01.make

2015-09-10 22:49:46 -0700

make
STATIC=
HDF5INCLUDEDIR=/usr/local/opt/hdf5/include
HDF5LIBDIR=/usr/local/opt/hdf5/lib

mkdir -p bin
gcc-5 -MM *.cpp  -I ../common -I /usr/local/opt/hdf5/include > make.dep 
mkdir -p bin
mkdir -p bin
gcc-5 -MM *.cpp  -I ..//common -I /usr/local/opt/hdf5/include > make.dep 
gcc-5 -MM *.cpp  -I ../common -I /usr/local/opt/hdf5/include > make.dep 
mkdir -p bin
gcc-5 -MM *.cpp  -I ../common -I /usr/local/opt/hdf5/include > make.dep 
..//MoveODependenciesToBin.pl make.dep make.dep2
mv make.dep2 make.dep							 
g++-5 -I ..//common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive -c SuffixArrayToBWT.cpp  -o bin/SuffixArrayToBWT.o
../MoveODependenciesToBin.pl make.dep make.dep2
mv make.dep2 make.dep							 
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -fno-trapping-math -c LoadPulses.cpp  -o bin/LoadPulses.o
../MoveODependenciesToBin.pl make.dep make.dep2
mv make.dep2 make.dep							 
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c Blasr.cpp  -o bin/Blasr.o
../MoveODependenciesToBin.pl make.dep make.dep2
mv make.dep2 make.dep							 
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c ConcatenateSequences.cpp  -o bin/ConcatenateSequences.o
g++-5 -I ..//common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive -c BwtToSuffixArray.cpp  -o bin/BwtToSuffixArray.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c Compress.cpp  -o bin/Compress.o
g++-5 -I ..//common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive -c BWTLocateList.cpp  -o bin/BWTLocateList.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c FilterSeq.cpp  -o bin/FilterSeq.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c BuildSequenceDB.cpp  -o bin/BuildSequenceDB.o
g++-5 -I ..//common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive -c PrintBWTSWBWT.cpp  -o bin/PrintBWTSWBWT.o
g++-5 -I ..//common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive -c PrintPBBWT.cpp  -o bin/PrintPBBWT.o
g++-5 -I ..//common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive -c BWTQuery.cpp  -o bin/BWTQuery.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c ConcatenateReads.cpp  -o bin/ConcatenateReads.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SimpleShredder.cpp  -o bin/SimpleShredder.o
#Mark, I added HDFLIBDIR b/c libz now gets compiled to that dir. Otherwise, -lz fails if libz is not installed. -johann
g++-5  -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive bin/SuffixArrayToBWT.o -o bin/sa2bwt -L/usr/local/opt/hdf5/lib -lz -lpthread
g++-5  -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive bin/BwtToSuffixArray.o -o bin/bwt2sa -L/usr/local/opt/hdf5/lib -lz -lpthread
g++-5  -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive bin/BWTLocateList.o -o bin/bwtLocateList -L/usr/local/opt/hdf5/lib -lz -lpthread
g++-5  -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive bin/PrintBWTSWBWT.o -o bin/bwtswPrint -L/usr/local/opt/hdf5/lib -lz -lpthread
g++-5  -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive bin/PrintPBBWT.o -o bin/bwtpbPrint -L/usr/local/opt/hdf5/lib -lz -lpthread
g++-5  -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive bin/BWTQuery.o -o bin/bwtquery -L/usr/local/opt/hdf5/lib -lz -lpthread
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c WriteHDFSubset.cpp  -o bin/WriteHDFSubset.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c CountUniqueNMers.cpp  -o bin/CountUniqueNMers.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c Evolve.cpp  -o bin/Evolve.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c WordCounter.cpp  -o bin/WordCounter.o
mkdir -p bin
gcc-5 -MM *.cpp  -I ../common -I /usr/local/opt/hdf5/include > make.dep 
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c ExtractSeq.cpp  -o bin/ExtractSeq.o
../MoveODependenciesToBin.pl make.dep make.dep2
mv make.dep2 make.dep							 
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c StoreQualityByContext.cpp  -o bin/StoreQualityByContext.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c ExtractRepeats.cpp  -o bin/ExtractRepeats.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PrintUngappedSequenceLengthHistogram.cpp  -o bin/PrintUngappedSequenceLengthHistogram.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PulseToFasta.cpp  -o bin/PulseToFasta.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c Dustoff.cpp  -o bin/Dustoff.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SplitContigs.cpp  -o bin/SplitContigs.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PrintUnalignedSequences.cpp  -o bin/PrintUnalignedSequences.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c ScrambleSequenceOrder.cpp  -o bin/ScrambleSequenceOrder.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c LoadContextOut.cpp  -o bin/LoadContextOut.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c BasH5Simulator.cpp  -o bin/BasH5Simulator.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c MaskSequence.cpp  -o bin/MaskSequence.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SelectRandomSubstrings.cpp  -o bin/SelectRandomSubstrings.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PrintHomopolymerCount.cpp  -o bin/PrintHomopolymerCount.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c ExtractReadsByTitle.cpp  -o bin/ExtractReadsByTitle.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PrintGCRank.cpp  -o bin/PrintGCRank.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c Hammer.cpp  -o bin/Hammer.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c StoreQualityByContextFromCmpH5.cpp  -o bin/StoreQualityByContextFromCmpH5.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c CheckForFilteredReads.cpp  -o bin/CheckForFilteredReads.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c NormalizeGCContent.cpp  -o bin/NormalizeGCContent.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c FilterHDFPls.cpp  -o bin/FilterHDFPls.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PrintReadWordCount.cpp  -o bin/PrintReadWordCount.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c ExciseRepeats.cpp  -o bin/ExciseRepeats.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SDPMatcher.cpp  -o bin/SDPMatcher.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PrintTitleTable.cpp  -o bin/PrintTitleTable.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c MakeBarcodeDatabase.cpp  -o bin/MakeBarcodeDatabase.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c TileGenome.cpp  -o bin/TileGenome.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PrintHDFPlsSummary.cpp  -o bin/PrintHDFPlsSummary.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c Sageify.cpp  -o bin/Sageify.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c FilterBySubreadAgreement.cpp  -o bin/FilterBySubreadAgreement.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SWMatcher.cpp  -o bin/SWMatcher.o
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/StoreQualityByContext.o  -o bin/storeQualityByContext  -L/usr/local/opt/hdf5/lib -lhdf5_cpp -lhdf5 -lz -lpthread -ldl
Undefined symbols for architecture x86_64:
  "H5::H5Location::iterateAttrs(void (*)(H5::H5Location&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, void*), unsigned int*, void*)", referenced from:
      HDFAttributable::ContainsAttribute(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) in StoreQualityByContext.o
  "H5::CommonFG::getObjnameByIdx[abi:cxx11](unsigned long long) const", referenced from:
      HDFGroup::ContainsObject(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) in StoreQualityByContext.o
  "H5::Attribute::read(H5::DataType const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&) const", referenced from:
      HDFAtom<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >::Read(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&) in StoreQualityByContext.o
  "H5::Attribute::write(H5::DataType const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const", referenced from:
      HDFAtom<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >::Write(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) in StoreQualityByContext.o
  "H5::Exception::getDetailMsg[abi:cxx11]() const", referenced from:
      HDFData::InitializeDataset(H5::CommonFG&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) in StoreQualityByContext.o
      BufferedHDF2DArray<short>::Initialize(HDFGroup&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, bool) in StoreQualityByContext.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[1]: *** [bin/storeQualityByContext] Error 1
make: *** [simulator-build] Error 2
make: *** Waiting for unfinished jobs....
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c TestAdvance.cpp  -o bin/TestAdvance.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c ComputeRefCoverage.cpp  -o bin/ComputeRefCoverage.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c KBandMatcher.cpp  -o bin/KBandMatcher.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SAWriter.cpp  -o bin/SAWriter.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SAQuery.cpp  -o bin/SAQuery.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c ToAfg.cpp  -o bin/ToAfg.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SAModify.cpp  -o bin/SAModify.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PrintTupleCountTable.cpp  -o bin/PrintTupleCountTable.o
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/ConcatenateSequences.o  -o bin/catseq
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/Compress.o  -o bin/compressseq
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c CmpH5View.cpp  -o bin/CmpH5View.o
g++-5 -c -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -DCOMPRESSED PrintTupleCountTable.cpp  -o bin/CmpPrintTupleCountTable.o
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/FilterSeq.o  -o bin/filterseq
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/BuildSequenceDB.o  -o bin/bsdb -L/usr/local/opt/hdf5/lib -lhdf5_cpp -lhdf5 -lz -lpthread -ldl 
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/ConcatenateReads.o  -o bin/catreads
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/SimpleShredder.o  -o bin/simpleShredder
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/CountUniqueNMers.o  -o bin/countKmers
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/Evolve.o  -o bin/evolve
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/ExtractSeq.o  -o bin/extractseq
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/ExtractRepeats.o  -o bin/extractrep
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/PrintUngappedSequenceLengthHistogram.o  -o bin/printUngappedLengths
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c MAlign.cpp  -o bin/MAlign.o
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/Dustoff.o  -o bin/dustoff
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/SplitContigs.o  -o bin/splitContigs
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/PrintUnalignedSequences.o  -o bin/printUnalignedSequences
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/ScrambleSequenceOrder.o  -o bin/scramble
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/MaskSequence.o  -o bin/maskSequence
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/SelectRandomSubstrings.o  -o bin/selectRandomSubstrings
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/PrintHomopolymerCount.o  -o bin/printHPC
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/PrintGCRank.o  -o bin/gcrank
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/Hammer.o  -o bin/hammer
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/CheckForFilteredReads.o  -o bin/checkfilt
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c RemoveAdapters.cpp  -o bin/RemoveAdapters.o
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/NormalizeGCContent.o  -o bin/normgc
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c CmpH5Information.cpp  -o bin/CmpH5Information.o
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/ExciseRepeats.o  -o bin/excrep
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/PrintTitleTable.o  -o bin/printTitleTable -lz -lpthread
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/MakeBarcodeDatabase.o  -o bin/makeBarcodeDatabase
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/TileGenome.o  -o bin/tileGenome
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/FilterBySubreadAgreement.o  -o bin/filterBySubreadAgreement -L/usr/local/opt/hdf5/lib -lhdf5_cpp -lhdf5 -lz -lpthread -ldl
Undefined symbols for architecture x86_64:
  "H5::H5Location::iterateAttrs(void (*)(H5::H5Location&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, void*), unsigned int*, void*)", referenced from:
      HDFAttributable::ContainsAttribute(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) in FilterBySubreadAgreement.o
  "H5::CommonFG::createGroup(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long) const", referenced from:
      HDFRegionTableWriter::CreateGroupStructure()       in FilterBySubreadAgreement.o
  "H5::CommonFG::getObjnameByIdx[abi:cxx11](unsigned long long) const", referenced from:
      HDFGroup::ContainsObject(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) in FilterBySubreadAgreement.o
  "H5::Attribute::read(H5::DataType const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&) const", referenced from:
      HDFAtom<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >::Read(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&) in FilterBySubreadAgreement.o
  "H5::Attribute::write(H5::DataType const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const", referenced from:
      HDFAtom<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >::Write(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) in FilterBySubreadAgreement.o
  "H5::Exception::getDetailMsg[abi:cxx11]() const", referenced from:
      HDFData::InitializeDataset(H5::CommonFG&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) in FilterBySubreadAgreement.o
      BufferedHDF2DArray<short>::Initialize(HDFGroup&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, bool) in FilterBySubreadAgreement.o
      BufferedHDF2DArray<int>::Initialize(HDFGroup&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, bool) in FilterBySubreadAgreement.o
      HDFRegionTableReader::Initialize(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, H5::FileAccPropList const&) in FilterBySubreadAgreement.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[1]: *** [bin/filterBySubreadAgreement] Error 1
make: *** [sequtils-build] Error 2
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c TabulateAlignment.cpp  -o bin/TabulateAlignment.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PrintMSA.cpp  -o bin/PrintMSA.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SAMatcher.cpp  -o bin/SAMatcher.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SAPrinter.cpp  -o bin/SAPrinter.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c BuildQualityValueProfile.cpp  -o bin/BuildQualityValueProfile.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PrintVariants.cpp  -o bin/PrintVariants.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c GuidedAlign.cpp  -o bin/GuidedAlign.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c DiffAlnInfoGroups.cpp  -o bin/DiffAlnInfoGroups.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c ExtendAlign.cpp  -o bin/ExtendAlign.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SamToCmpH5.cpp  -o bin/SamToCmpH5.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SamToM4.cpp  -o bin/SamToM4.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SALS.cpp  -o bin/SALS.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SamFilter.cpp  -o bin/SamFilter.o
g++-5 -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c Mask.cpp  -o bin/Mask.o
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/LoadPulses.o  -o bin/loadPulses  -L/usr/local/opt/hdf5/lib -lhdf5_cpp -lhdf5 -lz -lpthread -ldl 
Undefined symbols for architecture x86_64:
  "H5::H5Location::iterateAttrs(void (*)(H5::H5Location&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, void*), unsigned int*, void*)", referenced from:
      HDFAttributable::ContainsAttribute(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) in LoadPulses.o
  "H5::CommonFG::getObjnameByIdx[abi:cxx11](unsigned long long) const", referenced from:
      HDFGroup::ContainsObject(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) in LoadPulses.o
  "H5::Attribute::read(H5::DataType const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&) const", referenced from:
      HDFAtom<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >::Read(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&) in LoadPulses.o
  "H5::Attribute::write(H5::DataType const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const", referenced from:
      HDFAtom<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >::Write(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) in LoadPulses.o
  "H5::Exception::getDetailMsg[abi:cxx11]() const", referenced from:
      HDFData::InitializeDataset(H5::CommonFG&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) in LoadPulses.o
      BufferedHDF2DArray<unsigned int>::Initialize(HDFGroup&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, bool) in LoadPulses.o
      BufferedHDF2DArray<short>::Initialize(HDFGroup&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, bool) in LoadPulses.o
      BufferedHDF2DArray<unsigned short>::Initialize(HDFGroup&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, bool) in LoadPulses.o
      HDFCmpFile<CmpAlignment>::Initialize(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned int, H5::FileAccPropList) in LoadPulses.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[1]: *** [bin/loadPulses] Error 1
make[1]: *** Waiting for unfinished jobs....
g++-5 -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/Blasr.o   -L/usr/local/opt/hdf5/lib -lhdf5_cpp -lhdf5 -lz -lpthread -ldl  -o bin/blasr
Undefined symbols for architecture x86_64:
  "H5::H5Location::iterateAttrs(void (*)(H5::H5Location&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, void*), unsigned int*, void*)", referenced from:
      HDFAttributable::ContainsAttribute(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) in Blasr.o
  "H5::CommonFG::getObjnameByIdx[abi:cxx11](unsigned long long) const", referenced from:
      HDFGroup::ContainsObject(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) in Blasr.o
  "H5::Attribute::read(H5::DataType const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&) const", referenced from:
      HDFAtom<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >::Read(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&) in Blasr.o
  "H5::Attribute::write(H5::DataType const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const", referenced from:
      HDFAtom<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >::Write(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) in Blasr.o
  "H5::Exception::getDetailMsg[abi:cxx11]() const", referenced from:
      HDFData::InitializeDataset(H5::CommonFG&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) in Blasr.o
      BufferedHDF2DArray<short>::Initialize(HDFGroup&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, bool) in Blasr.o
      BufferedHDF2DArray<int>::Initialize(HDFGroup&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, bool) in Blasr.o
      HDFRegionTableReader::Initialize(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, H5::FileAccPropList const&) in Blasr.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[1]: *** [bin/blasr] Error 1
make[1]: *** Waiting for unfinished jobs....
make: *** [pbihdfutils-build] Error 2
make: *** [alignment-build] Error 2

HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/homebrew
HEAD: 85de42b8002b6a75b2af4cb6f6a8bd1a47fdc188
Last commit: 3 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_REPOSITORY: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://homebrew.bintray.com
CPU: quad-core 64-bit broadwell
OS X: 10.10.5-x86_64
Xcode: 6.4
CLT: N/A
Clang: 6.1 build 602
X11: 2.7.7 => /opt/X11
System Ruby: 2.0.0-p481
Perl: /usr/bin/perl
Python: /usr/bin/python
Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby
Java: N/A

HOMEBREW_CC: gcc-5
HOMEBREW_CXX: g++-5
MAKEFLAGS: -j4
CMAKE_PREFIX_PATH: /usr/local
CMAKE_INCLUDE_PATH: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2:/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2:/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
CMAKE_LIBRARY_PATH: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
CMAKE_FRAMEWORK_PATH: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks
PKG_CONFIG_LIBDIR: /usr/lib/pkgconfig:/usr/local/Library/ENV/pkgconfig/10.10
HOMEBREW_SDKROOT: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk
ACLOCAL_PATH: /usr/local/share/aclocal
PATH: /usr/local/Library/ENV/4.3:/usr/local/opt/hdf5/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/opt/gcc/bin

01.make.cc

gcc-5 called with: -dumpversion
superenv added:    -pipe -w -Os -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: gcc-5 -pipe -w -Os -dumpversion -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

gcc-5 called with: -dumpversion
superenv added:    -pipe -w -Os -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: gcc-5 -pipe -w -Os -dumpversion -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

gcc-5 called with: -dumpversion
superenv added:    -pipe -w -Os -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: gcc-5 -pipe -w -Os -dumpversion -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

gcc-5 called with: -dumpversion
superenv added:    -pipe -w -Os -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: gcc-5 -pipe -w -Os -dumpversion -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

gcc-5 called with: -MM CmpH5Information.cpp CmpH5ToCmpXML.cpp CmpH5View.cpp ComputeRefCoverage.cpp DiffAlnInfoGroups.cpp ExtractReadsByTitle.cpp FilterHDFPls.cpp LoadPulses.cpp PrintHDFPlsSummary.cpp PrintMSA.cpp PrintMapqvTrack.cpp PrintVariants.cpp PulseToFasta.cpp SamFilter.cpp SamToCmpH5.cpp SamToM4.cpp TestAdvance.cpp ToAfg.cpp WriteHDFSubset.cpp -I ../common -I /usr/local/opt/hdf5/include
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: gcc-5 -pipe -w -Os -MM CmpH5Information.cpp CmpH5ToCmpXML.cpp CmpH5View.cpp ComputeRefCoverage.cpp DiffAlnInfoGroups.cpp ExtractReadsByTitle.cpp FilterHDFPls.cpp LoadPulses.cpp PrintHDFPlsSummary.cpp PrintMSA.cpp PrintMapqvTrack.cpp PrintVariants.cpp PulseToFasta.cpp SamFilter.cpp SamToCmpH5.cpp SamToM4.cpp TestAdvance.cpp ToAfg.cpp WriteHDFSubset.cpp -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

gcc-5 called with: -MM BWTLocateList.cpp BWTQuery.cpp BwtToSuffixArray.cpp PrintBWTSWBWT.cpp PrintPBBWT.cpp SuffixArrayToBWT.cpp -I ..//common -I /usr/local/opt/hdf5/include
superenv removed:  -I ..//common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I..//common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: gcc-5 -pipe -w -Os -MM BWTLocateList.cpp BWTQuery.cpp BwtToSuffixArray.cpp PrintBWTSWBWT.cpp PrintPBBWT.cpp SuffixArrayToBWT.cpp -I..//common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

gcc-5 called with: -MM BuildSequenceDB.cpp CheckForFilteredReads.cpp Compress.cpp ConcatenateReads.cpp ConcatenateSequences.cpp Condense.cpp CountUniqueNMers.cpp Dustoff.cpp Evolve.cpp ExciseRepeats.cpp ExtractRepeats.cpp ExtractSeq.cpp FileGenome.cpp FilterBySubreadAgreement.cpp FilterSeq.cpp Hammer.cpp KnownGeneToSequence.cpp MakeBarcodeDatabase.cpp MaskSequence.cpp NormalizeGCContent.cpp OurMatch.cpp PrintGCRank.cpp PrintHomopolymerCount.cpp PrintReverseComplements.cpp PrintTitleTable.cpp PrintUnalignedSequences.cpp PrintUngappedSequenceLengthHistogram.cpp ReverseComplement.cpp ScrambleSequenceOrder.cpp SelectRandomSubstrings.cpp SimpleShredder.cpp SimulateConcatenates.cpp SplitContigs.cpp TileGenome.cpp -I ../common -I /usr/local/opt/hdf5/include
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: gcc-5 -pipe -w -Os -MM BuildSequenceDB.cpp CheckForFilteredReads.cpp Compress.cpp ConcatenateReads.cpp ConcatenateSequences.cpp Condense.cpp CountUniqueNMers.cpp Dustoff.cpp Evolve.cpp ExciseRepeats.cpp ExtractRepeats.cpp ExtractSeq.cpp FileGenome.cpp FilterBySubreadAgreement.cpp FilterSeq.cpp Hammer.cpp KnownGeneToSequence.cpp MakeBarcodeDatabase.cpp MaskSequence.cpp NormalizeGCContent.cpp OurMatch.cpp PrintGCRank.cpp PrintHomopolymerCount.cpp PrintReverseComplements.cpp PrintTitleTable.cpp PrintUnalignedSequences.cpp PrintUngappedSequenceLengthHistogram.cpp ReverseComplement.cpp ScrambleSequenceOrder.cpp SelectRandomSubstrings.cpp SimpleShredder.cpp SimulateConcatenates.cpp SplitContigs.cpp TileGenome.cpp -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

gcc-5 called with: -MM Blasr.cpp BuildQualityValueProfile.cpp ExtendAlign.cpp GuidedAlign.cpp KBandMatcher.cpp MAlign.cpp Mask.cpp OneGapAlign.cpp PositionTable.cpp PrintReadWordCount.cpp PrintTupleCountTable.cpp Prism.cpp RemoveAdapters.cpp SALS.cpp SAMatcher.cpp SAModify.cpp SAPrinter.cpp SAQuery.cpp SAWriter.cpp SDPMatcher.cpp SWMatcher.cpp SeqReader.cpp TabulateAlignment.cpp WordCounter.cpp -I ../common -I /usr/local/opt/hdf5/include
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: gcc-5 -pipe -w -Os -MM Blasr.cpp BuildQualityValueProfile.cpp ExtendAlign.cpp GuidedAlign.cpp KBandMatcher.cpp MAlign.cpp Mask.cpp OneGapAlign.cpp PositionTable.cpp PrintReadWordCount.cpp PrintTupleCountTable.cpp Prism.cpp RemoveAdapters.cpp SALS.cpp SAMatcher.cpp SAModify.cpp SAPrinter.cpp SAQuery.cpp SAWriter.cpp SDPMatcher.cpp SWMatcher.cpp SeqReader.cpp TabulateAlignment.cpp WordCounter.cpp -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

g++-5 called with: -I ..//common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive -c SuffixArrayToBWT.cpp -o bin/SuffixArrayToBWT.o
superenv removed:  -I ..//common -I /usr/local/opt/hdf5/include -O3 -I ..//common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I..//common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I..//common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c SuffixArrayToBWT.cpp -o bin/SuffixArrayToBWT.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -fno-trapping-math -c LoadPulses.cpp -o bin/LoadPulses.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -fno-trapping-math -c LoadPulses.cpp -o bin/LoadPulses.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c Blasr.cpp -o bin/Blasr.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c Blasr.cpp -o bin/Blasr.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c ConcatenateSequences.cpp -o bin/ConcatenateSequences.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c ConcatenateSequences.cpp -o bin/ConcatenateSequences.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ..//common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive -c BwtToSuffixArray.cpp -o bin/BwtToSuffixArray.o
superenv removed:  -I ..//common -I /usr/local/opt/hdf5/include -O3 -I ..//common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I..//common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I..//common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c BwtToSuffixArray.cpp -o bin/BwtToSuffixArray.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c Compress.cpp -o bin/Compress.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c Compress.cpp -o bin/Compress.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ..//common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive -c BWTLocateList.cpp -o bin/BWTLocateList.o
superenv removed:  -I ..//common -I /usr/local/opt/hdf5/include -O3 -I ..//common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I..//common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I..//common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c BWTLocateList.cpp -o bin/BWTLocateList.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c FilterSeq.cpp -o bin/FilterSeq.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c FilterSeq.cpp -o bin/FilterSeq.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c BuildSequenceDB.cpp -o bin/BuildSequenceDB.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c BuildSequenceDB.cpp -o bin/BuildSequenceDB.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ..//common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive -c PrintBWTSWBWT.cpp -o bin/PrintBWTSWBWT.o
superenv removed:  -I ..//common -I /usr/local/opt/hdf5/include -O3 -I ..//common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I..//common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I..//common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c PrintBWTSWBWT.cpp -o bin/PrintBWTSWBWT.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ..//common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive -c PrintPBBWT.cpp -o bin/PrintPBBWT.o
superenv removed:  -I ..//common -I /usr/local/opt/hdf5/include -O3 -I ..//common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I..//common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I..//common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c PrintPBBWT.cpp -o bin/PrintPBBWT.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ..//common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive -c BWTQuery.cpp -o bin/BWTQuery.o
superenv removed:  -I ..//common -I /usr/local/opt/hdf5/include -O3 -I ..//common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I..//common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I..//common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c BWTQuery.cpp -o bin/BWTQuery.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c ConcatenateReads.cpp -o bin/ConcatenateReads.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c ConcatenateReads.cpp -o bin/ConcatenateReads.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SimpleShredder.cpp -o bin/SimpleShredder.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c SimpleShredder.cpp -o bin/SimpleShredder.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive bin/SuffixArrayToBWT.o -o bin/sa2bwt -L/usr/local/opt/hdf5/lib -lz -lpthread
superenv removed:  -O3 -I ..//common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I..//common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I..//common -I/usr/local/opt/hdf5/include -fpermissive bin/SuffixArrayToBWT.o -o bin/sa2bwt -L/usr/local/opt/hdf5/lib -lz -lpthread -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/sa2bwt -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/SuffixArrayToBWT.o -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/sa2bwt -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/SuffixArrayToBWT.o -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive bin/BwtToSuffixArray.o -o bin/bwt2sa -L/usr/local/opt/hdf5/lib -lz -lpthread
superenv removed:  -O3 -I ..//common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I..//common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I..//common -I/usr/local/opt/hdf5/include -fpermissive bin/BwtToSuffixArray.o -o bin/bwt2sa -L/usr/local/opt/hdf5/lib -lz -lpthread -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/bwt2sa -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/BwtToSuffixArray.o -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/bwt2sa -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/BwtToSuffixArray.o -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive bin/BWTLocateList.o -o bin/bwtLocateList -L/usr/local/opt/hdf5/lib -lz -lpthread
superenv removed:  -O3 -I ..//common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I..//common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I..//common -I/usr/local/opt/hdf5/include -fpermissive bin/BWTLocateList.o -o bin/bwtLocateList -L/usr/local/opt/hdf5/lib -lz -lpthread -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/bwtLocateList -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/BWTLocateList.o -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/bwtLocateList -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/BWTLocateList.o -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive bin/PrintBWTSWBWT.o -o bin/bwtswPrint -L/usr/local/opt/hdf5/lib -lz -lpthread
superenv removed:  -O3 -I ..//common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I..//common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I..//common -I/usr/local/opt/hdf5/include -fpermissive bin/PrintBWTSWBWT.o -o bin/bwtswPrint -L/usr/local/opt/hdf5/lib -lz -lpthread -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/bwtswPrint -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/PrintBWTSWBWT.o -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/bwtswPrint -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/PrintBWTSWBWT.o -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive bin/PrintPBBWT.o -o bin/bwtpbPrint -L/usr/local/opt/hdf5/lib -lz -lpthread
superenv removed:  -O3 -I ..//common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I..//common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I..//common -I/usr/local/opt/hdf5/include -fpermissive bin/PrintPBBWT.o -o bin/bwtpbPrint -L/usr/local/opt/hdf5/lib -lz -lpthread -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/bwtpbPrint -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/PrintPBBWT.o -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/bwtpbPrint -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/PrintPBBWT.o -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include -fpermissive bin/BWTQuery.o -o bin/bwtquery -L/usr/local/opt/hdf5/lib -lz -lpthread
superenv removed:  -O3 -I ..//common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I..//common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I..//common -I/usr/local/opt/hdf5/include -fpermissive bin/BWTQuery.o -o bin/bwtquery -L/usr/local/opt/hdf5/lib -lz -lpthread -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/bwtquery -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/BWTQuery.o -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/bwtquery -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/BWTQuery.o -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c WriteHDFSubset.cpp -o bin/WriteHDFSubset.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c WriteHDFSubset.cpp -o bin/WriteHDFSubset.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c CountUniqueNMers.cpp -o bin/CountUniqueNMers.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c CountUniqueNMers.cpp -o bin/CountUniqueNMers.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c Evolve.cpp -o bin/Evolve.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c Evolve.cpp -o bin/Evolve.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c WordCounter.cpp -o bin/WordCounter.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c WordCounter.cpp -o bin/WordCounter.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

gcc-5 called with: -dumpversion
superenv added:    -pipe -w -Os -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: gcc-5 -pipe -w -Os -dumpversion -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

gcc-5 called with: -MM BasH5Simulator.cpp CmpH5ToMerProfile.cpp LoadContextOut.cpp PrintLengthHistogramFromCmph5.cpp Sageify.cpp StoreQualityByContext.cpp StoreQualityByContextFromCmpH5.cpp -I ../common -I /usr/local/opt/hdf5/include
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: gcc-5 -pipe -w -Os -MM BasH5Simulator.cpp CmpH5ToMerProfile.cpp LoadContextOut.cpp PrintLengthHistogramFromCmph5.cpp Sageify.cpp StoreQualityByContext.cpp StoreQualityByContextFromCmpH5.cpp -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c ExtractSeq.cpp -o bin/ExtractSeq.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c ExtractSeq.cpp -o bin/ExtractSeq.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c StoreQualityByContext.cpp -o bin/StoreQualityByContext.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c StoreQualityByContext.cpp -o bin/StoreQualityByContext.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c ExtractRepeats.cpp -o bin/ExtractRepeats.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c ExtractRepeats.cpp -o bin/ExtractRepeats.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PrintUngappedSequenceLengthHistogram.cpp -o bin/PrintUngappedSequenceLengthHistogram.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c PrintUngappedSequenceLengthHistogram.cpp -o bin/PrintUngappedSequenceLengthHistogram.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PulseToFasta.cpp -o bin/PulseToFasta.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c PulseToFasta.cpp -o bin/PulseToFasta.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c Dustoff.cpp -o bin/Dustoff.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c Dustoff.cpp -o bin/Dustoff.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SplitContigs.cpp -o bin/SplitContigs.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c SplitContigs.cpp -o bin/SplitContigs.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PrintUnalignedSequences.cpp -o bin/PrintUnalignedSequences.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c PrintUnalignedSequences.cpp -o bin/PrintUnalignedSequences.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c ScrambleSequenceOrder.cpp -o bin/ScrambleSequenceOrder.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c ScrambleSequenceOrder.cpp -o bin/ScrambleSequenceOrder.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c LoadContextOut.cpp -o bin/LoadContextOut.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c LoadContextOut.cpp -o bin/LoadContextOut.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c BasH5Simulator.cpp -o bin/BasH5Simulator.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c BasH5Simulator.cpp -o bin/BasH5Simulator.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c MaskSequence.cpp -o bin/MaskSequence.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c MaskSequence.cpp -o bin/MaskSequence.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SelectRandomSubstrings.cpp -o bin/SelectRandomSubstrings.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c SelectRandomSubstrings.cpp -o bin/SelectRandomSubstrings.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PrintHomopolymerCount.cpp -o bin/PrintHomopolymerCount.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c PrintHomopolymerCount.cpp -o bin/PrintHomopolymerCount.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c ExtractReadsByTitle.cpp -o bin/ExtractReadsByTitle.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c ExtractReadsByTitle.cpp -o bin/ExtractReadsByTitle.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PrintGCRank.cpp -o bin/PrintGCRank.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c PrintGCRank.cpp -o bin/PrintGCRank.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c Hammer.cpp -o bin/Hammer.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c Hammer.cpp -o bin/Hammer.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c StoreQualityByContextFromCmpH5.cpp -o bin/StoreQualityByContextFromCmpH5.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c StoreQualityByContextFromCmpH5.cpp -o bin/StoreQualityByContextFromCmpH5.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c CheckForFilteredReads.cpp -o bin/CheckForFilteredReads.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c CheckForFilteredReads.cpp -o bin/CheckForFilteredReads.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c NormalizeGCContent.cpp -o bin/NormalizeGCContent.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c NormalizeGCContent.cpp -o bin/NormalizeGCContent.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c FilterHDFPls.cpp -o bin/FilterHDFPls.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c FilterHDFPls.cpp -o bin/FilterHDFPls.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PrintReadWordCount.cpp -o bin/PrintReadWordCount.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c PrintReadWordCount.cpp -o bin/PrintReadWordCount.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c ExciseRepeats.cpp -o bin/ExciseRepeats.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c ExciseRepeats.cpp -o bin/ExciseRepeats.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SDPMatcher.cpp -o bin/SDPMatcher.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c SDPMatcher.cpp -o bin/SDPMatcher.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PrintTitleTable.cpp -o bin/PrintTitleTable.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c PrintTitleTable.cpp -o bin/PrintTitleTable.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c MakeBarcodeDatabase.cpp -o bin/MakeBarcodeDatabase.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c MakeBarcodeDatabase.cpp -o bin/MakeBarcodeDatabase.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c TileGenome.cpp -o bin/TileGenome.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c TileGenome.cpp -o bin/TileGenome.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PrintHDFPlsSummary.cpp -o bin/PrintHDFPlsSummary.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c PrintHDFPlsSummary.cpp -o bin/PrintHDFPlsSummary.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c Sageify.cpp -o bin/Sageify.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c Sageify.cpp -o bin/Sageify.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c FilterBySubreadAgreement.cpp -o bin/FilterBySubreadAgreement.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c FilterBySubreadAgreement.cpp -o bin/FilterBySubreadAgreement.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SWMatcher.cpp -o bin/SWMatcher.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c SWMatcher.cpp -o bin/SWMatcher.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/StoreQualityByContext.o -o bin/storeQualityByContext -L/usr/local/opt/hdf5/lib -lhdf5_cpp -lhdf5 -lz -lpthread -ldl
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/StoreQualityByContext.o -o bin/storeQualityByContext -L/usr/local/opt/hdf5/lib -lhdf5_cpp -lhdf5 -lz -lpthread -ldl -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/storeQualityByContext -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/StoreQualityByContext.o -lhdf5_cpp -lhdf5 -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/storeQualityByContext -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/StoreQualityByContext.o -lhdf5_cpp -lhdf5 -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c TestAdvance.cpp -o bin/TestAdvance.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c TestAdvance.cpp -o bin/TestAdvance.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c ComputeRefCoverage.cpp -o bin/ComputeRefCoverage.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c ComputeRefCoverage.cpp -o bin/ComputeRefCoverage.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c KBandMatcher.cpp -o bin/KBandMatcher.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c KBandMatcher.cpp -o bin/KBandMatcher.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SAWriter.cpp -o bin/SAWriter.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c SAWriter.cpp -o bin/SAWriter.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SAQuery.cpp -o bin/SAQuery.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c SAQuery.cpp -o bin/SAQuery.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c ToAfg.cpp -o bin/ToAfg.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c ToAfg.cpp -o bin/ToAfg.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SAModify.cpp -o bin/SAModify.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c SAModify.cpp -o bin/SAModify.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PrintTupleCountTable.cpp -o bin/PrintTupleCountTable.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c PrintTupleCountTable.cpp -o bin/PrintTupleCountTable.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/ConcatenateSequences.o -o bin/catseq
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/ConcatenateSequences.o -o bin/catseq -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/catseq -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/ConcatenateSequences.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/catseq -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/ConcatenateSequences.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/Compress.o -o bin/compressseq
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/Compress.o -o bin/compressseq -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

g++-5 called with: -c -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -DCOMPRESSED PrintTupleCountTable.cpp -o bin/CmpPrintTupleCountTable.o
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -c -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive -DCOMPRESSED PrintTupleCountTable.cpp -o bin/CmpPrintTupleCountTable.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c CmpH5View.cpp -o bin/CmpH5View.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c CmpH5View.cpp -o bin/CmpH5View.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/compressseq -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/Compress.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/compressseq -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/Compress.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/FilterSeq.o -o bin/filterseq
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/FilterSeq.o -o bin/filterseq -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/filterseq -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/FilterSeq.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/filterseq -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/FilterSeq.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/BuildSequenceDB.o -o bin/bsdb -L/usr/local/opt/hdf5/lib -lhdf5_cpp -lhdf5 -lz -lpthread -ldl
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/BuildSequenceDB.o -o bin/bsdb -L/usr/local/opt/hdf5/lib -lhdf5_cpp -lhdf5 -lz -lpthread -ldl -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/bsdb -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/BuildSequenceDB.o -lhdf5_cpp -lhdf5 -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/bsdb -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/BuildSequenceDB.o -lhdf5_cpp -lhdf5 -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/ConcatenateReads.o -o bin/catreads
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/ConcatenateReads.o -o bin/catreads -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/catreads -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/ConcatenateReads.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/catreads -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/ConcatenateReads.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/SimpleShredder.o -o bin/simpleShredder
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/SimpleShredder.o -o bin/simpleShredder -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/simpleShredder -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/SimpleShredder.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/simpleShredder -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/SimpleShredder.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/CountUniqueNMers.o -o bin/countKmers
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/CountUniqueNMers.o -o bin/countKmers -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/countKmers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/CountUniqueNMers.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/countKmers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/CountUniqueNMers.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/Evolve.o -o bin/evolve
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/Evolve.o -o bin/evolve -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/evolve -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/Evolve.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/evolve -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/Evolve.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/ExtractSeq.o -o bin/extractseq
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/ExtractSeq.o -o bin/extractseq -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/extractseq -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/ExtractSeq.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/extractseq -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/ExtractSeq.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/ExtractRepeats.o -o bin/extractrep
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/ExtractRepeats.o -o bin/extractrep -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/extractrep -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/ExtractRepeats.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/extractrep -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/ExtractRepeats.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/PrintUngappedSequenceLengthHistogram.o -o bin/printUngappedLengths
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/PrintUngappedSequenceLengthHistogram.o -o bin/printUngappedLengths -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/printUngappedLengths -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/PrintUngappedSequenceLengthHistogram.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/printUngappedLengths -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/PrintUngappedSequenceLengthHistogram.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c MAlign.cpp -o bin/MAlign.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c MAlign.cpp -o bin/MAlign.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/Dustoff.o -o bin/dustoff
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/Dustoff.o -o bin/dustoff -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/dustoff -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/Dustoff.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/dustoff -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/Dustoff.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/SplitContigs.o -o bin/splitContigs
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/SplitContigs.o -o bin/splitContigs -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/splitContigs -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/SplitContigs.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/splitContigs -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/SplitContigs.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/PrintUnalignedSequences.o -o bin/printUnalignedSequences
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/PrintUnalignedSequences.o -o bin/printUnalignedSequences -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/printUnalignedSequences -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/PrintUnalignedSequences.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/printUnalignedSequences -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/PrintUnalignedSequences.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/ScrambleSequenceOrder.o -o bin/scramble
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/ScrambleSequenceOrder.o -o bin/scramble -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/scramble -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/ScrambleSequenceOrder.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/scramble -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/ScrambleSequenceOrder.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/MaskSequence.o -o bin/maskSequence
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/MaskSequence.o -o bin/maskSequence -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/maskSequence -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/MaskSequence.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/maskSequence -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/MaskSequence.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/SelectRandomSubstrings.o -o bin/selectRandomSubstrings
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/SelectRandomSubstrings.o -o bin/selectRandomSubstrings -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/selectRandomSubstrings -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/SelectRandomSubstrings.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/selectRandomSubstrings -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/SelectRandomSubstrings.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/PrintHomopolymerCount.o -o bin/printHPC
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/PrintHomopolymerCount.o -o bin/printHPC -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/printHPC -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/PrintHomopolymerCount.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/printHPC -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/PrintHomopolymerCount.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/PrintGCRank.o -o bin/gcrank
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/PrintGCRank.o -o bin/gcrank -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/gcrank -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/PrintGCRank.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/gcrank -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/PrintGCRank.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/Hammer.o -o bin/hammer
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/Hammer.o -o bin/hammer -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/hammer -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/Hammer.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/hammer -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/Hammer.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/CheckForFilteredReads.o -o bin/checkfilt
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/CheckForFilteredReads.o -o bin/checkfilt -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c RemoveAdapters.cpp -o bin/RemoveAdapters.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c RemoveAdapters.cpp -o bin/RemoveAdapters.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/checkfilt -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/CheckForFilteredReads.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/checkfilt -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/CheckForFilteredReads.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/NormalizeGCContent.o -o bin/normgc
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/NormalizeGCContent.o -o bin/normgc -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/normgc -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/NormalizeGCContent.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/normgc -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/NormalizeGCContent.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c CmpH5Information.cpp -o bin/CmpH5Information.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c CmpH5Information.cpp -o bin/CmpH5Information.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/ExciseRepeats.o -o bin/excrep
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/ExciseRepeats.o -o bin/excrep -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/excrep -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/ExciseRepeats.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/excrep -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/ExciseRepeats.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/PrintTitleTable.o -o bin/printTitleTable -lz -lpthread
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/PrintTitleTable.o -o bin/printTitleTable -lz -lpthread -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/printTitleTable -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/PrintTitleTable.o -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/printTitleTable -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/PrintTitleTable.o -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/MakeBarcodeDatabase.o -o bin/makeBarcodeDatabase
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/MakeBarcodeDatabase.o -o bin/makeBarcodeDatabase -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/makeBarcodeDatabase -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/MakeBarcodeDatabase.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/makeBarcodeDatabase -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/MakeBarcodeDatabase.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/TileGenome.o -o bin/tileGenome
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/TileGenome.o -o bin/tileGenome -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/tileGenome -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/TileGenome.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/tileGenome -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/TileGenome.o -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/FilterBySubreadAgreement.o -o bin/filterBySubreadAgreement -L/usr/local/opt/hdf5/lib -lhdf5_cpp -lhdf5 -lz -lpthread -ldl
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/FilterBySubreadAgreement.o -o bin/filterBySubreadAgreement -L/usr/local/opt/hdf5/lib -lhdf5_cpp -lhdf5 -lz -lpthread -ldl -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/filterBySubreadAgreement -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/FilterBySubreadAgreement.o -lhdf5_cpp -lhdf5 -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/filterBySubreadAgreement -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/FilterBySubreadAgreement.o -lhdf5_cpp -lhdf5 -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c TabulateAlignment.cpp -o bin/TabulateAlignment.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c TabulateAlignment.cpp -o bin/TabulateAlignment.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PrintMSA.cpp -o bin/PrintMSA.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c PrintMSA.cpp -o bin/PrintMSA.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SAMatcher.cpp -o bin/SAMatcher.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c SAMatcher.cpp -o bin/SAMatcher.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SAPrinter.cpp -o bin/SAPrinter.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c SAPrinter.cpp -o bin/SAPrinter.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c BuildQualityValueProfile.cpp -o bin/BuildQualityValueProfile.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c BuildQualityValueProfile.cpp -o bin/BuildQualityValueProfile.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c PrintVariants.cpp -o bin/PrintVariants.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c PrintVariants.cpp -o bin/PrintVariants.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c GuidedAlign.cpp -o bin/GuidedAlign.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c GuidedAlign.cpp -o bin/GuidedAlign.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c DiffAlnInfoGroups.cpp -o bin/DiffAlnInfoGroups.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c DiffAlnInfoGroups.cpp -o bin/DiffAlnInfoGroups.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c ExtendAlign.cpp -o bin/ExtendAlign.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c ExtendAlign.cpp -o bin/ExtendAlign.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SamToCmpH5.cpp -o bin/SamToCmpH5.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c SamToCmpH5.cpp -o bin/SamToCmpH5.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SamToM4.cpp -o bin/SamToM4.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c SamToM4.cpp -o bin/SamToM4.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SALS.cpp -o bin/SALS.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c SALS.cpp -o bin/SALS.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c SamFilter.cpp -o bin/SamFilter.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c SamFilter.cpp -o bin/SamFilter.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -I ../common -I /usr/local/opt/hdf5/include -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive -c Mask.cpp -o bin/Mask.o
superenv removed:  -I ../common -I /usr/local/opt/hdf5/include -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: g++-5 -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -Wno-div-by-zero -fpermissive -c Mask.cpp -o bin/Mask.o -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/LoadPulses.o -o bin/loadPulses -L/usr/local/opt/hdf5/lib -lhdf5_cpp -lhdf5 -lz -lpthread -ldl
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/LoadPulses.o -o bin/loadPulses -L/usr/local/opt/hdf5/lib -lhdf5_cpp -lhdf5 -lz -lpthread -ldl -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/loadPulses -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/LoadPulses.o -lhdf5_cpp -lhdf5 -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/loadPulses -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/LoadPulses.o -lhdf5_cpp -lhdf5 -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

g++-5 called with: -O3 -Wno-div-by-zero -I ../common -I /usr/local/opt/hdf5/include -fpermissive bin/Blasr.o -L/usr/local/opt/hdf5/lib -lhdf5_cpp -lhdf5 -lz -lpthread -ldl -o bin/blasr
superenv removed:  -O3 -I ../common -I /usr/local/opt/hdf5/include
superenv added:    -pipe -w -Os -I../common -I/usr/local/opt/hdf5/include -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: g++-5 -pipe -w -Os -Wno-div-by-zero -I../common -I/usr/local/opt/hdf5/include -fpermissive bin/Blasr.o -L/usr/local/opt/hdf5/lib -lhdf5_cpp -lhdf5 -lz -lpthread -ldl -o bin/blasr -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -isystem/usr/local/include -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/apache2 -isystem/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names

ld called with: -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/blasr -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/Blasr.o -lhdf5_cpp -lhdf5 -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem
superenv executed: ld -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -headerpad_max_install_names -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -w -o bin/blasr -L/usr/local/opt/hdf5/lib -L/usr/local/lib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/../../.. -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib bin/Blasr.o -lhdf5_cpp -lhdf5 -lz -headerpad_max_install_names -lstdc++ -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lSystem -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk

config.out

HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/homebrew
HEAD: 85de42b8002b6a75b2af4cb6f6a8bd1a47fdc188
Last commit: 3 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_REPOSITORY: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://homebrew.bintray.com
CPU: quad-core 64-bit broadwell
OS X: 10.10.5-x86_64
Xcode: 6.4
CLT: N/A
Clang: 6.1 build 602
X11: 2.7.7 => /opt/X11
System Ruby: 2.0.0-p481
Perl: /usr/bin/perl
Python: /usr/local/bin/python => /usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/bin/python2.7
Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby
Java: N/A

doctor.out

Your system is ready to brew.

tap.out

Formula: blasr
Tap: homebrew/homebrew-science
Path: /usr/local/Library/Taps/homebrew/homebrew-science/blasr.rb