##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL enhancerHomologSearch
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'enhancerHomologSearch' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/alignment/Alignment.cpp -o ClustalW/alignment/Alignment.o
ClustalW/alignment/Alignment.cpp: In member function 'bool clustalw::Alignment::keepPortionOfSeqArray(int, int)':
ClustalW/alignment/Alignment.cpp:1715:24: warning: variable 'posToAddTo' set but not used [-Wunused-but-set-variable]
 1715 |     SeqArray::iterator posToAddTo = sectionToRealign.begin();
      |                        ^~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/alignment/AlignmentOutput.cpp -o ClustalW/alignment/AlignmentOutput.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/alignment/ObjectiveScore.cpp -o ClustalW/alignment/ObjectiveScore.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/alignment/Sequence.cpp -o ClustalW/alignment/Sequence.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/Clustal.cpp -o ClustalW/Clustal.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/fileInput/ClustalFileParser.cpp -o ClustalW/fileInput/ClustalFileParser.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/fileInput/EMBLFileParser.cpp -o ClustalW/fileInput/EMBLFileParser.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/fileInput/FileParser.cpp -o ClustalW/fileInput/FileParser.o
ClustalW/fileInput/FileParser.cpp: In member function 'std::vector<clustalw::Sequence> clustalw::FileParser::getSeqRangeR(int, int, std::string*, ClustalWInput*)':
ClustalW/fileInput/FileParser.cpp:38:21: warning: unused variable 'n' [-Wunused-variable]
   38 |                 int n = (*input).inputSeqs.size();
      |                     ^
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/fileInput/FileReader.cpp -o ClustalW/fileInput/FileReader.o
ClustalW/fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readCharacterSeqs(clustalw::Alignment*, int, std::string*, ClustalWInput*)':
ClustalW/fileInput/FileReader.cpp:421:17: warning: variable 'maxAlnLength' set but not used [-Wunused-but-set-variable]
  421 |             int maxAlnLength; // Get values from the Alignment object.
      |                 ^~~~~~~~~~~~
ClustalW/fileInput/FileReader.cpp:357:54: warning: 'this' pointer is null [-Wnonnull]
  357 |             seqRangeVector = fileParser->getSeqRangeR(1, noSeqs, offendingSeq, input);
      |                              ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ClustalW/fileInput/FileReader.h:16,
                 from ClustalW/fileInput/FileReader.cpp:29:
ClustalW/fileInput/FileParser.h:44:26: note: in a call to non-static member function 'std::vector<clustalw::Sequence> clustalw::FileParser::getSeqRangeR(int, int, std::string*, ClustalWInput*)'
   44 |         vector<Sequence> getSeqRangeR(int firstSeq, int num, string *offendingSeq, ClustalWInput *input);
      |                          ^~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/fileInput/GDEFileParser.cpp -o ClustalW/fileInput/GDEFileParser.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/fileInput/InFileStream.cpp -o ClustalW/fileInput/InFileStream.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/fileInput/MSFFileParser.cpp -o ClustalW/fileInput/MSFFileParser.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/fileInput/PearsonFileParser.cpp -o ClustalW/fileInput/PearsonFileParser.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/fileInput/PIRFileParser.cpp -o ClustalW/fileInput/PIRFileParser.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/fileInput/RSFFileParser.cpp -o ClustalW/fileInput/RSFFileParser.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/general/ClustalWResources.cpp -o ClustalW/general/ClustalWResources.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/general/DebugLog.cpp -o ClustalW/general/DebugLog.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/general/InvalidCombination.cpp -o ClustalW/general/InvalidCombination.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/general/OutputFile.cpp -o ClustalW/general/OutputFile.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/general/Stats.cpp -o ClustalW/general/Stats.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/general/SymMatrix.cpp -o ClustalW/general/SymMatrix.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/general/UserParameters.cpp -o ClustalW/general/UserParameters.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/general/Utility.cpp -o ClustalW/general/Utility.o
ClustalW/general/Utility.cpp: In member function 'bool clustalw::Utility::lineType(char*, const char*)':
ClustalW/general/Utility.cpp:251:8: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  251 |    int n;
      |        ^
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/general/VectorOutOfRange.cpp -o ClustalW/general/VectorOutOfRange.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/Help.cpp -o ClustalW/Help.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/interface/CommandLineParser.cpp -o ClustalW/interface/CommandLineParser.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/multipleAlign/Iteration.cpp -o ClustalW/multipleAlign/Iteration.o
ClustalW/multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)':
ClustalW/multipleAlign/Iteration.cpp:171:9: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  171 |     int count;
      |         ^~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/multipleAlign/LowScoreSegProfile.cpp -o ClustalW/multipleAlign/LowScoreSegProfile.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/multipleAlign/MSA.cpp -o ClustalW/multipleAlign/MSA.o
ClustalW/multipleAlign/MSA.cpp: In member function 'int clustalw::MSA::multiSeqAlign(clustalw::Alignment*, clustalw::DistMatrix*, std::vector<int>*, clustalw::AlignmentSteps*, int)':
ClustalW/multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable]
  340 |       int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18
      |           ^~~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/multipleAlign/MyersMillerProfileAlign.cpp -o ClustalW/multipleAlign/MyersMillerProfileAlign.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/multipleAlign/ProfileBase.cpp -o ClustalW/multipleAlign/ProfileBase.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/multipleAlign/ProfileStandard.cpp -o ClustalW/multipleAlign/ProfileStandard.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/multipleAlign/ProfileWithSub.cpp -o ClustalW/multipleAlign/ProfileWithSub.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/pairwise/FastPairwiseAlign.cpp -o ClustalW/pairwise/FastPairwiseAlign.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/pairwise/FullPairwiseAlign.cpp -o ClustalW/pairwise/FullPairwiseAlign.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/substitutionMatrix/SubMatrix.cpp -o ClustalW/substitutionMatrix/SubMatrix.o
ClustalW/substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeriesFromR(Rcpp::NumericMatrix, clustalw::Matrix&, clustalw::Xref&)':
ClustalW/substitutionMatrix/SubMatrix.cpp:1305:10: warning: unused variable 'inline1' [-Wunused-variable]
 1305 |     char inline1[1024];
      |          ^~~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp:1307:9: warning: unused variable 'nmat' [-Wunused-variable]
 1307 |     int nmat;
      |         ^~~~
ClustalW/substitutionMatrix/SubMatrix.cpp:1308:9: warning: unused variable 'n' [-Wunused-variable]
 1308 |     int n, llimit, ulimit;
      |         ^
ClustalW/substitutionMatrix/SubMatrix.cpp:1308:12: warning: unused variable 'llimit' [-Wunused-variable]
 1308 |     int n, llimit, ulimit;
      |            ^~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp:1308:20: warning: unused variable 'ulimit' [-Wunused-variable]
 1308 |     int n, llimit, ulimit;
      |                    ^~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readUserMatrixFromR(Rcpp::NumericMatrix, clustalw::Matrix&, clustalw::Xref&)':
ClustalW/substitutionMatrix/SubMatrix.cpp:1361:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 1361 |                 for (j = 0; j < curline.length(); j++) {
      |                             ~~^~~~~~~~~~~~~~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForHistogram(int (*)[32])':
ClustalW/substitutionMatrix/SubMatrix.cpp:1845:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
 1845 |     int maxRes;
      |         ^~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForLowScoreSeg(int (*)[32])':
ClustalW/substitutionMatrix/SubMatrix.cpp:1905:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
 1905 |     int maxRes;
      |         ^~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeries(const char*, clustalw::Matrix&, clustalw::Xref&)':
ClustalW/substitutionMatrix/SubMatrix.cpp:1128:19: warning: 'n' may be used uninitialized [-Wmaybe-uninitialized]
 1128 |     return (maxRes);
      |                   ^
ClustalW/substitutionMatrix/SubMatrix.cpp:1023:9: note: 'n' was declared here
 1023 |     int n, llimit, ulimit;
      |         ^
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/tree/AlignmentSteps.cpp -o ClustalW/tree/AlignmentSteps.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/tree/ClusterTree.cpp -o ClustalW/tree/ClusterTree.o
ClustalW/tree/ClusterTree.cpp: In member function 'void clustalw::ClusterTree::calcPercIdentity(std::ofstream*, clustalw::Alignment*)':
ClustalW/tree/ClusterTree.cpp:580:9: warning: variable 'rs' set but not used [-Wunused-but-set-variable]
  580 |     int rs = 0, rl = 0;
      |         ^~
ClustalW/tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable]
  580 |     int rs = 0, rl = 0;
      |                 ^~
ClustalW/tree/ClusterTree.cpp: In member function 'void clustalw::ClusterTree::promptForBoolSeedAndNumTrials()':
ClustalW/tree/ClusterTree.cpp:967:22: warning: variable 'tempSeed' set but not used [-Wunused-but-set-variable]
  967 |         unsigned int tempSeed;
      |                      ^~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/tree/ClusterTreeOutput.cpp -o ClustalW/tree/ClusterTreeOutput.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/tree/NJTree.cpp -o ClustalW/tree/NJTree.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/tree/RandomGenerator.cpp -o ClustalW/tree/RandomGenerator.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/tree/Tree.cpp -o ClustalW/tree/Tree.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/tree/TreeInterface.cpp -o ClustalW/tree/TreeInterface.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/tree/UnRootedClusterTree.cpp -o ClustalW/tree/UnRootedClusterTree.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/tree/UPGMA/Node.cpp -o ClustalW/tree/UPGMA/Node.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/tree/UPGMA/RootedClusterTree.cpp -o ClustalW/tree/UPGMA/RootedClusterTree.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/tree/UPGMA/RootedGuideTree.cpp -o ClustalW/tree/UPGMA/RootedGuideTree.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/tree/UPGMA/RootedTreeOutput.cpp -o ClustalW/tree/UPGMA/RootedTreeOutput.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClustalW/tree/UPGMA/UPGMAAlgorithm.cpp -o ClustalW/tree/UPGMA/UPGMAAlgorithm.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/aligngivenpath.cpp -o Muscle/aligngivenpath.o
Muscle/aligngivenpath.cpp: In function 'void AppendTplInserts(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)':
Muscle/aligngivenpath.cpp:186:24: warning: unused variable 'uLengthA' [-Wunused-variable]
  186 |         const unsigned uLengthA = msaA.GetColCount();
      |                        ^~~~~~~~
Muscle/aligngivenpath.cpp:187:24: warning: unused variable 'uLengthB' [-Wunused-variable]
  187 |         const unsigned uLengthB = msaB.GetColCount();
      |                        ^~~~~~~~
Muscle/aligngivenpath.cpp: In function 'void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)':
Muscle/aligngivenpath.cpp:335:40: warning: unused variable 'uColA' [-Wunused-variable]
  335 |                         const unsigned uColA = uPrefixLengthA - 1;
      |                                        ^~~~~
Muscle/aligngivenpath.cpp:336:40: warning: unused variable 'uColB' [-Wunused-variable]
  336 |                         const unsigned uColB = uPrefixLengthB - 1;
      |                                        ^~~~~
Muscle/aligngivenpath.cpp:346:40: warning: unused variable 'uColA' [-Wunused-variable]
  346 |                         const unsigned uColA = uPrefixLengthA - 1;
      |                                        ^~~~~
Muscle/aligngivenpath.cpp:354:40: warning: unused variable 'uColB' [-Wunused-variable]
  354 |                         const unsigned uColB = uPrefixLengthB - 1;
      |                                        ^~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/aligngivenpath.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/aligngivenpathsw.cpp -o Muscle/aligngivenpathsw.o
Muscle/aligngivenpathsw.cpp: In function 'void AppendUnalignedTerminals(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)':
Muscle/aligngivenpathsw.cpp:58:24: warning: unused variable 'uLengthA' [-Wunused-variable]
   58 |         const unsigned uLengthA = msaA.GetColCount();
      |                        ^~~~~~~~
Muscle/aligngivenpathsw.cpp:59:24: warning: unused variable 'uLengthB' [-Wunused-variable]
   59 |         const unsigned uLengthB = msaB.GetColCount();
      |                        ^~~~~~~~
Muscle/aligngivenpathsw.cpp: In function 'void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)':
Muscle/aligngivenpathsw.cpp:204:40: warning: unused variable 'uColA' [-Wunused-variable]
  204 |                         const unsigned uColA = uPrefixLengthA - 1;
      |                                        ^~~~~
Muscle/aligngivenpathsw.cpp:205:40: warning: unused variable 'uColB' [-Wunused-variable]
  205 |                         const unsigned uColB = uPrefixLengthB - 1;
      |                                        ^~~~~
Muscle/aligngivenpathsw.cpp:215:40: warning: unused variable 'uColA' [-Wunused-variable]
  215 |                         const unsigned uColA = uPrefixLengthA - 1;
      |                                        ^~~~~
Muscle/aligngivenpathsw.cpp:223:40: warning: unused variable 'uColB' [-Wunused-variable]
  223 |                         const unsigned uColB = uPrefixLengthB - 1;
      |                                        ^~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/aligngivenpathsw.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/aligntwomsas.cpp -o Muscle/aligntwomsas.o
In file included from Muscle/aligntwomsas.cpp:6:
Muscle/timing.h:5: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
    5 | #pragma warning(disable:4035)
      | 
Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
   24 | static double TicksToSecs(TICKS t)
      |               ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/aligntwomsas.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/aligntwoprofs.cpp -o Muscle/aligntwoprofs.o
In file included from Muscle/muscle.h:37,
                 from Muscle/aligntwoprofs.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/aln.cpp -o Muscle/aln.o
In file included from Muscle/muscle.h:37,
                 from Muscle/aln.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/alpha.cpp -o Muscle/alpha.o
In file included from Muscle/muscle.h:37,
                 from Muscle/alpha.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/anchors.cpp -o Muscle/anchors.o
Muscle/anchors.cpp: In function 'void MergeBestCols(const SCORE*, const unsigned int*, unsigned int, unsigned int, unsigned int*, unsigned int*)':
Muscle/anchors.cpp:162:34: warning: unused variable 'uWindowCenter' [-Wunused-variable]
  162 |                         unsigned uWindowCenter = uBestColIndex + uWindowLength/2;
      |                                  ^~~~~~~~~~~~~
Muscle/anchors.cpp: At global scope:
Muscle/anchors.cpp:105:13: warning: 'void ListBestCols(const MSA&, const SCORE*, const SCORE*, unsigned int*, unsigned int)' defined but not used [-Wunused-function]
  105 | static void ListBestCols(const MSA &msa, const SCORE Score[], const SCORE SmoothScore[],
      |             ^~~~~~~~~~~~
Muscle/anchors.cpp:53:13: warning: 'void FindBestColsGrade(const SCORE*, unsigned int, double, unsigned int*, unsigned int*)' defined but not used [-Wunused-function]
   53 | static void FindBestColsGrade(const SCORE Score[], unsigned uCount,
      |             ^~~~~~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/anchors.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/bittraceback.cpp -o Muscle/bittraceback.o
Muscle/bittraceback.cpp: In function 'void BitTraceBack(char**, unsigned int, unsigned int, char, PWPath&)':
Muscle/bittraceback.cpp:146:14: warning: unused variable 'Bits' [-Wunused-variable]
  146 |         char Bits = TraceBack[uLengthA][uLengthB];
      |              ^~~~
Muscle/bittraceback.cpp: At global scope:
Muscle/bittraceback.cpp:15:20: warning: 'const char* BitsToStr(char)' defined but not used [-Wunused-function]
   15 | static const char *BitsToStr(char Bits)
      |                    ^~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/bittraceback.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/blosum62.cpp -o Muscle/blosum62.o
In file included from Muscle/muscle.h:37,
                 from Muscle/blosum62.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/blosumla.cpp -o Muscle/blosumla.o
Muscle/blosumla.cpp:7:14: warning: 'Blosum62LA' defined but not used [-Wunused-variable]
    7 | static float Blosum62LA[20][20] =
      |              ^~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/blosumla.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/clust.cpp -o Muscle/clust.o
Muscle/clust.cpp: In member function 'void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)':
Muscle/clust.cpp:186:24: warning: unused variable 'uClusterCount' [-Wunused-variable]
  186 |         const unsigned uClusterCount = GetClusterCount();
      |                        ^~~~~~~~~~~~~
Muscle/clust.cpp: In member function 'void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)':
Muscle/clust.cpp:206:24: warning: unused variable 'uClusterCount' [-Wunused-variable]
  206 |         const unsigned uClusterCount = GetClusterCount();
      |                        ^~~~~~~~~~~~~
Muscle/clust.cpp: In member function 'float Clust::ComputeDistMAFFT(unsigned int, unsigned int)':
Muscle/clust.cpp:365:21: warning: unused variable 'dDistLR' [-Wunused-variable]
  365 |         const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex);
      |                     ^~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/clust.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/cluster.cpp -o Muscle/cluster.o
Muscle/cluster.cpp: In member function 'void ClusterTree::Create(const DistFunc&)':
Muscle/cluster.cpp:284:22: warning: variable 'bFound' set but not used [-Wunused-but-set-variable]
  284 |                 bool bFound = false;
      |                      ^~~~~~
Muscle/cluster.cpp:267:16: warning: unused variable 'dMaxDist' [-Wunused-variable]
  267 |         double dMaxDist = 0.0;
      |                ^~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/cluster.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
Muscle/cluster.cpp: In member function 'void ClusterTree::Create(const DistFunc&)':
Muscle/cluster.cpp:307:47: warning: 'uIndexClosest1' may be used uninitialized [-Wmaybe-uninitialized]
  307 |                 ClusterNode &Child1 = m_Nodes[uIndexClosest1];
      |                                               ^~~~~~~~~~~~~~
Muscle/cluster.cpp:282:26: note: 'uIndexClosest1' was declared here
  282 |                 unsigned uIndexClosest1;
      |                          ^~~~~~~~~~~~~~
Muscle/cluster.cpp:308:47: warning: 'uIndexClosest2' may be used uninitialized [-Wmaybe-uninitialized]
  308 |                 ClusterNode &Child2 = m_Nodes[uIndexClosest2];
      |                                               ^~~~~~~~~~~~~~
Muscle/cluster.cpp:283:26: note: 'uIndexClosest2' was declared here
  283 |                 unsigned uIndexClosest2;
      |                          ^~~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/clwwt.cpp -o Muscle/clwwt.o
In file included from Muscle/muscle.h:37,
                 from Muscle/clwwt.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/color.cpp -o Muscle/color.o
Muscle/color.cpp:72:12: warning: 'int BlosumScore(char, char)' defined but not used [-Wunused-function]
   72 | static int BlosumScore(char c1, char c2)
      |            ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/color.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/cons.cpp -o Muscle/cons.o
In file included from Muscle/muscle.h:37,
                 from Muscle/cons.cpp:7:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/diaglist.cpp -o Muscle/diaglist.o
In file included from Muscle/muscle.h:37,
                 from Muscle/diaglist.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/diffobjscore.cpp -o Muscle/diffobjscore.o
Muscle/diffobjscore.cpp: In function 'SCORE ScoreLetters(const MSA&, const unsigned int*, unsigned int)':
Muscle/diffobjscore.cpp:76:24: warning: unused variable 'uSeqCount' [-Wunused-variable]
   76 |         const unsigned uSeqCount = msa.GetSeqCount();
      |                        ^~~~~~~~~
Muscle/diffobjscore.cpp:77:24: warning: unused variable 'uColCount' [-Wunused-variable]
   77 |         const unsigned uColCount = msa.GetColCount();
      |                        ^~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/diffobjscore.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/diffpaths.cpp -o Muscle/diffpaths.o
In file included from Muscle/muscle.h:37,
                 from Muscle/diffpaths.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/difftrees.cpp -o Muscle/difftrees.o
Muscle/difftrees.cpp: In function 'void DiffTrees(const Tree&, const Tree&, Tree&, unsigned int*)':
Muscle/difftrees.cpp:161:24: warning: unused variable 'uLeafCount2' [-Wunused-variable]
  161 |         const unsigned uLeafCount2 = Tree2.GetLeafCount();
      |                        ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/difftrees.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/difftreese.cpp -o Muscle/difftreese.o
In file included from Muscle/muscle.h:37,
                 from Muscle/difftreese.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/distcalc.cpp -o Muscle/distcalc.o
In file included from Muscle/muscle.h:37,
                 from Muscle/distcalc.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/distfunc.cpp -o Muscle/distfunc.o
In file included from Muscle/muscle.h:37,
                 from Muscle/distfunc.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/distpwkimura.cpp -o Muscle/distpwkimura.o
In file included from Muscle/muscle.h:37,
                 from Muscle/distpwkimura.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/domuscle.cpp -o Muscle/domuscle.o
In file included from Muscle/domuscle.cpp:9:
Muscle/timing.h:5: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
    5 | #pragma warning(disable:4035)
      | 
Muscle/domuscle.cpp: In function 'void DoMuscle(MuscleInput*, MuscleOutput*)':
Muscle/domuscle.cpp:169:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  169 |                 if (g_bClusterOnly)
      |                 ^~
Muscle/domuscle.cpp:172:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  172 |                         return;
      |                         ^~~~~~
Muscle/domuscle.cpp:180:13: warning: unused variable 'PNlength' [-Wunused-variable]
  180 |         int PNlength = (msaInput->inputSeqs).Length();
      |             ^~~~~~~~
Muscle/timing.h: At global scope:
Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
   24 | static double TicksToSecs(TICKS t)
      |               ^~~~~~~~~~~
In file included from ./Muscle/muscle.h:37,
                 from ./RMuscle.h:4,
                 from Muscle/domuscle.cpp:1:
./Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/dosp.cpp -o Muscle/dosp.o
In file included from Muscle/muscle.h:37,
                 from Muscle/dosp.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/dpreglist.cpp -o Muscle/dpreglist.o
Muscle/dpreglist.cpp: In function 'void DiagListToDPRegionList(const DiagList&, DPRegionList&, unsigned int, unsigned int)':
Muscle/dpreglist.cpp:82:40: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable]
   82 |                         const unsigned uDiagLengthMinusCaps = uEndVertexA - uStartVertexA - 1;
      |                                        ^~~~~~~~~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/dpreglist.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/drawtree.cpp -o Muscle/drawtree.o
In file included from Muscle/muscle.h:37,
                 from Muscle/drawtree.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/edgelist.cpp -o Muscle/edgelist.o
In file included from Muscle/muscle.h:37,
                 from Muscle/edgelist.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/enumopts.cpp -o Muscle/enumopts.o
In file included from Muscle/muscle.h:37,
                 from Muscle/enumopts.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/enumtostr.cpp -o Muscle/enumtostr.o
In file included from Muscle/muscle.h:37,
                 from Muscle/enumtostr.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/estring.cpp -o Muscle/estring.o
Muscle/estring.cpp:464:13: warning: 'bool CanMultiplyEstrings(const short int*, const short int*)' defined but not used [-Wunused-function]
  464 | static bool CanMultiplyEstrings(const short es1[], const short es2[])
      |             ^~~~~~~~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/estring.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
Muscle/estring.cpp: In function 'void EstringsToPath(const short int*, const short int*, PWPath&)':
Muscle/estring.cpp:409:17: warning: 'cType' may be used uninitialized [-Wmaybe-uninitialized]
  409 |                 switch (cType)
      |                 ^~~~~~
Muscle/estring.cpp:377:22: note: 'cType' was declared here
  377 |                 char cType;
      |                      ^~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/fasta.cpp -o Muscle/fasta.o
Muscle/fasta.cpp: In member function 'void MSA::FromFASTAFile(TextFile&)':
Muscle/fasta.cpp:15:18: warning: unused variable 'uSeqCount' [-Wunused-variable]
   15 |         unsigned uSeqCount = 0;
      |                  ^~~~~~~~~
Muscle/fasta.cpp:16:18: warning: unused variable 'uColCount' [-Wunused-variable]
   16 |         unsigned uColCount = uInsane;
      |                  ^~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/fasta.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/fasta2.cpp -o Muscle/fasta2.o
In file included from Muscle/muscle.h:37,
                 from Muscle/fasta2.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/fastclust.cpp -o Muscle/fastclust.o
In file included from Muscle/muscle.h:37,
                 from Muscle/fastclust.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/fastdist.cpp -o Muscle/fastdist.o
In file included from Muscle/muscle.h:37,
                 from Muscle/fastdist.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/fastdistjones.cpp -o Muscle/fastdistjones.o
In file included from Muscle/muscle.h:37,
                 from Muscle/fastdistjones.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/fastdistkbit.cpp -o Muscle/fastdistkbit.o
In file included from Muscle/muscle.h:37,
                 from Muscle/fastdistkbit.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/fastdistkmer.cpp -o Muscle/fastdistkmer.o
Muscle/fastdistkmer.cpp: In function 'void FastDistKmer(const SeqVect&, DistFunc&)':
Muscle/fastdistkmer.cpp:235:32: warning: unused variable 'KD' [-Wunused-variable]
  235 |                         double KD = KimuraDist(EstimatedPctId);
      |                                ^~
In file included from Muscle/muscle.h:37,
                 from Muscle/fastdistkmer.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/fastdistmafft.cpp -o Muscle/fastdistmafft.o
Muscle/fastdistmafft.cpp: In function 'void DistKmer6_6(const SeqVect&, DistFunc&)':
Muscle/fastdistmafft.cpp:239:29: warning: unused variable 'pName1' [-Wunused-variable]
  239 |                 const char *pName1 = s1.GetName();
      |                             ^~~~~~
Muscle/fastdistmafft.cpp: At global scope:
Muscle/fastdistmafft.cpp:104:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function]
  104 | static void ListCount(const unsigned char Count[])
      |             ^~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/fastdistmafft.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/fastdistnuc.cpp -o Muscle/fastdistnuc.o
Muscle/fastdistnuc.cpp: In function 'void DistKmer4_6(const SeqVect&, DistFunc&)':
Muscle/fastdistnuc.cpp:223:29: warning: unused variable 'pName1' [-Wunused-variable]
  223 |                 const char *pName1 = s1.GetName();
      |                             ^~~~~~
Muscle/fastdistnuc.cpp: At global scope:
Muscle/fastdistnuc.cpp:85:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function]
   85 | static void ListCount(const unsigned char Count[])
      |             ^~~~~~~~~
Muscle/fastdistnuc.cpp:33:17: warning: 'uResidueGroupCount' defined but not used [-Wunused-variable]
   33 | static unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]);
      |                 ^~~~~~~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/fastdistnuc.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/fastscorepath2.cpp -o Muscle/fastscorepath2.o
In file included from Muscle/muscle.h:37,
                 from Muscle/fastscorepath2.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/finddiags.cpp -o Muscle/finddiags.o
Muscle/finddiags.cpp:11:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function]
   11 | static char *TupleToStr(int t)
      |              ^~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/finddiags.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/finddiagsn.cpp -o Muscle/finddiagsn.o
Muscle/finddiagsn.cpp: In function 'char* TupleToStr(int)':
Muscle/finddiagsn.cpp:16:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
   16 |         for (int i = 0; i < K; ++i)
      |                         ~~^~~
Muscle/finddiagsn.cpp: At global scope:
Muscle/finddiagsn.cpp:12:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function]
   12 | static char *TupleToStr(int t)
      |              ^~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/finddiagsn.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/glbalign.cpp -o Muscle/glbalign.o
In file included from Muscle/glbalign.cpp:3:
Muscle/timing.h:5: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
    5 | #pragma warning(disable:4035)
      | 
Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
   24 | static double TicksToSecs(TICKS t)
      |               ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/glbalign.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/glbalign352.cpp -o Muscle/glbalign352.o
In file included from Muscle/glbalign352.cpp:3:
Muscle/timing.h:5: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
    5 | #pragma warning(disable:4035)
      | 
Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
   24 | static double TicksToSecs(TICKS t)
      |               ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/glbalign352.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/glbaligndiag.cpp -o Muscle/glbaligndiag.o
In file included from Muscle/glbaligndiag.cpp:6:
Muscle/timing.h:5: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
    5 | #pragma warning(disable:4035)
      | 
Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
   24 | static double TicksToSecs(TICKS t)
      |               ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/glbaligndiag.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/glbalignla.cpp -o Muscle/glbalignla.o
In file included from Muscle/muscle.h:37,
                 from Muscle/glbalignla.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
Muscle/glbalignla.cpp: In function 'SCORE GlobalAlignLA(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
Muscle/glbalignla.cpp:366:52: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized]
  366 |                                 *ptrTraceBack_ij = (int) uInsertPos - (int) j;
      |                                                    ^~~~~~~~~~~~~~~~
Muscle/glbalignla.cpp:333:26: note: 'uInsertPos' was declared here
  333 |                 unsigned uInsertPos;
      |                          ^~~~~~~~~~
Muscle/glbalignla.cpp:427:30: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized]
  427 |                 iTraceBack = (int) uInsertPos - (int) uLengthB;
      |                              ^~~~~~~~~~~~~~~~
Muscle/glbalignla.cpp:400:18: note: 'uInsertPos' was declared here
  400 |         unsigned uInsertPos;
      |                  ^~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/glbalignle.cpp -o Muscle/glbalignle.o
In file included from Muscle/muscle.h:37,
                 from Muscle/glbalignle.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
Muscle/glbalignle.cpp: In function 'SCORE GlobalAlignLE(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
Muscle/glbalignle.cpp:431:30: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized]
  431 |                 iTraceBack = (int) uInsertPos - (int) uLengthB;
      |                              ^~~~~~~~~~~~~~~~
Muscle/glbalignle.cpp:404:18: note: 'uInsertPos' was declared here
  404 |         unsigned uInsertPos;
      |                  ^~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/glbalignns.cpp -o Muscle/glbalignns.o
In file included from Muscle/muscle.h:37,
                 from Muscle/glbalignns.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
Muscle/glbalignns.cpp: In function 'SCORE GlobalAlignNS(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
Muscle/glbalignns.cpp:305:52: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized]
  305 |                                 *ptrTraceBack_ij = (int) uInsertPos - (int) j;
      |                                                    ^~~~~~~~~~~~~~~~
Muscle/glbalignns.cpp:272:26: note: 'uInsertPos' was declared here
  272 |                 unsigned uInsertPos;
      |                          ^~~~~~~~~~
Muscle/glbalignns.cpp:366:30: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized]
  366 |                 iTraceBack = (int) uInsertPos - (int) uLengthB;
      |                              ^~~~~~~~~~~~~~~~
Muscle/glbalignns.cpp:339:18: note: 'uInsertPos' was declared here
  339 |         unsigned uInsertPos;
      |                  ^~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/glbalignsimple.cpp -o Muscle/glbalignsimple.o
Muscle/glbalignsimple.cpp:52:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
   52 | static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
      |             ^~~~~~
Muscle/glbalignsimple.cpp:28:13: warning: 'void ListTB(const char*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
   28 | static void ListTB(const char *TBM_, const ProfPos *PA, const ProfPos *PB,
      |             ^~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/glbalignsimple.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/glbalignsp.cpp -o Muscle/glbalignsp.o
In file included from Muscle/muscle.h:37,
                 from Muscle/glbalignsp.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
Muscle/glbalignsp.cpp: In function 'SCORE GlobalAlignSP(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
Muscle/glbalignsp.cpp:305:52: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized]
  305 |                                 *ptrTraceBack_ij = (int) uInsertPos - (int) j;
      |                                                    ^~~~~~~~~~~~~~~~
Muscle/glbalignsp.cpp:272:26: note: 'uInsertPos' was declared here
  272 |                 unsigned uInsertPos;
      |                          ^~~~~~~~~~
Muscle/glbalignsp.cpp:366:30: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized]
  366 |                 iTraceBack = (int) uInsertPos - (int) uLengthB;
      |                              ^~~~~~~~~~~~~~~~
Muscle/glbalignsp.cpp:339:18: note: 'uInsertPos' was declared here
  339 |         unsigned uInsertPos;
      |                  ^~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/glbalignspn.cpp -o Muscle/glbalignspn.o
In file included from Muscle/muscle.h:37,
                 from Muscle/glbalignspn.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
Muscle/glbalignspn.cpp: In function 'SCORE GlobalAlignSPN(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
Muscle/glbalignspn.cpp:340:52: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized]
  340 |                                 *ptrTraceBack_ij = (int) uInsertPos - (int) j;
      |                                                    ^~~~~~~~~~~~~~~~
Muscle/glbalignspn.cpp:307:26: note: 'uInsertPos' was declared here
  307 |                 unsigned uInsertPos;
      |                          ^~~~~~~~~~
Muscle/glbalignspn.cpp:401:30: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized]
  401 |                 iTraceBack = (int) uInsertPos - (int) uLengthB;
      |                              ^~~~~~~~~~~~~~~~
Muscle/glbalignspn.cpp:374:18: note: 'uInsertPos' was declared here
  374 |         unsigned uInsertPos;
      |                  ^~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/glbalignss.cpp -o Muscle/glbalignss.o
Muscle/glbalignss.cpp: In function 'SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)':
Muscle/glbalignss.cpp:177:30: warning: unused variable 'ptrRowA' [-Wunused-variable]
  177 |                 const SCORE *ptrRowA = MxRowA[i];
      |                              ^~~~~~~
Muscle/glbalignss.cpp:119:24: warning: unused variable 'uPrefixCountA' [-Wunused-variable]
  119 |         const unsigned uPrefixCountA = uLengthA + 1;
      |                        ^~~~~~~~~~~~~
Muscle/glbalignss.cpp:120:24: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
  120 |         const unsigned uPrefixCountB = uLengthB + 1;
      |                        ^~~~~~~~~~~~~
Muscle/glbalignss.cpp: At global scope:
Muscle/glbalignss.cpp:11:14: warning: 'SCORE Subst(const Seq&, const Seq&, unsigned int, unsigned int)' defined but not used [-Wunused-function]
   11 | static SCORE Subst(const Seq &seqA, const Seq &seqB, unsigned i, unsigned j)
      |              ^~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/glbalignss.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
Muscle/glbalignss.cpp: In function 'SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)':
Muscle/glbalignss.cpp:252:52: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized]
  252 |                                 *ptrTraceBack_ij = (int) uInsertPos - (int) j;
      |                                                    ^~~~~~~~~~~~~~~~
Muscle/glbalignss.cpp:221:26: note: 'uInsertPos' was declared here
  221 |                 unsigned uInsertPos;
      |                          ^~~~~~~~~~
Muscle/glbalignss.cpp:310:30: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized]
  310 |                 iTraceBack = (int) uInsertPos - (int) uLengthB;
      |                              ^~~~~~~~~~~~~~~~
Muscle/glbalignss.cpp:283:18: note: 'uInsertPos' was declared here
  283 |         unsigned uInsertPos;
      |                  ^~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/glbalndimer.cpp -o Muscle/glbalndimer.o
Muscle/glbalndimer.cpp:14:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function]
   14 | static const char *LocalScoreToStr(SCORE s)
      |                    ^~~~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/glbalndimer.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/globals.cpp -o Muscle/globals.o
In file included from Muscle/muscle.h:37,
                 from Muscle/globals.cpp:6:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/globalslinux.cpp -o Muscle/globalslinux.o
In file included from Muscle/muscle.h:37,
                 from Muscle/globalslinux.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/globalsosx.cpp -o Muscle/globalsosx.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/globalsother.cpp -o Muscle/globalsother.o
In file included from Muscle/muscle.h:37,
                 from Muscle/globalsother.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/globalswin32.cpp -o Muscle/globalswin32.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/gonnet.cpp -o Muscle/gonnet.o
Muscle/gonnet.cpp:137:14: warning: 'Gonnet160' defined but not used [-Wunused-variable]
  137 | static SCORE Gonnet160[20][20] =
      |              ^~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/gonnet.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/gotowt.cpp -o Muscle/gotowt.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/henikoffweight.cpp -o Muscle/henikoffweight.o
In file included from Muscle/muscle.h:37,
                 from Muscle/henikoffweight.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/henikoffweightpb.cpp -o Muscle/henikoffweightpb.o
In file included from Muscle/muscle.h:37,
                 from Muscle/henikoffweightpb.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/html.cpp -o Muscle/html.o
In file included from Muscle/muscle.h:37,
                 from Muscle/html.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/hydro.cpp -o Muscle/hydro.o
In file included from Muscle/muscle.h:37,
                 from Muscle/hydro.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/intmath.cpp -o Muscle/intmath.o
In file included from Muscle/muscle.h:37,
                 from Muscle/intmath.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/local.cpp -o Muscle/local.o
In file included from Muscle/muscle.h:37,
                 from Muscle/local.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/main.cpp -o Muscle/main.o
In file included from Muscle/muscle.h:37,
                 from Muscle/main.cpp:3:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/makerootmsa.cpp -o Muscle/makerootmsa.o
Muscle/makerootmsa.cpp: In function 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)':
Muscle/makerootmsa.cpp:18:24: warning: unused variable 'uSeqLength' [-Wunused-variable]
   18 |         const unsigned uSeqLength = s.Length();
      |                        ^~~~~~~~~~
Muscle/makerootmsa.cpp: In function 'short int* MakeRootSeqE(const Seq&, const Tree&, unsigned int, const ProgNode*, Seq&, short int*, short int*)':
Muscle/makerootmsa.cpp:94:31: warning: unused variable 'Path' [-Wunused-variable]
   94 |                 const PWPath &Path = Nodes[uNodeIndex].m_Path;
      |                               ^~~~
Muscle/makerootmsa.cpp: In function 'void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)':
Muscle/makerootmsa.cpp:168:24: warning: unused variable 'uTreeNodeCount' [-Wunused-variable]
  168 |         const unsigned uTreeNodeCount = GuideTree.GetNodeCount();
      |                        ^~~~~~~~~~~~~~
Muscle/makerootmsa.cpp: At global scope:
Muscle/makerootmsa.cpp:12:13: warning: 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)' defined but not used [-Wunused-function]
   12 | static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut)
      |             ^~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/makerootmsa.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/makerootmsab.cpp -o Muscle/makerootmsab.o
In file included from Muscle/muscle.h:37,
                 from Muscle/makerootmsab.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/maketree.cpp -o Muscle/maketree.o
In file included from Muscle/muscle.h:37,
                 from Muscle/maketree.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/mhack.cpp -o Muscle/mhack.o
In file included from Muscle/muscle.h:37,
                 from Muscle/mhack.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/mpam200.cpp -o Muscle/mpam200.o
In file included from Muscle/muscle.h:37,
                 from Muscle/mpam200.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/msa.cpp -o Muscle/msa.o
Muscle/msa.cpp:419:13: warning: 'void FmtPad(unsigned int)' defined but not used [-Wunused-function]
  419 | static void FmtPad(unsigned n)
      |             ^~~~~~
Muscle/msa.cpp:407:13: warning: 'void FmtInt0(unsigned int, unsigned int)' defined but not used [-Wunused-function]
  407 | static void FmtInt0(unsigned u, unsigned uWidth)
      |             ^~~~~~~
Muscle/msa.cpp:392:13: warning: 'void FmtInt(unsigned int, unsigned int)' defined but not used [-Wunused-function]
  392 | static void FmtInt(unsigned u, unsigned uWidth)
      |             ^~~~~~
Muscle/msa.cpp:385:13: warning: 'void FmtChar(char, unsigned int)' defined but not used [-Wunused-function]
  385 | static void FmtChar(char c, unsigned uWidth)
      |             ^~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/msa.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/msa2.cpp -o Muscle/msa2.o
Muscle/msa2.cpp: In function 'void MSAAppend(MSA&, const MSA&)':
Muscle/msa2.cpp:479:24: warning: unused variable 'uColCountCat' [-Wunused-variable]
  479 |         const unsigned uColCountCat = uColCount1 + uColCount2;
      |                        ^~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/msa2.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/msadistkimura.cpp -o Muscle/msadistkimura.o
In file included from Muscle/muscle.h:37,
                 from Muscle/msadistkimura.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/msf.cpp -o Muscle/msf.o
Muscle/msf.cpp:24:20: warning: 'const char* strfind(const char*, const char*)' defined but not used [-Wunused-function]
   24 | static const char *strfind(const char *s, const char *t)
      |                    ^~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/msf.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/muscle.cpp -o Muscle/muscle.o
In file included from Muscle/muscle.h:37,
                 from Muscle/muscle.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/muscleout.cpp -o Muscle/muscleout.o
In file included from Muscle/muscle.h:37,
                 from Muscle/muscleout.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/nucmx.cpp -o Muscle/nucmx.o
In file included from Muscle/muscle.h:37,
                 from Muscle/nucmx.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/nwdasimple.cpp -o Muscle/nwdasimple.o
In file included from Muscle/muscle.h:37,
                 from Muscle/nwdasimple.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/nwdasimple2.cpp -o Muscle/nwdasimple2.o
In file included from Muscle/muscle.h:37,
                 from Muscle/nwdasimple2.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/nwdasmall.cpp -o Muscle/nwdasmall.o
In file included from Muscle/muscle.h:37,
                 from Muscle/nwdasmall.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/nwrec.cpp -o Muscle/nwrec.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/nwsmall.cpp -o Muscle/nwsmall.o
In file included from Muscle/muscle.h:37,
                 from Muscle/nwsmall.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/objscore.cpp -o Muscle/objscore.o
In file included from Muscle/objscore.cpp:5:
Muscle/timing.h:5: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
    5 | #pragma warning(disable:4035)
      | 
Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
   24 | static double TicksToSecs(TICKS t)
      |               ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/objscore.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/objscore2.cpp -o Muscle/objscore2.o
Muscle/objscore2.cpp: In function 'SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)':
Muscle/objscore2.cpp:65:15: warning: unused variable 'scoreGaps' [-Wunused-variable]
   65 |         SCORE scoreGaps = 0;
      |               ^~~~~~~~~
Muscle/objscore2.cpp:66:14: warning: unused variable 'bGapping1' [-Wunused-variable]
   66 |         bool bGapping1 = false;
      |              ^~~~~~~~~
Muscle/objscore2.cpp:67:14: warning: unused variable 'bGapping2' [-Wunused-variable]
   67 |         bool bGapping2 = false;
      |              ^~~~~~~~~
Muscle/objscore2.cpp:70:14: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
   70 |         bool bLeftTermGap = false;
      |              ^~~~~~~~~~~~
Muscle/objscore2.cpp:85:14: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
   85 |         bool bRightTermGap = false;
      |              ^~~~~~~~~~~~~
Muscle/objscore2.cpp: In function 'SCORE ScoreSeqPairGaps(const MSA&, unsigned int, const MSA&, unsigned int)':
Muscle/objscore2.cpp:143:14: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
  143 |         bool bLeftTermGap = false;
      |              ^~~~~~~~~~~~
Muscle/objscore2.cpp:158:14: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
  158 |         bool bRightTermGap = false;
      |              ^~~~~~~~~~~~~
Muscle/objscore2.cpp: In function 'SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)':
Muscle/objscore2.cpp:317:24: warning: unused variable 'uColCount2' [-Wunused-variable]
  317 |         const unsigned uColCount2 = msa2.GetColCount();
      |                        ^~~~~~~~~~
Muscle/objscore2.cpp: In function 'SCORE ObjScoreXP(const MSA&, const MSA&)':
Muscle/objscore2.cpp:496:38: warning: unused variable 'w' [-Wunused-variable]
  496 |                         const WEIGHT w = w1*w2;
      |                                      ^
In file included from Muscle/muscle.h:37,
                 from Muscle/objscore2.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/objscoreda.cpp -o Muscle/objscoreda.o
In file included from Muscle/muscle.h:37,
                 from Muscle/objscoreda.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/onexception.cpp -o Muscle/onexception.o
In file included from Muscle/muscle.h:37,
                 from Muscle/onexception.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/options.cpp -o Muscle/options.o
In file included from Muscle/muscle.h:37,
                 from Muscle/options.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/outweights.cpp -o Muscle/outweights.o
In file included from Muscle/muscle.h:37,
                 from Muscle/outweights.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/pam200mafft.cpp -o Muscle/pam200mafft.o
Muscle/pam200mafft.cpp:6:14: warning: 'PAM200' defined but not used [-Wunused-variable]
    6 | static float PAM200[23][23] =
      |              ^~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/pam200mafft.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/params.cpp -o Muscle/params.o
In file included from Muscle/muscle.h:37,
                 from Muscle/params.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/phy.cpp -o Muscle/phy.o
Muscle/phy.cpp: In member function 'void Tree::RootUnrootedTree(ROOT)':
Muscle/phy.cpp:665:16: warning: unused variable 'dEdgeLength' [-Wunused-variable]
  665 |         double dEdgeLength = GetEdgeLength(uNode1, uNode2);
      |                ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/phy.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/phy2.cpp -o Muscle/phy2.o
In file included from Muscle/muscle.h:37,
                 from Muscle/phy2.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/phy3.cpp -o Muscle/phy3.o
Muscle/phy3.cpp: In function 'void CalcInfo(const Tree&, unsigned int, unsigned int, EdgeInfo**)':
Muscle/phy3.cpp:125:22: warning: unused variable 'dThisDist' [-Wunused-variable]
  125 |         const double dThisDist = tree.GetEdgeLength(uNode1, uNode2);
      |                      ^~~~~~~~~
Muscle/phy3.cpp: In function 'void FindRoot(const Tree&, unsigned int*, unsigned int*, double*, double*, ROOT)':
Muscle/phy3.cpp:167:24: warning: unused variable 'uLeafCount' [-Wunused-variable]
  167 |         const unsigned uLeafCount = tree.GetLeafCount();
      |                        ^~~~~~~~~~
Muscle/phy3.cpp:190:16: warning: unused variable 'dAllMaxDist' [-Wunused-variable]
  190 |         double dAllMaxDist = -1e20;
      |                ^~~~~~~~~~~
Muscle/phy3.cpp:191:18: warning: unused variable 'uMaxFrom' [-Wunused-variable]
  191 |         unsigned uMaxFrom = NULL_NEIGHBOR;
      |                  ^~~~~~~~
Muscle/phy3.cpp:192:18: warning: unused variable 'uMaxTo' [-Wunused-variable]
  192 |         unsigned uMaxTo = NULL_NEIGHBOR;
      |                  ^~~~~~
Muscle/phy3.cpp: In function 'void RootByMidLongestSpan(const Tree&, EdgeInfo**, unsigned int*, unsigned int*, double*, double*)':
Muscle/phy3.cpp:263:18: warning: variable 'uMostDistantLeaf' set but not used [-Wunused-but-set-variable]
  263 |         unsigned uMostDistantLeaf = NULL_NEIGHBOR;
      |                  ^~~~~~~~~~~~~~~~
Muscle/phy3.cpp: At global scope:
Muscle/phy3.cpp:45:13: warning: 'void ListEIs(EdgeInfo**, unsigned int)' defined but not used [-Wunused-function]
   45 | static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount)
      |             ^~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/phy3.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/phy4.cpp -o Muscle/phy4.o
In file included from Muscle/muscle.h:37,
                 from Muscle/phy4.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/phyfromclust.cpp -o Muscle/phyfromclust.o
In file included from Muscle/muscle.h:37,
                 from Muscle/phyfromclust.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/phyfromfile.cpp -o Muscle/phyfromfile.o
In file included from Muscle/muscle.h:37,
                 from Muscle/phyfromfile.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/physeq.cpp -o Muscle/physeq.o
Muscle/physeq.cpp: In member function 'void MSA::ToPhySequentialFile(TextFile&) const':
Muscle/physeq.cpp:60:41: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
   60 |                                 if (Col == ColCount)
      |                                     ~~~~^~~~~~~~~~~
Muscle/physeq.cpp:71:33: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
   71 |                         if (Col == ColCount)
      |                             ~~~~^~~~~~~~~~~
Muscle/physeq.cpp: In member function 'void MSA::ToPhyInterleavedFile(TextFile&) const':
Muscle/physeq.cpp:112:41: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  112 |                                 if (Col == ColCount)
      |                                     ~~~~^~~~~~~~~~~
Muscle/physeq.cpp:124:25: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  124 |                 if (Col == ColCount)
      |                     ~~~~^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/physeq.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/phytofile.cpp -o Muscle/phytofile.o
In file included from Muscle/muscle.h:37,
                 from Muscle/phytofile.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/posgap.cpp -o Muscle/posgap.o
In file included from Muscle/muscle.h:37,
                 from Muscle/posgap.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/ppscore.cpp -o Muscle/ppscore.o
In file included from Muscle/muscle.h:37,
                 from Muscle/ppscore.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/profdb.cpp -o Muscle/profdb.o
In file included from Muscle/muscle.h:37,
                 from Muscle/profdb.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/profile.cpp -o Muscle/profile.o
In file included from Muscle/muscle.h:37,
                 from Muscle/profile.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/profilefrommsa.cpp -o Muscle/profilefrommsa.o
Muscle/profilefrommsa.cpp: In function 'void ListProfile(const ProfPos*, unsigned int, const MSA*)':
Muscle/profilefrommsa.cpp:131:24: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  131 |                 if (-1 == PP.m_uResidueGroup)
      |                     ~~~^~~~~~~~~~~~~~~~~~~~~
Muscle/profilefrommsa.cpp: In function 'ProfPos* ProfileFromMSA(const MSA&)':
Muscle/profilefrommsa.cpp:248:24: warning: unused variable 'uSeqCount' [-Wunused-variable]
  248 |         const unsigned uSeqCount = a.GetSeqCount();
      |                        ^~~~~~~~~
Muscle/profilefrommsa.cpp:256:18: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable]
  256 |         unsigned uHydrophobicRunLength = 0;
      |                  ^~~~~~~~~~~~~~~~~~~~~
Muscle/profilefrommsa.cpp: At global scope:
Muscle/profilefrommsa.cpp:15:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function]
   15 | static const char *LocalScoreToStr(SCORE s)
      |                    ^~~~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/profilefrommsa.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/progalign.cpp -o Muscle/progalign.o
Muscle/progalign.cpp: In function 'ProgNode* ProgressiveAlignE(const SeqVect&, const Tree&, MSA&)':
Muscle/progalign.cpp:41:24: warning: unused variable 'uIterCount' [-Wunused-variable]
   41 |         const unsigned uIterCount = uSeqCount - 1;
      |                        ^~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/progalign.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/progress.cpp -o Muscle/progress.o
In file included from Muscle/muscle.h:37,
                 from Muscle/progress.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/progressivealign.cpp -o Muscle/progressivealign.o
In file included from Muscle/muscle.h:37,
                 from Muscle/progressivealign.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/pwpath.cpp -o Muscle/pwpath.o
Muscle/pwpath.cpp: In member function 'void PWPath::Validate() const':
Muscle/pwpath.cpp:80:23: warning: unused variable 'LastEdge' [-Wunused-variable]
   80 |         const PWEdge &LastEdge = GetEdge(uEdgeCount - 1);
      |                       ^~~~~~~~
Muscle/pwpath.cpp: In member function 'void PWPath::FromFile(TextFile&)':
Muscle/pwpath.cpp:213:18: warning: unused variable 'uEdgeIndex' [-Wunused-variable]
  213 |         unsigned uEdgeIndex = 0;
      |                  ^~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/pwpath.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/readmx.cpp -o Muscle/readmx.o
Muscle/readmx.cpp: In function 'float (* ReadMx(TextFile&))[32][32]':
Muscle/readmx.cpp:83:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
   83 |         for (int i = 0; i < MAX_ALPHA; ++i)
      |                         ~~^~~~~~~~~~~
Muscle/readmx.cpp:84:35: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
   84 |                 for (int j = 0; j < MAX_ALPHA; ++j)
      |                                 ~~^~~~~~~~~~~
Muscle/readmx.cpp: In function 'float (* ReadMxFromR(std::vector<std::__cxx11::basic_string<char> >, float (*)[32]))[32][32]':
Muscle/readmx.cpp:184:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  184 |         for (int i = 0; i < MAX_ALPHA; ++i)
      |                         ~~^~~~~~~~~~~
Muscle/readmx.cpp:185:35: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  185 |                 for (int j = 0; j < MAX_ALPHA; ++j)
      |                                 ~~^~~~~~~~~~~
Muscle/readmx.cpp: At global scope:
Muscle/readmx.cpp:30:17: warning: 'unsigned int MxCharToLetter(char)' defined but not used [-Wunused-function]
   30 | static unsigned MxCharToLetter(char c)
      |                 ^~~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/readmx.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/realigndiffs.cpp -o Muscle/realigndiffs.o
In file included from Muscle/muscle.h:37,
                 from Muscle/realigndiffs.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/realigndiffse.cpp -o Muscle/realigndiffse.o
Muscle/realigndiffse.cpp: In function 'void RealignDiffsE(const MSA&, const SeqVect&, const Tree&, const Tree&, const unsigned int*, MSA&, ProgNode*)':
Muscle/realigndiffse.cpp:77:34: warning: unused variable 'uNewRight' [-Wunused-variable]
   77 |                         unsigned uNewRight = NewTree.GetRight(uNewNodeIndex);
      |                                  ^~~~~~~~~
Muscle/realigndiffse.cpp:80:34: warning: unused variable 'uOldRight' [-Wunused-variable]
   80 |                         unsigned uOldRight = OldTree.GetRight(uOld);
      |                                  ^~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/realigndiffse.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/refine.cpp -o Muscle/refine.o
In file included from Muscle/muscle.h:37,
                 from Muscle/refine.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/refinehoriz.cpp -o Muscle/refinehoriz.o
In file included from Muscle/muscle.h:37,
                 from Muscle/refinehoriz.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
In function 'void RefineHeightParts(MSA&, const Tree&, const unsigned int*, bool, bool, unsigned int, ScoreHistory&, bool*, bool*, bool, bool)',
    inlined from 'bool RefineHoriz(MSA&, const Tree&, unsigned int, bool, bool)' at Muscle/refinehoriz.cpp:263:21:
Muscle/refinehoriz.cpp:187:58: warning: 'scoreBefore' may be used uninitialized [-Wmaybe-uninitialized]
  187 |                 SCORE scoreMax = scoreAfter > scoreBefore? scoreAfter : scoreBefore;
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
Muscle/refinehoriz.cpp: In function 'bool RefineHoriz(MSA&, const Tree&, unsigned int, bool, bool)':
Muscle/refinehoriz.cpp:173:23: note: 'scoreBefore' was declared here
  173 |                 SCORE scoreBefore;
      |                       ^~~~~~~~~~~
In function 'void RefineHeightParts(MSA&, const Tree&, const unsigned int*, bool, bool, unsigned int, ScoreHistory&, bool*, bool*, bool, bool)',
    inlined from 'bool RefineHoriz(MSA&, const Tree&, unsigned int, bool, bool)' at Muscle/refinehoriz.cpp:263:21:
Muscle/refinehoriz.cpp:187:58: warning: 'scoreAfter' may be used uninitialized [-Wmaybe-uninitialized]
  187 |                 SCORE scoreMax = scoreAfter > scoreBefore? scoreAfter : scoreBefore;
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
Muscle/refinehoriz.cpp: In function 'bool RefineHoriz(MSA&, const Tree&, unsigned int, bool, bool)':
Muscle/refinehoriz.cpp:174:23: note: 'scoreAfter' was declared here
  174 |                 SCORE scoreAfter;
      |                       ^~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/refinesubfams.cpp -o Muscle/refinesubfams.o
Muscle/refinesubfams.cpp: In function 'bool RefineSubfams(MSA&, const Tree&, unsigned int)':
Muscle/refinesubfams.cpp:63:24: warning: unused variable 'uNodeCount' [-Wunused-variable]
   63 |         const unsigned uNodeCount = tree.GetNodeCount();
      |                        ^~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/refinesubfams.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/refinetree.cpp -o Muscle/refinetree.o
In file included from Muscle/muscle.h:37,
                 from Muscle/refinetree.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/refinetreee.cpp -o Muscle/refinetreee.o
In file included from Muscle/muscle.h:37,
                 from Muscle/refinetreee.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/refinevert.cpp -o Muscle/refinevert.o
In file included from Muscle/muscle.h:37,
                 from Muscle/refinevert.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/refinew.cpp -o Muscle/refinew.o
Muscle/refinew.cpp: In function 'void AppendMSA(MSA&, const MSA&)':
Muscle/refinew.cpp:23:24: warning: unused variable 'uColCountCat' [-Wunused-variable]
   23 |         const unsigned uColCountCat = uColCount1 + uColCount2;
      |                        ^~~~~~~~~~~~
Muscle/refinew.cpp: In function 'void RefineW(const MSA&, MSA&)':
Muscle/refinew.cpp:128:34: warning: unused variable 'uOutCols' [-Wunused-variable]
  128 |                         unsigned uOutCols = msaOut.GetColCount();
      |                                  ^~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/refinew.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/savebest.cpp -o Muscle/savebest.o
In file included from Muscle/muscle.h:37,
                 from Muscle/savebest.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/scoredist.cpp -o Muscle/scoredist.o
In file included from Muscle/muscle.h:37,
                 from Muscle/scoredist.cpp:3:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/scoregaps.cpp -o Muscle/scoregaps.o
Muscle/scoregaps.cpp:80:14: warning: 'SCORE Penalty(unsigned int, bool)' defined but not used [-Wunused-function]
   80 | static SCORE Penalty(unsigned Length, bool Term)
      |              ^~~~~~~
Muscle/scoregaps.cpp:37:13: warning: 'void FreeGapInfo(GAPINFO*)' defined but not used [-Wunused-function]
   37 | static void FreeGapInfo(GAPINFO *GI)
      |             ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/scoregaps.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/scorehistory.cpp -o Muscle/scorehistory.o
In file included from Muscle/muscle.h:37,
                 from Muscle/scorehistory.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/scorepp.cpp -o Muscle/scorepp.o
In file included from Muscle/muscle.h:37,
                 from Muscle/scorepp.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/seq.cpp -o Muscle/seq.o
In file included from Muscle/muscle.h:37,
                 from Muscle/seq.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/seqvect.cpp -o Muscle/seqvect.o
In file included from Muscle/muscle.h:37,
                 from Muscle/seqvect.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/setblosumweights.cpp -o Muscle/setblosumweights.o
In file included from Muscle/muscle.h:37,
                 from Muscle/setblosumweights.cpp:42:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/setgscweights.cpp -o Muscle/setgscweights.o
In file included from Muscle/muscle.h:37,
                 from Muscle/setgscweights.cpp:104:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/setnewhandler.cpp -o Muscle/setnewhandler.o
In file included from Muscle/muscle.h:37,
                 from Muscle/setnewhandler.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/spfast.cpp -o Muscle/spfast.o
Muscle/spfast.cpp: In function 'SCORE ObjScoreSPDimer(const MSA&)':
Muscle/spfast.cpp:252:24: warning: unused variable 'uSeqCount' [-Wunused-variable]
  252 |         const unsigned uSeqCount = msa.GetSeqCount();
      |                        ^~~~~~~~~
Muscle/spfast.cpp: At global scope:
Muscle/spfast.cpp:59:14: warning: 'SCORE SPColBrute(const MSA&, unsigned int)' defined but not used [-Wunused-function]
   59 | static SCORE SPColBrute(const MSA &msa, unsigned uColIndex)
      |              ^~~~~~~~~~
Muscle/spfast.cpp:14:20: warning: 'const char* GapTypeToStr(int)' defined but not used [-Wunused-function]
   14 | static const char *GapTypeToStr(int GapType)
      |                    ^~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/spfast.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/sptest.cpp -o Muscle/sptest.o
In file included from Muscle/muscle.h:37,
                 from Muscle/sptest.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/stabilize.cpp -o Muscle/stabilize.o
In file included from Muscle/muscle.h:37,
                 from Muscle/stabilize.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/subfam.cpp -o Muscle/subfam.o
Muscle/subfam.cpp: In function 'void AlignSubFam(SeqVect&, const Tree&, unsigned int, MSA&)':
Muscle/subfam.cpp:173:13: warning: unused variable 'NotUsed' [-Wunused-variable]
  173 |         int NotUsed = system(CmdLine);
      |             ^~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/subfam.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/subfams.cpp -o Muscle/subfams.o
Muscle/subfams.cpp:52:13: warning: 'void Relax(DistFunc&, unsigned int, unsigned int)' defined but not used [-Wunused-function]
   52 | static void Relax(DistFunc &DF, unsigned u, unsigned v)
      |             ^~~~~
Muscle/subfams.cpp:40:13: warning: 'void InitializeSingleSource(DistFunc&, unsigned int)' defined but not used [-Wunused-function]
   40 | static void InitializeSingleSource(DistFunc &DF, unsigned uIndex)
      |             ^~~~~~~~~~~~~~~~~~~~~~
Muscle/subfams.cpp:10:13: warning: 'void GetMostDistantPair(DistFunc&, unsigned int*, unsigned int*)' defined but not used [-Wunused-function]
   10 | static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2)
      |             ^~~~~~~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/subfams.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/sw.cpp -o Muscle/sw.o
Muscle/sw.cpp:20:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
   20 | static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
      |             ^~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/sw.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/termgaps.cpp -o Muscle/termgaps.o
In file included from Muscle/muscle.h:37,
                 from Muscle/termgaps.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/textfile.cpp -o Muscle/textfile.o
Muscle/textfile.cpp: In member function 'void TextFile::PutChar(char)':
Muscle/textfile.cpp:107:13: warning: unused variable 'i' [-Wunused-variable]
  107 |         int i = fputc(c, m_ptrFile);
      |             ^
Muscle/textfile.cpp: In member function 'void TextFile::PutString(const char*)':
Muscle/textfile.cpp:120:13: warning: unused variable 'iError' [-Wunused-variable]
  120 |         int iError = fputs(szLine, m_ptrFile);
      |             ^~~~~~
Muscle/textfile.cpp: In member function 'TEXTFILEPOS TextFile::GetPos()':
Muscle/textfile.cpp:220:13: warning: unused variable 'i' [-Wunused-variable]
  220 |         int i = fgetpos(m_ptrFile, &p);
      |             ^
Muscle/textfile.cpp: In member function 'void TextFile::SetPos(TEXTFILEPOS)':
Muscle/textfile.cpp:233:13: warning: unused variable 'i' [-Wunused-variable]
  233 |         int i = fsetpos(m_ptrFile, &p);
      |             ^
In file included from Muscle/muscle.h:37,
                 from Muscle/textfile.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/threewaywt.cpp -o Muscle/threewaywt.o
In file included from Muscle/muscle.h:37,
                 from Muscle/threewaywt.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/tomhydro.cpp -o Muscle/tomhydro.o
In file included from Muscle/muscle.h:37,
                 from Muscle/tomhydro.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/traceback.cpp -o Muscle/traceback.o
Muscle/traceback.cpp: In function 'SCORE TraceBack(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, PWPath&)':
Muscle/traceback.cpp:21:24: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
   21 |         const unsigned uPrefixCountB = uLengthB + 1;
      |                        ^~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/traceback.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/tracebackopt.cpp -o Muscle/tracebackopt.o
In file included from Muscle/muscle.h:37,
                 from Muscle/tracebackopt.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/tracebacksw.cpp -o Muscle/tracebacksw.o
Muscle/tracebacksw.cpp: In function 'void TraceBackSW(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, unsigned int, unsigned int, PWPath&)':
Muscle/tracebacksw.cpp:22:24: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
   22 |         const unsigned uPrefixCountB = uLengthB + 1;
      |                        ^~~~~~~~~~~~~
Muscle/tracebacksw.cpp:29:15: warning: unused variable 'scoreMax' [-Wunused-variable]
   29 |         SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB);
      |               ^~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/tracebacksw.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/treefrommsa.cpp -o Muscle/treefrommsa.o
In file included from Muscle/muscle.h:37,
                 from Muscle/treefrommsa.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/typetostr.cpp -o Muscle/typetostr.o
In file included from Muscle/muscle.h:37,
                 from Muscle/typetostr.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/upgma2.cpp -o Muscle/upgma2.o
Muscle/upgma2.cpp:68:13: warning: 'void ListState()' defined but not used [-Wunused-function]
   68 | static void ListState()
      |             ^~~~~~~~~
In file included from Muscle/muscle.h:37,
                 from Muscle/upgma2.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
Muscle/upgma2.cpp: In function 'void UPGMA2(const DistCalc&, Tree&, LINKAGE)':
Muscle/upgma2.cpp:292:36: warning: 'dtNewDist' may be used uninitialized [-Wmaybe-uninitialized]
  292 |                         g_Dist[vL] = dtNewDist;
      |                         ~~~~~~~~~~~^~~~~~~~~~~
Muscle/upgma2.cpp:252:32: note: 'dtNewDist' was declared here
  252 |                         dist_t dtNewDist;
      |                                ^~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/usage.cpp -o Muscle/usage.o
In file included from Muscle/muscle.h:37,
                 from Muscle/usage.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/validateids.cpp -o Muscle/validateids.o
In file included from Muscle/muscle.h:37,
                 from Muscle/validateids.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/vtml2.cpp -o Muscle/vtml2.o
In file included from Muscle/muscle.h:37,
                 from Muscle/vtml2.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Muscle/writescorefile.cpp -o Muscle/writescorefile.o
In file included from Muscle/muscle.h:37,
                 from Muscle/writescorefile.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
In function 'double GetColScore(const MSA&, unsigned int)',
    inlined from 'void WriteScoreFile(const MSA&)' at Muscle/writescorefile.cpp:59:29:
Muscle/writescorefile.cpp:40:30: warning: 'Score' may be used uninitialized [-Wmaybe-uninitialized]
   40 |                         dSum += Score;
      |                         ~~~~~^~~~~~~~
Muscle/writescorefile.cpp: In function 'void WriteScoreFile(const MSA&)':
Muscle/writescorefile.cpp:27:32: note: 'Score' was declared here
   27 |                         double Score;
      |                                ^~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RClustalW.cpp -o RClustalW.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RClustalWMain.cpp -o RClustalWMain.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RMuscle.cpp -o RMuscle.o
In file included from Muscle/muscle.h:37,
                 from RMuscle.h:4,
                 from RMuscle.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ushuffle.c -o ushuffle.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -I"./ClustalW" -I"./Muscle" -pthread   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ushuffler.cpp -o ushuffler.o
g++ -std=gnu++17 -shared -s -static-libgcc -o enhancerHomologSearch.dll tmp.def ClustalW/alignment/Alignment.o ClustalW/alignment/AlignmentOutput.o ClustalW/alignment/ObjectiveScore.o ClustalW/alignment/Sequence.o ClustalW/Clustal.o ClustalW/fileInput/ClustalFileParser.o ClustalW/fileInput/EMBLFileParser.o ClustalW/fileInput/FileParser.o ClustalW/fileInput/FileReader.o ClustalW/fileInput/GDEFileParser.o ClustalW/fileInput/InFileStream.o ClustalW/fileInput/MSFFileParser.o ClustalW/fileInput/PearsonFileParser.o ClustalW/fileInput/PIRFileParser.o ClustalW/fileInput/RSFFileParser.o ClustalW/general/ClustalWResources.o ClustalW/general/DebugLog.o ClustalW/general/InvalidCombination.o ClustalW/general/OutputFile.o ClustalW/general/Stats.o ClustalW/general/SymMatrix.o ClustalW/general/UserParameters.o ClustalW/general/Utility.o ClustalW/general/VectorOutOfRange.o ClustalW/Help.o ClustalW/interface/CommandLineParser.o ClustalW/multipleAlign/Iteration.o ClustalW/multipleAlign/LowScoreSegProfile.o ClustalW/multipleAlign/MSA.o ClustalW/multipleAlign/MyersMillerProfileAlign.o ClustalW/multipleAlign/ProfileBase.o ClustalW/multipleAlign/ProfileStandard.o ClustalW/multipleAlign/ProfileWithSub.o ClustalW/pairwise/FastPairwiseAlign.o ClustalW/pairwise/FullPairwiseAlign.o ClustalW/substitutionMatrix/SubMatrix.o ClustalW/tree/AlignmentSteps.o ClustalW/tree/ClusterTree.o ClustalW/tree/ClusterTreeOutput.o ClustalW/tree/NJTree.o ClustalW/tree/RandomGenerator.o ClustalW/tree/Tree.o ClustalW/tree/TreeInterface.o ClustalW/tree/UnRootedClusterTree.o ClustalW/tree/UPGMA/Node.o ClustalW/tree/UPGMA/RootedClusterTree.o ClustalW/tree/UPGMA/RootedGuideTree.o ClustalW/tree/UPGMA/RootedTreeOutput.o ClustalW/tree/UPGMA/UPGMAAlgorithm.o Muscle/aligngivenpath.o Muscle/aligngivenpathsw.o Muscle/aligntwomsas.o Muscle/aligntwoprofs.o Muscle/aln.o Muscle/alpha.o Muscle/anchors.o Muscle/bittraceback.o Muscle/blosum62.o Muscle/blosumla.o Muscle/clust.o Muscle/cluster.o Muscle/clwwt.o Muscle/color.o Muscle/cons.o Muscle/diaglist.o Muscle/diffobjscore.o Muscle/diffpaths.o Muscle/difftrees.o Muscle/difftreese.o Muscle/distcalc.o Muscle/distfunc.o Muscle/distpwkimura.o Muscle/domuscle.o Muscle/dosp.o Muscle/dpreglist.o Muscle/drawtree.o Muscle/edgelist.o Muscle/enumopts.o Muscle/enumtostr.o Muscle/estring.o Muscle/fasta.o Muscle/fasta2.o Muscle/fastclust.o Muscle/fastdist.o Muscle/fastdistjones.o Muscle/fastdistkbit.o Muscle/fastdistkmer.o Muscle/fastdistmafft.o Muscle/fastdistnuc.o Muscle/fastscorepath2.o Muscle/finddiags.o Muscle/finddiagsn.o Muscle/glbalign.o Muscle/glbalign352.o Muscle/glbaligndiag.o Muscle/glbalignla.o Muscle/glbalignle.o Muscle/glbalignns.o Muscle/glbalignsimple.o Muscle/glbalignsp.o Muscle/glbalignspn.o Muscle/glbalignss.o Muscle/glbalndimer.o Muscle/globals.o Muscle/globalslinux.o Muscle/globalsosx.o Muscle/globalsother.o Muscle/globalswin32.o Muscle/gonnet.o Muscle/gotowt.o Muscle/henikoffweight.o Muscle/henikoffweightpb.o Muscle/html.o Muscle/hydro.o Muscle/intmath.o Muscle/local.o Muscle/main.o Muscle/makerootmsa.o Muscle/makerootmsab.o Muscle/maketree.o Muscle/mhack.o Muscle/mpam200.o Muscle/msa.o Muscle/msa2.o Muscle/msadistkimura.o Muscle/msf.o Muscle/muscle.o Muscle/muscleout.o Muscle/nucmx.o Muscle/nwdasimple.o Muscle/nwdasimple2.o Muscle/nwdasmall.o Muscle/nwrec.o Muscle/nwsmall.o Muscle/objscore.o Muscle/objscore2.o Muscle/objscoreda.o Muscle/onexception.o Muscle/options.o Muscle/outweights.o Muscle/pam200mafft.o Muscle/params.o Muscle/phy.o Muscle/phy2.o Muscle/phy3.o Muscle/phy4.o Muscle/phyfromclust.o Muscle/phyfromfile.o Muscle/physeq.o Muscle/phytofile.o Muscle/posgap.o Muscle/ppscore.o Muscle/profdb.o Muscle/profile.o Muscle/profilefrommsa.o Muscle/progalign.o Muscle/progress.o Muscle/progressivealign.o Muscle/pwpath.o Muscle/readmx.o Muscle/realigndiffs.o Muscle/realigndiffse.o Muscle/refine.o Muscle/refinehoriz.o Muscle/refinesubfams.o Muscle/refinetree.o Muscle/refinetreee.o Muscle/refinevert.o Muscle/refinew.o Muscle/savebest.o Muscle/scoredist.o Muscle/scoregaps.o Muscle/scorehistory.o Muscle/scorepp.o Muscle/seq.o Muscle/seqvect.o Muscle/setblosumweights.o Muscle/setgscweights.o Muscle/setnewhandler.o Muscle/spfast.o Muscle/sptest.o Muscle/stabilize.o Muscle/subfam.o Muscle/subfams.o Muscle/sw.o Muscle/termgaps.o Muscle/textfile.o Muscle/threewaywt.o Muscle/tomhydro.o Muscle/traceback.o Muscle/tracebackopt.o Muscle/tracebacksw.o Muscle/treefrommsa.o Muscle/typetostr.o Muscle/upgma2.o Muscle/usage.o Muscle/validateids.o Muscle/vtml2.o Muscle/writescorefile.o RClustalW.o RClustalWMain.o RcppExports.o RMuscle.o ushuffle.o ushuffler.o -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRlapack -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -lpthread -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-enhancerHomologSearch/00new/enhancerHomologSearch/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (enhancerHomologSearch)