STAR-2.4.0d does not build on OS X

[lgautier]

make STARforMac

ends with:

bamRemoveDuplicates.cpp:23:25: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
        for (int ii=0;ii<la;ii++) {
                      ~~^~~
bamRemoveDuplicates.cpp:74:41: error: arithmetic on a pointer to void
    uint32* pa2=(uint32*) *(uint32**) (a+8);
                                       ~^
bamRemoveDuplicates.cpp:77:41: error: arithmetic on a pointer to void
    uint32* pb2=(uint32*) *(uint32**) (b+8);
                                       ~^
bamRemoveDuplicates.cpp:106:18: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
        for (; ii<pa2[5]; ii+=2) {
               ~~^~~~~~~
2 warnings and 2 errors generated.
make: *** [bamRemoveDuplicates.o] Error 1

[alexdobin]

Hi Laurent,

I have pushed the fix into the master branch - could you please test it and let me know if it works. I will make a tag after that. Apparently your compiler on Mac has stricter rules for poitner arithmetic than gcc.

Cheers
Alex

[lgautier]

Thanks.

On OS X, clang is the compiler behind g++.

The fix lets the build progress a little further, but it is still failing:

g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Oct 2 15:26:00 EDT 2014 :/Users/foo/STAR-master"'   bam_cat.c
clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated
clang: warning: argument unused during compilation: '-fopenmp'
g++ -o STAR -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Oct 2 15:26:00 EDT 2014 :/Users/foo/STAR-master"'   -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz PackedArray.o SuffixArrayFuns.o STAR.o Parameters.o InOutStreams.o SequenceFuns.o Genome.o Transcript.o Stats.o ReadAlign.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputAlignments.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_chimericDetection.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o alignSmithWaterman.o genomeGenerate.o TimeFunctions.o ErrorWarning.o loadGTF.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o ReadAlign_quantTranscriptome.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o mapThreadsSpawn.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o bam_cat.o
ld: library not found for -lgomp

[lgautier]

The work around was to force the use of gcc.

If gcc 4.9 was installed with homebrew (currently the default/latest), one can edit the Makefile from CC := g++ to CC := g++-4.9.

The build is completing with that change.