install error

[awakumaya]

Hi,

I'm stuck at do 'make' in the Mach2VCF directory. The output message including errors is the below:

make[1]: Entering directory '/home/awakumaya/Mach2VCF/src'
make -C ../Library/libStatGenForMinimac3 --no-print-directory opt
ar -cru ../libStatGen.a obj/bgzf.o obj/knetfile.o
ar: `u' modifier ignored since `D' is the default (see `U')
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
ar: `u' modifier ignored since `D' is the default (see `U')
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
ar: `u' modifier ignored since `D' is the default (see `U')
ar -cru ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o
ar: `u' modifier ignored since `D' is the default (see `U')
ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o
ar: `u' modifier ignored since `D' is the default (see `U')
g++  -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\""
In file included from VcfRecord.h:29:0,
                 from VcfFileReader.h:24,
                 from VcfFileReader.cpp:20:
VcfRecordDiscardRules.h:72:18: error: 'unordered_set' in namespace 'std' does not name a template type
     typedef std::unordered_set<vcfIDtype> IDList;
                  ^~~~~~~~~~~~~
VcfRecordDiscardRules.h:80:17: error: 'IDList' has not been declared
     bool setIDs(IDList& idlist, const char* filename);
                 ^~~~~~
VcfRecordDiscardRules.h:82:5: error: 'IDList' does not name a type
     IDList myExcludeIDs;
     ^~~~~~
VcfRecordDiscardRules.h:83:5: error: 'IDList' does not name a type
     IDList myIncludeIDs;
     ^~~~~~
VcfRecordDiscardRules.h: In constructor 'VcfRecordDiscardRules::VcfRecordDiscardRules()':
VcfRecordDiscardRules.h:33:11: error: class 'VcfRecordDiscardRules' does not have any field named 'myExcludeIDs'
         : myExcludeIDs(),
           ^~~~~~~~~~~~
VcfRecordDiscardRules.h:34:11: error: class 'VcfRecordDiscardRules' does not have any field named 'myIncludeIDs'
           myIncludeIDs(),
           ^~~~~~~~~~~~
../Makefiles/Makefile.common:81: recipe for target 'obj/VcfFileReader.o' failed
make[3]: *** [obj/VcfFileReader.o] Error 1
Makefiles/Makefile.base:15: recipe for target 'vcf' failed
make[2]: *** [vcf] Error 2
../Library/libStatGenForMinimac3/Makefiles/Makefile.ext:50: recipe for target '../Library/libStatGenForMinimac3/libStatGen.a' failed
make[1]: *** [../Library/libStatGenForMinimac3/libStatGen.a] Error 2
make[1]: Leaving directory '/home/awakumaya/Mach2VCF/src'
Library/libStatGenForMinimac3/Makefiles/Makefile.base:15: recipe for target 'src' failed
make: *** [src] Error 2

Could anyone help me to solve it?

[Diwadkar]

I am experiencing the exact same issue. Is there any fix available?

[awakumaya]

Sorry. I couldn't to response it for long time. I can't solve the error. But currently,I don't need to use the tool.