GraphImplementationExperimental.o CXX RayPlatform/routing/GraphImplementationGroup.o CXX RayPlatform/routing/Polytope.o CXX RayPlatform/routing/Torus.o CXX RayPlatform/communication/mpi_tags.o CXX RayPlatform/communication/VirtualCommunicator.o CXX RayPlatform/communication/BufferedData.o CXX RayPlatform/communication/Message.o CXX RayPlatform/communication/MessagesHandler.o CXX RayPlatform/communication/MessageQueue.o CXX RayPlatform/communication/MessageRouter.o CXX RayPlatform/scheduling/VirtualProcessor.o CXX RayPlatform/scheduling/TaskCreator.o CXX RayPlatform/scheduling/SwitchMan.o CXX RayPlatform/core/ComputeCore.o CXX RayPlatform/core/MiniRank.o core/MiniRank.h:36: warning: ‘class MiniRank’ has virtual functions but non-virtual destructor CXX RayPlatform/core/slave_modes.o CXX RayPlatform/core/OperatingSystem.o CXX RayPlatform/core/master_modes.o CXX RayPlatform/core/statistics.o CXX RayPlatform/plugins/CorePlugin.o CXX RayPlatform/plugins/RegisteredPlugin.o CXX RayPlatform/structures/StaticVector.o CXX RayPlatform/profiling/Profiler.o CXX RayPlatform/profiling/Derivative.o CXX RayPlatform/profiling/TickLogger.o CXX RayPlatform/profiling/TimePrinter.o CXX RayPlatform/handlers/MasterModeExecutor.o CXX RayPlatform/handlers/SlaveModeExecutor.o CXX RayPlatform/handlers/MessageTagExecutor.o CXX RayPlatform/cryptography/crypto.o AR libRayPlatform.a make[1]: Leaving directory `/scratch/aborneman/bin/Ray-v2.2.0/RayPlatform' CXX code/Partitioner/Partitioner.o ./code/SequencesIndexer/PairedRead.h:42: error: ‘LibraryHandle’ does not name a type ./code/SequencesIndexer/PairedRead.h:45: error: ‘Rank’ does not name a type ./code/SequencesIndexer/PairedRead.h:47: error: ‘ReadHandle’ does not name a type ./code/SequencesLoader/Read.h:63: error: ‘Kmer’ does not name a type ./code/SequencesLoader/Read.h:83: error: conflicting declaration ‘Read ATTRIBUTE_PACKED’ ./code/SequencesIndexer/PairedRead.h:52: error: ‘ATTRIBUTE_PACKED’ has a previous declaration as ‘PairedRead ATTRIBUTE_PACKED’ ./code/SequencesLoader/ArrayOfReads.h:38: error: ‘LargeCount’ does not name a type ./code/SequencesLoader/ArrayOfReads.h:39: error: ‘LargeCount’ does not name a type ./code/SequencesLoader/ArrayOfReads.h:49: error: expected ‘;’ before ‘(’ token ./code/SequencesLoader/ArrayOfReads.h:50: error: declaration of ‘operator[]’ as non-function ./code/SequencesLoader/ArrayOfReads.h:50: error: expected ‘;’ before ‘(’ token ./code/SequencesLoader/ArrayOfReads.h:51: error: ‘LargeCount’ does not name a type ./code/SequencesLoader/LoaderInterface.h:36: warning: ‘class LoaderInterface’ has virtual functions but non-virtual destructor ./code/SequencesLoader/FastqLoader.h:41: warning: ‘class FastqLoader’ has virtual functions but non-virtual destructor ./code/SequencesLoader/FastaLoaderForReads.h:42: warning: ‘class FastaLoaderForReads’ has virtual functions but non-virtual destructor ./code/SequencesLoader/ExportLoader.h:46: warning: ‘class ExportLoader’ has virtual functions but non-virtual destructor ./code/SequencesLoader/ColorSpaceLoader.h:42: warning: ‘class ColorSpaceLoader’ has virtual functions but non-virtual destructor ./code/SequencesLoader/SffLoader.h:42: warning: ‘class SffLoader’ has virtual functions but non-virtual destructor ./code/SequencesLoader/FastqGzLoader.h:43: warning: ‘class FastqGzLoader’ has virtual functions but non-virtual destructor ./code/SequencesLoader/FastaGzLoader.h:43: warning: ‘class FastaGzLoader’ has virtual functions but non-virtual destructor ./code/SequencesLoader/FastqBz2Loader.h:41: warning: ‘class FastqBz2Loader’ has virtual functions but non-virtual destructor ./code/SequencesLoader/FastaBz2Loader.h:41: warning: ‘class FastaBz2Loader’ has virtual functions but non-virtual destructor ./code/SequencesLoader/Loader.h:49: error: ‘Rank’ does not name a type ./code/SequencesLoader/Loader.h:56: error: ‘LargeIndex’ does not name a type ./code/SequencesLoader/Loader.h:58: error: ‘LargeCount’ does not name a type ./code/SequencesLoader/Loader.h:64: error: ‘Rank’ has not been declared ./code/SequencesLoader/Loader.h:66: error: ‘LargeCount’ does not name a type ./code/SequencesLoader/Loader.h:67: error: expected ‘;’ before ‘(’ token code/Partitioner/Partitioner.h:88: error: ‘LargeCount’ was not declared in this scope code/Partitioner/Partitioner.h:88: error: template argument 2 is invalid code/Partitioner/Partitioner.h:88: error: template argument 4 is invalid code/Partitioner/Partitioner.h:90: error: ‘LargeCount’ was not declared in this scope code/Partitioner/Partitioner.h:90: error: template argument 2 is invalid code/Partitioner/Partitioner.h:90: error: template argument 4 is invalid code/Partitioner/Partitioner.h:100: error: ISO C++ forbids declaration of ‘Parameters’ with no type code/Partitioner/Partitioner.h:100: error: expected ‘;’ before ‘*’ token code/Partitioner/Partitioner.h:105: error: ‘Parameters’ has not been declared code/Partitioner/Partitioner.cpp:33: error: ‘Parameters’ has not been declared code/Partitioner/Partitioner.cpp: In member function ‘void Partitioner::constructor(RingAllocator*, StaticVector*, StaticVector*, int*, SwitchMan*)’: code/Partitioner/Partitioner.cpp:40: error: ‘m_parameters’ was not declared in this scope code/Partitioner/Partitioner.cpp: In member function ‘void Partitioner::call_RAY_MASTER_MODE_COUNT_FILE_ENTRIES()’: code/Partitioner/Partitioner.cpp:53: error: ‘m_parameters’ was not declared in this scope code/Partitioner/Partitioner.cpp:61: error: ‘m_parameters’ was not declared in this scope code/Partitioner/Partitioner.cpp:71: error: ‘LargeCount’ was not declared in this scope code/Partitioner/Partitioner.cpp:71: error: expected `;' before ‘count’ code/Partitioner/Partitioner.cpp:72: error: invalid types ‘int[int]’ for array subscript code/Partitioner/Partitioner.cpp:74: error: ‘m_parameters’ was not declared in this scope code/Partitioner/Partitioner.cpp:77: error: ‘m_parameters’ was not declared in this scope code/Partitioner/Partitioner.cpp:83: error: ‘m_parameters’ was not declared in this scope code/Partitioner/Partitioner.cpp:85: error: request for member ‘size’ in ‘((Partitioner*)this)->Partitioner::m_masterCounts’, which is of non-class type ‘int’ code/Partitioner/Partitioner.cpp:87: error: invalid types ‘int[int]’ for array subscript code/Partitioner/Partitioner.cpp:88: error: invalid types ‘int[int]’ for array subscript code/Partitioner/Partitioner.cpp:90: error: request for member ‘clear’ in ‘((Partitioner*)this)->Partitioner::m_masterCounts’, which is of non-class type ‘int’ code/Partitioner/Partitioner.cpp:111: error: ‘LargeCount’ was not declared in this scope code/Partitioner/Partitioner.cpp:111: error: expected `;' before ‘totalSequences’ code/Partitioner/Partitioner.cpp:116: error: expected `;' before ‘entries’ code/Partitioner/Partitioner.cpp:117: error: ‘entries’ was not declared in this scope code/Partitioner/Partitioner.cpp:120: error: ‘totalSequences’ was not declared in this scope code/Partitioner/Partitioner.cpp:128: error: ‘totalSequences’ was not declared in this scope code/Partitioner/Partitioner.cpp:133: error: ‘totalSequences’ was not declared in this scope code/Partitioner/Partitioner.cpp:140: error: ‘totalSequences’ was not declared in this scope code/Partitioner/Partitioner.cpp:153: error: expected `;' before ‘perRank’ code/Partitioner/Partitioner.cpp:156: error: ‘LargeIndex’ was not declared in this scope code/Partitioner/Partitioner.cpp:156: error: expected `;' before ‘first’ code/Partitioner/Partitioner.cpp:157: error: expected `;' before ‘last’ code/Partitioner/Partitioner.cpp:160: error: ‘last’ was not declared in this scope code/Partitioner/Partitioner.cpp:163: error: expected `;' before ‘count’ code/Partitioner/Partitioner.cpp:165: error: ‘first’ was not declared in this scope code/Partitioner/Partitioner.cpp:165: error: ‘last’ was not declared in this scope code/Partitioner/Partitioner.cpp: In member function ‘void Partitioner::call_RAY_SLAVE_MODE_COUNT_FILE_ENTRIES()’: code/Partitioner/Partitioner.cpp:184: error: ‘m_parameters’ was not declared in this scope code/Partitioner/Partitioner.cpp:191: error: ‘LargeCount’ was not declared in this scope code/Partitioner/Partitioner.cpp:191: error: expected `;' before ‘sequences’ code/Partitioner/Partitioner.cpp:193: error: ‘sequences’ was not declared in this scope code/Partitioner/Partitioner.cpp:200: error: invalid types ‘int[int]’ for array subscript code/Partitioner/Partitioner.cpp:211: error: ‘m_parameters’ was not declared in this scope code/Partitioner/Partitioner.cpp:221: error: request for member ‘size’ in ‘((Partitioner*)this)->Partitioner::m_slaveCounts’, which is of non-class type ‘int’ code/Partitioner/Partitioner.cpp:224: error: ‘LargeCount’ was not declared in this scope code/Partitioner/Partitioner.cpp:224: error: template argument 2 is invalid code/Partitioner/Partitioner.cpp:224: error: template argument 4 is invalid code/Partitioner/Partitioner.cpp:224: error: expected initializer before ‘i’ code/Partitioner/Partitioner.cpp:225: error: ‘i’ was not declared in this scope code/Partitioner/Partitioner.cpp:225: error: request for member ‘end’ in ‘((Partitioner*)this)->Partitioner::m_slaveCounts’, which is of non-class type ‘int’ code/Partitioner/Partitioner.cpp:227: error: expected `;' before ‘sequences’ code/Partitioner/Partitioner.cpp:229: error: ‘sequences’ was not declared in this scope code/Partitioner/Partitioner.cpp:245: error: invalid types ‘int[int]’ for array subscript code/Partitioner/Partitioner.cpp:245: error: ‘class Loader’ has no member named ‘size’ code/Partitioner/Partitioner.cpp:249: error: invalid types ‘int[int]’ for array subscript code/Partitioner/Partitioner.cpp:268: error: invalid types ‘int[int]’ for array subscript code/Partitioner/Partitioner.cpp:281: error: request for member ‘clear’ in ‘((Partitioner*)this)->Partitioner::m_slaveCounts’, which is of non-class type ‘int’ make: *** [code/Partitioner/Partitioner.o] Error 1 Anthony Borneman Principal Research Scientist - Molecular Biology | The Australian Wine Research Institute Waite Precinct, Hartley Grove cnr Paratoo Road, Urrbrae (Adelaide) SA 5064 | Map PO Box 197, Glen Osmond SA 5064, Australia T: +61 8 83136613 (direct) | F: +61 8 83136601 | www: www.awri.com.au | AWRI Events This communication, including attachments, is intended only for the addressee(s) and contains information which might be confidential and/or the copyright of The Australian Wine Research Institute (AWRI) or a third party. 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