building on OSX 10.6.8

[splaisan]

did as in README (git) These files provide some programs for working on SAM/BAM files.-------------------------------------------------------------------------------- To use git to clone the required statgen library: make cloneLib Next, to build libStatGen & this program: make

many lines ...... then ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o /opt/local/bin/ranlib: file: ../libStatGen.a(LongHash.o) has no symbols /opt/local/bin/ranlib: file: ../libStatGen.a(TrimSequence.o) has no symbols /opt/local/bin/ranlib: file: ../libStatGen.a(WindowsHelper.o) has no symbols /opt/local/bin/ranlib: file: ../libStatGen.a(SamFlag.o) has no symbols mkdir -p ../obj g++ -O4 -pipe -Wall -I../../libStatGen/include -I. -DZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -DSTDC_LIMIT_MACROS -std=c++0x -DDATE="\"Sat Aug 25 12:23:40 CEST 2012\"" -DVERSION="\"1.0.2\"" -DUSER="\"splaisan\"" -o ../obj/BamExecutable.o -c BamExecutable.cpp -DVERSION="\"1.0.2\"" cc1plus: error: unrecognized command line option "-std=c++0x" make[1]: * [../obj/BamExecutable.o] Error 1 make: * [src] Error 2

Any idea what is missing here? It worked fine on RHEL but not on my laptop Thanks

[douganger]

I got the same error on Mac OS X 10.7.3.

[mktrost]

-std=c++0x includes the new C++11 standards. It is only supported in GCC 4.3. I will add an option to disable it. Hopefully I can get that done today. Sorry for the delay in the response. My notifications were screwed up and I only just now saw this issue. I will let you know when the update is in place.

[mktrost]

This should now be updated in the latest development version. The Makefiles should now detect if you are using a gcc version that supports C++11.

If the automatic check does not work and you still get a failure, try adding: CXX11_AVAIL=0 to your Makefile command (or to your environment). Example: make CXX11_AVAIL=0

Let me know if this fixes your problem or if you still are having issues. Again, sorry for the troubles and the delay in resolving it.

[mj343]

I tried what you suggested with make CVV11_AVAIL=0 but I still get

ar -cru ../libStatGen.a obj/bgzf.o obj/knetfile.o /usr/bin/ranlib: file: ../libStatGen.a(LongHash.o) has no symbols /usr/bin/ranlib: file: ../libStatGen.a(TrimSequence.o) has no symbols /usr/bin/ranlib: file: ../libStatGen.a(WindowsHelper.o) has no symbols /usr/bin/ranlib: file: ../libStatGen.a(SamFlag.o) has no symbols ar -cru ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/TrimSequence.o obj/UncompressedFileType.o obj/WindowsHelper.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o /usr/bin/ranlib: file: ../libStatGen.a(LongHash.o) has no symbols /usr/bin/ranlib: file: ../libStatGen.a(TrimSequence.o) has no symbols /usr/bin/ranlib: file: ../libStatGen.a(WindowsHelper.o) has no symbols /usr/bin/ranlib: file: ../libStatGen.a(SamFlag.o) has no symbols ar -cru ../libStatGen.a obj/ErrorHandler.o obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatus.o obj/SamFlag.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o /usr/bin/ranlib: file: ../libStatGen.a(LongHash.o) has no symbols /usr/bin/ranlib: file: ../libStatGen.a(TrimSequence.o) has no symbols /usr/bin/ranlib: file: ../libStatGen.a(WindowsHelper.o) has no symbols /usr/bin/ranlib: file: ../libStatGen.a(SamFlag.o) has no symbols ar -cru ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o /usr/bin/ranlib: file: ../libStatGen.a(LongHash.o) has no symbols /usr/bin/ranlib: file: ../libStatGen.a(TrimSequence.o) has no symbols /usr/bin/ranlib: file: ../libStatGen.a(WindowsHelper.o) has no symbols /usr/bin/ranlib: file: ../libStatGen.a(SamFlag.o) has no symbols ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o /usr/bin/ranlib: file: ../libStatGen.a(LongHash.o) has no symbols /usr/bin/ranlib: file: ../libStatGen.a(TrimSequence.o) has no symbols /usr/bin/ranlib: file: ../libStatGen.a(WindowsHelper.o) has no symbols /usr/bin/ranlib: file: ../libStatGen.a(SamFlag.o) has no symbols

Any suggestions?

[mktrost]

Did you use: CVV11_AVAIL=0 or CXX11_AVAIL=0 ? It should be CXX11_AVAIL=0 I just wanted to check...

Also, can you try a: cd libStatGen (use the correct path to get to yours.) make clean; make CXX11_AVAIL=0

Let me know how that goes. Thanks. Sorry for the difficulties.

[mj343]

hey, thanks for the quick reply. Apologies for before it was a typo in my message, but it still doesn't work!:( I tried with make clean too but no luck.!

....

g++ -O4 -pipe -Wall -I../include -I. -DZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -DSTDC_LIMIT_MACROS -o obj/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.6\"" g++ -O4 -pipe -Wall -I../include -I. -DZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -DSTDC_LIMIT_MACROS -o obj/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.6\"" g++ -O4 -pipe -Wall -I../include -I. -DZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -DSTDC_LIMIT_MACROS -o obj/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.6\"" g++ -O4 -pipe -Wall -I../include -I. -DZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -DSTDC_LIMIT_MACROS -o obj/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.6\"" g++ -O4 -pipe -Wall -I../include -I. -DZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -DSTDC_LIMIT_MACROS -o obj/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.6\"" g++ -O4 -pipe -Wall -I../include -I. -DZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -DSTDC_LIMIT_MACROS -o obj/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.6\"" ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o /usr/bin/ranlib: file: ../libStatGen.a(LongHash.o) has no symbols /usr/bin/ranlib: file: ../libStatGen.a(TrimSequence.o) has no symbols /usr/bin/ranlib: file: ../libStatGen.a(WindowsHelper.o) has no symbols /usr/bin/ranlib: file: ../libStatGen.a(SamFlag.o) has no symbols

is there anything else I should have installed/downloaded except libstatgen?

[mktrost]

Oh, I think I get it now.

It looks like we have a couple of .cpp files that have no code in them. Your ranlib is warning about that. I should clean this up a bit so those files don't exist if they aren't needed.
But I wonder if everything else works properly. Are you able to compile bamUtil and do you get: bamUtil/bin/bam even with these messages?

If you do get the binary and can run that, great. Then it is just a warning message that can be ignored for now, and I will clean that up in the next release. If it doesn't work, let me know and I'll get you a fix sooner.