bamUtil Compiling issue

Compiling issue

Open kbaySA opened this issue 8 years ago • 6 comments

When I run "make" to compile libStatGen and bamUtil, I get the following errors:

In file included from ClipOverlap.cpp:22:
In file included from ./ClipOverlap.h:27:
./MateMapByCoord.h:70:19: error: no type named 'unordered_multimap' in namespace 'std'
     typedef std::unordered_multimap<uint64_t, SamRecord*> MATE_MAP; 
             ~~~~~^
./MateMapByCoord.h:70:37: error: expected member name or ';' after declaration specifiers
     typedef std::unordered_multimap<uint64_t, SamRecord*> MATE_MAP; 
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
./MateMapByCoord.h:73:5: error: unknown type name 'MATE_MAP'
    MATE_MAP myMateBuffer;
    ^
2 warnings and 3 errors generated.
make[1]: *** [../obj/ClipOverlap.o] Error 1
make: *** [src] Error 2

Then, running make install INSTALLDIR=mydirectory fails to install files into the specified directory and yields the same errors as above.

I've tried fresh installing and updating with no change.

Thanks for your help.

Dec 30 '15 19:12 kbaySA

What's your g++ version? (see by running 'g++ --version')? My guess is that you need more recent version of gcc compiler.

Thanks, Hyun.

On Wed, Dec 30, 2015 at 2:49 PM kbaySA [email protected] wrote:

When I run "make" to compile libStatGen and bamUtil, I get the following errors:

In file included from ClipOverlapcpp:22: In file included from /ClipOverlaph:27: /MateMapByCoordh:70:19: error: no type named 'unordered_multimap' in namespace 'std' typedef std::unordered_multimap MATE_MAP;

/MateMapByCoordh:70:37: error: expected member name or ';' after
declaration specifiers
typedef std::unordered_multimap MATE_MAP;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
/MateMapByCoordh:73:5: error: unknown type name 'MATE_MAP'
MATE_MAP myMateBuffer;
^
2 warnings and 3 errors generated
make[1]: *** [/obj/ClipOverlapo] Error 1
make: *** [src] Error 2

Then, running "make install INSTALLDIR=mydirectory" fails to install files
into the specified directory and yields the same errors as above

I've tried fresh installing and updating with no change

Thanks for your help

—
Reply to this email directly or view it on GitHub
<https://github.com/statgen/bamUtil/issues/18>.

Dec 30 '15 20:12 hyunminkang

You may not have C++11 (which includes unordered_map). If you want to compile without C++11, you can try one of the following:

Update bamUtil/Makefile.inc, line 7, change CXX11_AVAIL ?= 1 to CXX11_AVAIL = 0
Set CXX11_AVAIL to 0 on the command line: make CXX11_AVAIL=0
Set CXX11_AVAIL = 0 in your environment

Let me know if none of those work for you.

Jan 02 '16 16:01 mktrost

Same problem. g++ version = Apple LLVM version 7.3.0 (clang-703.0.31) Target: x86_64-apple-darwin15.6.0 Thread model: posix

mktrost, i tried your second option, outcome: 2 warnings and 3 errors generated. make[1]: *** [../obj/ClipOverlap.o] Error 1 make: *** [src] Error 2

when I use make, same thing: 2 warnings and 3 errors generated. make[1]: *** [../obj/ClipOverlap.o] Error 1 make: *** [src] Error 2

Aug 09 '16 12:08 TiongSun

Run "make CFLAGS=-std=c++11" when compiling with clang.

Aug 09 '16 14:08 jonathonl

Hi Jonathonl, I tried but got this:

/Applications/Xcode.app/Contents/Developer/usr/bin/make -C ../../libStatGen --no-print-directory opt ar -cru ../libStatGen.a obj/bgzf.o obj/knetfile.o /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../libStatGen.a(SmithWaterman.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../libStatGen.a(VcfRecordField.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/ErrorHandler.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/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.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/PhoneHome.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../libStatGen.a(SmithWaterman.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../libStatGen.a(VcfRecordField.o) has no symbols ar -cru ../libStatGen.a 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/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 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../libStatGen.a(SmithWaterman.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../libStatGen.a(VcfRecordField.o) has no symbols ar -cru ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../libStatGen.a(SmithWaterman.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../libStatGen.a(VcfRecordField.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 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../libStatGen.a(SmithWaterman.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../libStatGen.a(VcfRecordField.o) has no symbols ar -cru ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o obj/VcfRecordDiscardRules.o /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../libStatGen.a(SmithWaterman.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../libStatGen.a(VcfRecordField.o) has no symbols g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:03 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/ClipOverlap.o -c ClipOverlap.cpp -DVERSION=""1.0.14"" g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:04 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/MateMapByCoord.o -c MateMapByCoord.cpp -DVERSION=""1.0.14"" g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:05 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/SplitBam.o -c SplitBam.cpp -DVERSION=""1.0.14"" SplitBam.cpp:271:16: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] if ( (idx >= 0 ) && ( idx < vsRGIDs.size () ) ) { ~~~ ^ ~ 1 warning generated. g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:05 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/TrimBam.o -c TrimBam.cpp -DVERSION=""1.0.14"" g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:06 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/MergeBam.o -c MergeBam.cpp -DVERSION=""1.0.14"" g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:07 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/PolishBam.o -c PolishBam.cpp -DVERSION=""1.0.14"" g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:07 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/GapInfo.o -c GapInfo.cpp -DVERSION=""1.0.14"" g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:08 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/Logger.o -c Logger.cpp -DVERSION=""1.0.14"" g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:08 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/Bam2FastQ.o -c Bam2FastQ.cpp -DVERSION=""1.0.14"" g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:09 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/Dedup.o -c Dedup.cpp -DVERSION=""1.0.14"" g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:10 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/Dedup_LowMem.o -c Dedup_LowMem.cpp -DVERSION=""1.0.14"" g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:11 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/Prediction.o -c Prediction.cpp -DVERSION=""1.0.14"" g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:11 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/LogisticRegression.o -c LogisticRegression.cpp -DVERSION=""1.0.14"" g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:11 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/MathCholesky.o -c MathCholesky.cpp -DVERSION=""1.0.14"" g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:12 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/HashErrorModel.o -c HashErrorModel.cpp -DVERSION=""1.0.14"" g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:12 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/Recab.o -c Recab.cpp -DVERSION=""1.0.14"" g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:13 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/OverlapHandler.o -c OverlapHandler.cpp -DVERSION=""1.0.14"" g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:13 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/OverlapClipLowerBaseQual.o -c OverlapClipLowerBaseQual.cpp -DVERSION=""1.0.14"" g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:14 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/ExplainFlags.o -c ExplainFlags.cpp -DVERSION=""1.0.14"" g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:14 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/Main.o -c Main.cpp -DVERSION=""1.0.14"" g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:15 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../obj/BamExecutable.o -c BamExecutable.cpp -DVERSION=""1.0.14"" mkdir -p ../bin g++ -std=c++11 -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE=""Tue 9 Aug 2016 15:50:16 BST"" -DVERSION=""1.0.14"" -DUSER=""tiong"" -o ../bin/bam ../obj/BamExecutable.o ../obj/Validate.o ../obj/Convert.o ../obj/Diff.o ../obj/DumpHeader.o ../obj/SplitChromosome.o ../obj/WriteRegion.o ../obj/DumpIndex.o ../obj/ReadIndexedBam.o ../obj/DumpRefInfo.o ../obj/Filter.o ../obj/ReadReference.o ../obj/Revert.o ../obj/Squeeze.o ../obj/FindCigars.o ../obj/Stats.o ../obj/PileupElementBaseQCStats.o ../obj/ClipOverlap.o ../obj/MateMapByCoord.o ../obj/SplitBam.o ../obj/TrimBam.o ../obj/MergeBam.o ../obj/PolishBam.o ../obj/GapInfo.o ../obj/Logger.o ../obj/Bam2FastQ.o ../obj/Dedup.o ../obj/Dedup_LowMem.o ../obj/Prediction.o ../obj/LogisticRegression.o ../obj/MathCholesky.o ../obj/HashErrorModel.o ../obj/Recab.o ../obj/OverlapHandler.o ../obj/OverlapClipLowerBaseQual.o ../obj/ExplainFlags.o ../obj/Main.o ../../libStatGen/libStatGen.a -lm -lz

Aug 09 '16 15:08 TiongSun

Hi Jonathonl, it installed successfully! Thanks a lots!!!!!!

Aug 09 '16 15:08 TiongSun

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