############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/enhancerHomologSearch_1.0.1.tar.gz && rm -rf enhancerHomologSearch.buildbin-libdir && mkdir enhancerHomologSearch.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=enhancerHomologSearch.buildbin-libdir enhancerHomologSearch_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL enhancerHomologSearch_1.0.1.zip && rm enhancerHomologSearch_1.0.1.tar.gz enhancerHomologSearch_1.0.1.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 737k 100 737k 0 0 1310k 0 --:--:-- --:--:-- --:--:-- 1313k install for i386 * installing *source* package 'enhancerHomologSearch' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] SeqArray::iterator posToAddTo = sectionToRealign.begin(); ^~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/alignment/AlignmentOutput.cpp -o ClustalW/alignment/AlignmentOutput.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/alignment/ObjectiveScore.cpp -o ClustalW/alignment/ObjectiveScore.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/alignment/Sequence.cpp -o ClustalW/alignment/Sequence.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/Clustal.cpp -o ClustalW/Clustal.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/ClustalFileParser.cpp -o ClustalW/fileInput/ClustalFileParser.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/EMBLFileParser.cpp -o ClustalW/fileInput/EMBLFileParser.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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::FileParser::getSeqRangeR(int, int, std::__cxx11::string*, ClustalWInput*)': ClustalW/fileInput/FileParser.cpp:38:7: warning: unused variable 'n' [-Wunused-variable] int n = (*input).inputSeqs.size(); ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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::__cxx11::string*, ClustalWInput*)': ClustalW/fileInput/FileReader.cpp:421:10: warning: variable 'maxAlnLength' set but not used [-Wunused-but-set-variable] int maxAlnLength; // Get values from the Alignment object. ^~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/GDEFileParser.cpp -o ClustalW/fileInput/GDEFileParser.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/InFileStream.cpp -o ClustalW/fileInput/InFileStream.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/MSFFileParser.cpp -o ClustalW/fileInput/MSFFileParser.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/PearsonFileParser.cpp -o ClustalW/fileInput/PearsonFileParser.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/PIRFileParser.cpp -o ClustalW/fileInput/PIRFileParser.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/RSFFileParser.cpp -o ClustalW/fileInput/RSFFileParser.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/ClustalWResources.cpp -o ClustalW/general/ClustalWResources.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/DebugLog.cpp -o ClustalW/general/DebugLog.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/InvalidCombination.cpp -o ClustalW/general/InvalidCombination.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/OutputFile.cpp -o ClustalW/general/OutputFile.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/Stats.cpp -o ClustalW/general/Stats.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/SymMatrix.cpp -o ClustalW/general/SymMatrix.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/UserParameters.cpp -o ClustalW/general/UserParameters.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] int n; ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/VectorOutOfRange.cpp -o ClustalW/general/VectorOutOfRange.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/Help.cpp -o ClustalW/Help.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/interface/CommandLineParser.cpp -o ClustalW/interface/CommandLineParser.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] int count; ^~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/multipleAlign/LowScoreSegProfile.cpp -o ClustalW/multipleAlign/LowScoreSegProfile.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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*, clustalw::AlignmentSteps*, int)': ClustalW/multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable] int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18 ^~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/multipleAlign/MyersMillerProfileAlign.cpp -o ClustalW/multipleAlign/MyersMillerProfileAlign.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/multipleAlign/ProfileBase.cpp -o ClustalW/multipleAlign/ProfileBase.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/multipleAlign/ProfileStandard.cpp -o ClustalW/multipleAlign/ProfileStandard.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/multipleAlign/ProfileWithSub.cpp -o ClustalW/multipleAlign/ProfileWithSub.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/pairwise/FastPairwiseAlign.cpp -o ClustalW/pairwise/FastPairwiseAlign.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/pairwise/FullPairwiseAlign.cpp -o ClustalW/pairwise/FullPairwiseAlign.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] char inline1[1024]; ^~~~~~~ ClustalW/substitutionMatrix/SubMatrix.cpp:1307:9: warning: unused variable 'nmat' [-Wunused-variable] int nmat; ^~~~ ClustalW/substitutionMatrix/SubMatrix.cpp:1308:9: warning: unused variable 'n' [-Wunused-variable] int n, llimit, ulimit; ^ ClustalW/substitutionMatrix/SubMatrix.cpp:1308:12: warning: unused variable 'llimit' [-Wunused-variable] int n, llimit, ulimit; ^~~~~~ ClustalW/substitutionMatrix/SubMatrix.cpp:1308:20: warning: unused variable 'ulimit' [-Wunused-variable] 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:1361:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] 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] 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] 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 in this function [-Wmaybe-uninitialized] return (maxRes); ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/AlignmentSteps.cpp -o ClustalW/tree/AlignmentSteps.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] int rs = 0, rl = 0; ^~ ClustalW/tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable] 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] unsigned int tempSeed; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/ClusterTreeOutput.cpp -o ClustalW/tree/ClusterTreeOutput.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/NJTree.cpp -o ClustalW/tree/NJTree.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/RandomGenerator.cpp -o ClustalW/tree/RandomGenerator.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/Tree.cpp -o ClustalW/tree/Tree.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/TreeInterface.cpp -o ClustalW/tree/TreeInterface.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/UnRootedClusterTree.cpp -o ClustalW/tree/UnRootedClusterTree.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:186:17: warning: unused variable 'uLengthA' [-Wunused-variable] const unsigned uLengthA = msaA.GetColCount(); ^~~~~~~~ Muscle/aligngivenpath.cpp:187:17: warning: unused variable 'uLengthB' [-Wunused-variable] const unsigned uLengthB = msaB.GetColCount(); ^~~~~~~~ Muscle/aligngivenpath.cpp: In function 'void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)': Muscle/aligngivenpath.cpp:335:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^~~~~ Muscle/aligngivenpath.cpp:336:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^~~~~ Muscle/aligngivenpath.cpp:346:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^~~~~ Muscle/aligngivenpath.cpp:354:19: warning: unused variable 'uColB' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:58:17: warning: unused variable 'uLengthA' [-Wunused-variable] const unsigned uLengthA = msaA.GetColCount(); ^~~~~~~~ Muscle/aligngivenpathsw.cpp:59:17: warning: unused variable 'uLengthB' [-Wunused-variable] const unsigned uLengthB = msaB.GetColCount(); ^~~~~~~~ Muscle/aligngivenpathsw.cpp: In function 'void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)': Muscle/aligngivenpathsw.cpp:204:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^~~~~ Muscle/aligngivenpathsw.cpp:205:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^~~~~ Muscle/aligngivenpathsw.cpp:215:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^~~~~ Muscle/aligngivenpathsw.cpp:223:19: warning: unused variable 'uColB' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] #pragma warning(disable:4035) Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/alpha.cpp -o Muscle/alpha.o Muscle/alpha.cpp: In function 'unsigned int GetAlphaSize(ALPHA)': Muscle/alpha.cpp:84:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] switch (Alpha) ^ In file included from Muscle/muscle.h:37, from Muscle/alpha.cpp:1: Muscle/intmath.h: At global scope: Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:162:13: warning: unused variable 'uWindowCenter' [-Wunused-variable] 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] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:146:7: warning: unused variable 'Bits' [-Wunused-variable] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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::ChooseJoin(unsigned int*, unsigned int*, float*, float*)': Muscle/clust.cpp:167:9: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] switch (m_JoinStyle) ^ Muscle/clust.cpp: In member function 'void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)': Muscle/clust.cpp:184:17: warning: unused variable 'uClusterCount' [-Wunused-variable] const unsigned uClusterCount = GetClusterCount(); ^~~~~~~~~~~~~ Muscle/clust.cpp: In member function 'void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)': Muscle/clust.cpp:204:17: warning: unused variable 'uClusterCount' [-Wunused-variable] const unsigned uClusterCount = GetClusterCount(); ^~~~~~~~~~~~~ Muscle/clust.cpp: In member function 'float Clust::ComputeDist(unsigned int, unsigned int)': Muscle/clust.cpp:295:9: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch] switch (m_CentroidStyle) ^ Muscle/clust.cpp: In member function 'float Clust::ComputeDistMAFFT(unsigned int, unsigned int)': Muscle/clust.cpp:360:14: warning: unused variable 'dDistLR' [-Wunused-variable] const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex); ^~~~~~~ Muscle/clust.cpp: In member function 'float Clust::ComputeMetric(unsigned int, unsigned int) const': Muscle/clust.cpp:611:9: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] switch (m_JoinStyle) ^ 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:284:8: warning: variable 'bFound' set but not used [-Wunused-but-set-variable] bool bFound = false; ^~~~~~ Muscle/cluster.cpp:267:9: warning: unused variable 'dMaxDist' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/cluster.cpp: In member function 'void ClusterTree::Create(const DistFunc&)': Muscle/cluster.cpp:308:47: warning: 'uIndexClosest2' may be used uninitialized in this function [-Wmaybe-uninitialized] ClusterNode &Child2 = m_Nodes[uIndexClosest2]; ^ Muscle/cluster.cpp:307:47: warning: 'uIndexClosest1' may be used uninitialized in this function [-Wmaybe-uninitialized] ClusterNode &Child1 = m_Nodes[uIndexClosest1]; ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/diaglist.cpp: In member function 'void DiagList::FromPath(const PWPath&)': Muscle/diaglist.cpp:20:17: warning: 'uStartPosB' may be used uninitialized in this function [-Wmaybe-uninitialized] d.m_uStartPosB = uStartPosB; ~~~~~~~~~~~~~~~^~~~~~~~~~~~ Muscle/diaglist.cpp:52:11: note: 'uStartPosB' was declared here unsigned uStartPosB; ^~~~~~~~~~ Muscle/diaglist.cpp:19:17: warning: 'uStartPosA' may be used uninitialized in this function [-Wmaybe-uninitialized] d.m_uStartPosA = uStartPosA; ~~~~~~~~~~~~~~~^~~~~~~~~~~~ Muscle/diaglist.cpp:51:11: note: 'uStartPosA' was declared here unsigned uStartPosA; ^~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable] const unsigned uSeqCount = msa.GetSeqCount(); ^~~~~~~~~ Muscle/diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:161:17: warning: unused variable 'uLeafCount2' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] #pragma warning(disable:4035) Muscle/domuscle.cpp: In function 'void DoMuscle(MuscleInput*, MuscleOutput*)': Muscle/domuscle.cpp:169:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (g_bClusterOnly) ^~ Muscle/domuscle.cpp:172:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' return; ^~~~~~ Muscle/domuscle.cpp:180:6: warning: unused variable 'PNlength' [-Wunused-variable] int PNlength = (msaInput->inputSeqs).Length(); ^~~~~~~~ In file included from Muscle/domuscle.cpp:9: Muscle/timing.h: At global scope: Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:82:19: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/estring.cpp: In function 'void EstringsToPath(const short int*, const short int*, PWPath&)': Muscle/estring.cpp:424:14: warning: 'cType' may be used uninitialized in this function [-Wmaybe-uninitialized] Edge.cType = cType; ~~~~~~~~~~~^~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:15:11: warning: unused variable 'uSeqCount' [-Wunused-variable] unsigned uSeqCount = 0; ^~~~~~~~~ Muscle/fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:235:11: warning: unused variable 'KD' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:239:15: warning: unused variable 'pName1' [-Wunused-variable] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:223:15: warning: unused variable 'pName1' [-Wunused-variable] 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] static void ListCount(const unsigned char Count[]) ^~~~~~~~~ Muscle/fastdistnuc.cpp:33:17: warning: 'uResidueGroupCount' defined but not used [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:16:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] #pragma warning(disable:4035) Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] #pragma warning(disable:4035) Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] #pragma warning(disable:4035) Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/glbalignla.cpp: In function 'SCORE GlobalAlignLA(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': Muscle/glbalignla.cpp:427:16: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] iTraceBack = (int) uInsertPos - (int) uLengthB; ^~~~~~~~~~~~~~~~ Muscle/glbalignla.cpp:366:24: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] *ptrTraceBack_ij = (int) uInsertPos - (int) j; ^~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/glbalignle.cpp: In function 'SCORE GlobalAlignLE(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': Muscle/glbalignle.cpp:431:16: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] iTraceBack = (int) uInsertPos - (int) uLengthB; ^~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/glbalignns.cpp: In function 'SCORE GlobalAlignNS(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': Muscle/glbalignns.cpp:366:16: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] iTraceBack = (int) uInsertPos - (int) uLengthB; ^~~~~~~~~~~~~~~~ Muscle/glbalignns.cpp:305:24: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] *ptrTraceBack_ij = (int) uInsertPos - (int) j; ^~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/glbalignsp.cpp: In function 'SCORE GlobalAlignSP(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': Muscle/glbalignsp.cpp:366:16: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] iTraceBack = (int) uInsertPos - (int) uLengthB; ^~~~~~~~~~~~~~~~ Muscle/glbalignsp.cpp:305:24: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] *ptrTraceBack_ij = (int) uInsertPos - (int) j; ^~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/glbalignspn.cpp: In function 'SCORE GlobalAlignSPN(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': Muscle/glbalignspn.cpp:401:16: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] iTraceBack = (int) uInsertPos - (int) uLengthB; ^~~~~~~~~~~~~~~~ Muscle/glbalignspn.cpp:340:24: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] *ptrTraceBack_ij = (int) uInsertPos - (int) j; ^~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:177:16: warning: unused variable 'ptrRowA' [-Wunused-variable] const SCORE *ptrRowA = MxRowA[i]; ^~~~~~~ Muscle/glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable] const unsigned uPrefixCountA = uLengthA + 1; ^~~~~~~~~~~~~ Muscle/glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/glbalignss.cpp: In function 'SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)': Muscle/glbalignss.cpp:310:16: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] iTraceBack = (int) uInsertPos - (int) uLengthB; ^~~~~~~~~~~~~~~~ Muscle/glbalignss.cpp:252:24: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] *ptrTraceBack_ij = (int) uInsertPos - (int) j; ^~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/glbalndimer.cpp -o Muscle/glbalndimer.o Muscle/glbalndimer.cpp: In function 'SCORE ScoreProfPosDimer(const ProfPos&, const ProfPos&)': Muscle/glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch] switch (g_PPScore) ^ Muscle/glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_SPN' not handled in switch [-Wswitch] Muscle/glbalndimer.cpp: At global scope: Muscle/glbalndimer.cpp:14:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/globalsosx.cpp -o Muscle/globalsosx.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/globalswin32.cpp -o Muscle/globalswin32.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/gotowt.cpp -o Muscle/gotowt.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:18:17: warning: unused variable 'uSeqLength' [-Wunused-variable] 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:94:17: warning: unused variable 'Path' [-Wunused-variable] const PWPath &Path = Nodes[uNodeIndex].m_Path; ^~~~ Muscle/makerootmsa.cpp: In function 'void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)': Muscle/makerootmsa.cpp:168:17: warning: unused variable 'uTreeNodeCount' [-Wunused-variable] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static void FmtPad(unsigned n) ^~~~~~ Muscle/msa.cpp:407:13: warning: 'void FmtInt0(unsigned int, unsigned int)' defined but not used [-Wunused-function] 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] static void FmtInt(unsigned u, unsigned uWidth) ^~~~~~ Muscle/msa.cpp:385:13: warning: 'void FmtChar(char, unsigned int)' defined but not used [-Wunused-function] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 SetMSAWeightsMuscle(MSA&)': Muscle/msa2.cpp:357:9: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch] switch (Method) ^ Muscle/msa2.cpp: In function 'void MSAAppend(MSA&, const MSA&)': Muscle/msa2.cpp:476:17: warning: unused variable 'uColCountCat' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/nwrec.cpp -o Muscle/nwrec.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] #pragma warning(disable:4035) Muscle/objscore.cpp: In function 'SCORE ObjScore(const MSA&, const unsigned int*, unsigned int, const unsigned int*, unsigned int)': Muscle/objscore.cpp:31:9: warning: enumeration value 'OBJSCORE_Undefined' not handled in switch [-Wswitch] switch (OS) ^ Muscle/objscore.cpp:31:9: warning: enumeration value 'OBJSCORE_SPM' not handled in switch [-Wswitch] In file included from Muscle/objscore.cpp:5: Muscle/timing.h: At global scope: Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 TermGapScore(bool)': Muscle/objscore2.cpp:22:9: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch] switch (g_TermGaps) ^ Muscle/objscore2.cpp: In function 'SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)': Muscle/objscore2.cpp:62:8: warning: unused variable 'scoreGaps' [-Wunused-variable] SCORE scoreGaps = 0; ^~~~~~~~~ Muscle/objscore2.cpp:63:7: warning: unused variable 'bGapping1' [-Wunused-variable] bool bGapping1 = false; ^~~~~~~~~ Muscle/objscore2.cpp:64:7: warning: unused variable 'bGapping2' [-Wunused-variable] bool bGapping2 = false; ^~~~~~~~~ Muscle/objscore2.cpp:67:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable] bool bLeftTermGap = false; ^~~~~~~~~~~~ Muscle/objscore2.cpp:82:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable] bool bRightTermGap = false; ^~~~~~~~~~~~~ Muscle/objscore2.cpp: In function 'SCORE ScoreSeqPairGaps(const MSA&, unsigned int, const MSA&, unsigned int)': Muscle/objscore2.cpp:140:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable] bool bLeftTermGap = false; ^~~~~~~~~~~~ Muscle/objscore2.cpp:155:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable] bool bRightTermGap = false; ^~~~~~~~~~~~~ Muscle/objscore2.cpp: In function 'SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)': Muscle/objscore2.cpp:314:17: warning: unused variable 'uColCount2' [-Wunused-variable] const unsigned uColCount2 = msa2.GetColCount(); ^~~~~~~~~~ Muscle/objscore2.cpp: In function 'SCORE ObjScoreXP(const MSA&, const MSA&)': Muscle/objscore2.cpp:493:17: warning: unused variable 'w' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/params.cpp -o Muscle/params.o Muscle/params.cpp: In function 'void SetPPScore(bool)': Muscle/params.cpp:441:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch] switch (g_PPScore) ^ In file included from Muscle/muscle.h:37, from Muscle/params.cpp:1: Muscle/intmath.h: At global scope: Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:665:9: warning: unused variable 'dEdgeLength' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:125:15: warning: unused variable 'dThisDist' [-Wunused-variable] 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:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable] const unsigned uLeafCount = tree.GetLeafCount(); ^~~~~~~~~~ Muscle/phy3.cpp:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable] double dAllMaxDist = -1e20; ^~~~~~~~~~~ Muscle/phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable] unsigned uMaxFrom = NULL_NEIGHBOR; ^~~~~~~~ Muscle/phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable] unsigned uMaxTo = NULL_NEIGHBOR; ^~~~~~ Muscle/phy3.cpp: In function 'void RootByMidLongestSpan(const Tree&, EdgeInfo**, unsigned int*, unsigned int*, double*, double*)': Muscle/phy3.cpp:263:11: warning: variable 'uMostDistantLeaf' set but not used [-Wunused-but-set-variable] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:60:13: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] if (Col == ColCount) ~~~~^~~~~~~~~~~ Muscle/physeq.cpp:71:12: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] if (Col == ColCount) ~~~~^~~~~~~~~~~ Muscle/physeq.cpp: In member function 'void MSA::ToPhyInterleavedFile(TextFile&) const': Muscle/physeq.cpp:112:13: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] if (Col == ColCount) ~~~~^~~~~~~~~~~ Muscle/physeq.cpp:124:11: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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/clustsetmsa.h:8, from Muscle/profdb.cpp:9: Muscle/msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch] switch(m_Distance) ^ Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch] In file included from Muscle/muscle.h:37, from Muscle/profdb.cpp:1: Muscle/intmath.h: At global scope: Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:131:10: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] if (-1 == PP.m_uResidueGroup) ~~~^~~~~~~~~~~~~~~~~~~~~ Muscle/profilefrommsa.cpp: In function 'unsigned int ResidueGroupFromFCounts(const FCOUNT*)': Muscle/profilefrommsa.cpp:230:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] switch (g_Alpha) ^ Muscle/profilefrommsa.cpp: In function 'ProfPos* ProfileFromMSA(const MSA&)': Muscle/profilefrommsa.cpp:245:17: warning: unused variable 'uSeqCount' [-Wunused-variable] const unsigned uSeqCount = a.GetSeqCount(); ^~~~~~~~~ Muscle/profilefrommsa.cpp:253:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:41:17: warning: unused variable 'uIterCount' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:80:16: warning: unused variable 'LastEdge' [-Wunused-variable] const PWEdge &LastEdge = GetEdge(uEdgeCount - 1); ^~~~~~~~ Muscle/pwpath.cpp: In member function 'void PWPath::FromFile(TextFile&)': Muscle/pwpath.cpp:213:11: warning: unused variable 'uEdgeIndex' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:83:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int i = 0; i < MAX_ALPHA; ++i) ~~^~~~~~~~~~~ Muscle/readmx.cpp:84:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int j = 0; j < MAX_ALPHA; ++j) ~~^~~~~~~~~~~ Muscle/readmx.cpp: In function 'float (* ReadMxFromR(std::vector >, float (*)[32]))[32][32]': Muscle/readmx.cpp:184:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int i = 0; i < MAX_ALPHA; ++i) ~~^~~~~~~~~~~ Muscle/readmx.cpp:185:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:77:13: warning: unused variable 'uNewRight' [-Wunused-variable] unsigned uNewRight = NewTree.GetRight(uNewNodeIndex); ^~~~~~~~~ Muscle/realigndiffse.cpp:80:13: warning: unused variable 'uOldRight' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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/clustsetmsa.h:8, from Muscle/refine.cpp:9: Muscle/msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch] switch(m_Distance) ^ Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch] In file included from Muscle/muscle.h:37, from Muscle/refine.cpp:1: Muscle/intmath.h: At global scope: Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/refinehoriz.cpp: In function 'bool RefineHoriz(MSA&, const Tree&, unsigned int, bool, bool)': Muscle/refinehoriz.cpp:187:44: warning: 'scoreAfter' may be used uninitialized in this function [-Wmaybe-uninitialized] SCORE scoreMax = scoreAfter > scoreBefore? scoreAfter : scoreBefore; ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ Muscle/refinehoriz.cpp:174:9: note: 'scoreAfter' was declared here SCORE scoreAfter; ^~~~~~~~~~ Muscle/refinehoriz.cpp:187:44: warning: 'scoreBefore' may be used uninitialized in this function [-Wmaybe-uninitialized] SCORE scoreMax = scoreAfter > scoreBefore? scoreAfter : scoreBefore; ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ Muscle/refinehoriz.cpp:173:9: note: 'scoreBefore' was declared here SCORE scoreBefore; ^~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:63:17: warning: unused variable 'uNodeCount' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:22:17: warning: unused variable 'uColCountCat' [-Wunused-variable] const unsigned uColCountCat = uColCount1 + uColCount2; ^~~~~~~~~~~~ Muscle/refinew.cpp: In function 'void RefineW(const MSA&, MSA&)': Muscle/refinew.cpp:125:13: warning: unused variable 'uOutCols' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static SCORE Penalty(unsigned Length, bool Term) ^~~~~~~ Muscle/scoregaps.cpp:37:13: warning: 'void FreeGapInfo(GAPINFO*)' defined but not used [-Wunused-function] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:252:17: warning: unused variable 'uSeqCount' [-Wunused-variable] 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] static SCORE SPColBrute(const MSA &msa, unsigned uColIndex) ^~~~~~~~~~ Muscle/spfast.cpp:14:20: warning: 'const char* GapTypeToStr(int)' defined but not used [-Wunused-function] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:173:6: warning: unused variable 'NotUsed' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:111:6: warning: unused variable 'i' [-Wunused-variable] int i = fputc(c, m_ptrFile); ^ Muscle/textfile.cpp: In member function 'void TextFile::PutString(const char*)': Muscle/textfile.cpp:124:6: warning: unused variable 'iError' [-Wunused-variable] int iError = fputs(szLine, m_ptrFile); ^~~~~~ Muscle/textfile.cpp: In member function 'TEXTFILEPOS TextFile::GetPos()': Muscle/textfile.cpp:224:6: warning: unused variable 'i' [-Wunused-variable] int i = fgetpos(m_ptrFile, &p); ^ Muscle/textfile.cpp: In member function 'void TextFile::SetPos(TEXTFILEPOS)': Muscle/textfile.cpp:237:6: warning: unused variable 'i' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:21:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ 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:72:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wmaybe-uninitialized] switch (cEdgeType) ^~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:22:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] const unsigned uPrefixCountB = uLengthB + 1; ^~~~~~~~~~~~~ Muscle/tracebacksw.cpp:29:8: warning: unused variable 'scoreMax' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ 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:47:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wmaybe-uninitialized] switch (cEdgeType) ^~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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/clustsetmsa.h:8, from Muscle/treefrommsa.cpp:5: Muscle/msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch] switch(m_Distance) ^ Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch] In file included from Muscle/muscle.h:37, from Muscle/treefrommsa.cpp:1: Muscle/intmath.h: At global scope: Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/upgma2.cpp: In function 'void UPGMA2(const DistCalc&, Tree&, LINKAGE)': Muscle/upgma2.cpp:292:15: warning: 'dtNewDist' may be used uninitialized in this function [-Wmaybe-uninitialized] g_Dist[vL] = dtNewDist; ~~~~~~~~~~~^~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/writescorefile.cpp: In function 'void WriteScoreFile(const MSA&)': Muscle/writescorefile.cpp:40:9: warning: 'Score' may be used uninitialized in this function [-Wmaybe-uninitialized] dSum += Score; ~~~~~^~~~~~~~ Muscle/writescorefile.cpp:27:11: note: 'Score' was declared here double Score; ^~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RClustalW.cpp -o RClustalW.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RClustalWMain.cpp -o RClustalWMain.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ C:/rtools40/mingw32/bin/g++ -std=gnu++11 -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 -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -lpthread -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/enhancerHomologSearch.buildbin-libdir/00LOCK-enhancerHomologSearch/00new/enhancerHomologSearch/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'enhancerHomologSearch' finding HTML links ... done Enhancers-class html alignment html alignmentOne html conservedMotifs html getENCODEdata html motifs html queryEncode html saveAlignments html searchTFBPS html ** 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 install for x64 * installing *source* package 'enhancerHomologSearch' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] SeqArray::iterator posToAddTo = sectionToRealign.begin(); ^~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/alignment/AlignmentOutput.cpp -o ClustalW/alignment/AlignmentOutput.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/alignment/ObjectiveScore.cpp -o ClustalW/alignment/ObjectiveScore.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/alignment/Sequence.cpp -o ClustalW/alignment/Sequence.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/Clustal.cpp -o ClustalW/Clustal.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/ClustalFileParser.cpp -o ClustalW/fileInput/ClustalFileParser.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/EMBLFileParser.cpp -o ClustalW/fileInput/EMBLFileParser.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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::FileParser::getSeqRangeR(int, int, std::__cxx11::string*, ClustalWInput*)': ClustalW/fileInput/FileParser.cpp:38:7: warning: unused variable 'n' [-Wunused-variable] int n = (*input).inputSeqs.size(); ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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::__cxx11::string*, ClustalWInput*)': ClustalW/fileInput/FileReader.cpp:421:10: warning: variable 'maxAlnLength' set but not used [-Wunused-but-set-variable] int maxAlnLength; // Get values from the Alignment object. ^~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/GDEFileParser.cpp -o ClustalW/fileInput/GDEFileParser.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/InFileStream.cpp -o ClustalW/fileInput/InFileStream.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/MSFFileParser.cpp -o ClustalW/fileInput/MSFFileParser.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/PearsonFileParser.cpp -o ClustalW/fileInput/PearsonFileParser.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/PIRFileParser.cpp -o ClustalW/fileInput/PIRFileParser.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/RSFFileParser.cpp -o ClustalW/fileInput/RSFFileParser.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/ClustalWResources.cpp -o ClustalW/general/ClustalWResources.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/DebugLog.cpp -o ClustalW/general/DebugLog.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/InvalidCombination.cpp -o ClustalW/general/InvalidCombination.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/OutputFile.cpp -o ClustalW/general/OutputFile.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/Stats.cpp -o ClustalW/general/Stats.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/SymMatrix.cpp -o ClustalW/general/SymMatrix.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/UserParameters.cpp -o ClustalW/general/UserParameters.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] int n; ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/VectorOutOfRange.cpp -o ClustalW/general/VectorOutOfRange.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/Help.cpp -o ClustalW/Help.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/interface/CommandLineParser.cpp -o ClustalW/interface/CommandLineParser.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] int count; ^~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/multipleAlign/LowScoreSegProfile.cpp -o ClustalW/multipleAlign/LowScoreSegProfile.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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*, clustalw::AlignmentSteps*, int)': ClustalW/multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable] int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18 ^~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/multipleAlign/MyersMillerProfileAlign.cpp -o ClustalW/multipleAlign/MyersMillerProfileAlign.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/multipleAlign/ProfileBase.cpp -o ClustalW/multipleAlign/ProfileBase.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/multipleAlign/ProfileStandard.cpp -o ClustalW/multipleAlign/ProfileStandard.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/multipleAlign/ProfileWithSub.cpp -o ClustalW/multipleAlign/ProfileWithSub.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/pairwise/FastPairwiseAlign.cpp -o ClustalW/pairwise/FastPairwiseAlign.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/pairwise/FullPairwiseAlign.cpp -o ClustalW/pairwise/FullPairwiseAlign.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] char inline1[1024]; ^~~~~~~ ClustalW/substitutionMatrix/SubMatrix.cpp:1307:9: warning: unused variable 'nmat' [-Wunused-variable] int nmat; ^~~~ ClustalW/substitutionMatrix/SubMatrix.cpp:1308:9: warning: unused variable 'n' [-Wunused-variable] int n, llimit, ulimit; ^ ClustalW/substitutionMatrix/SubMatrix.cpp:1308:12: warning: unused variable 'llimit' [-Wunused-variable] int n, llimit, ulimit; ^~~~~~ ClustalW/substitutionMatrix/SubMatrix.cpp:1308:20: warning: unused variable 'ulimit' [-Wunused-variable] 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:1361:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 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] 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] 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 in this function [-Wmaybe-uninitialized] return (maxRes); ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/AlignmentSteps.cpp -o ClustalW/tree/AlignmentSteps.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] int rs = 0, rl = 0; ^~ ClustalW/tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable] 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] unsigned int tempSeed; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/ClusterTreeOutput.cpp -o ClustalW/tree/ClusterTreeOutput.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/NJTree.cpp -o ClustalW/tree/NJTree.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/RandomGenerator.cpp -o ClustalW/tree/RandomGenerator.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/Tree.cpp -o ClustalW/tree/Tree.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/TreeInterface.cpp -o ClustalW/tree/TreeInterface.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/UnRootedClusterTree.cpp -o ClustalW/tree/UnRootedClusterTree.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:186:17: warning: unused variable 'uLengthA' [-Wunused-variable] const unsigned uLengthA = msaA.GetColCount(); ^~~~~~~~ Muscle/aligngivenpath.cpp:187:17: warning: unused variable 'uLengthB' [-Wunused-variable] const unsigned uLengthB = msaB.GetColCount(); ^~~~~~~~ Muscle/aligngivenpath.cpp: In function 'void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)': Muscle/aligngivenpath.cpp:335:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^~~~~ Muscle/aligngivenpath.cpp:336:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^~~~~ Muscle/aligngivenpath.cpp:346:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^~~~~ Muscle/aligngivenpath.cpp:354:19: warning: unused variable 'uColB' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:58:17: warning: unused variable 'uLengthA' [-Wunused-variable] const unsigned uLengthA = msaA.GetColCount(); ^~~~~~~~ Muscle/aligngivenpathsw.cpp:59:17: warning: unused variable 'uLengthB' [-Wunused-variable] const unsigned uLengthB = msaB.GetColCount(); ^~~~~~~~ Muscle/aligngivenpathsw.cpp: In function 'void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)': Muscle/aligngivenpathsw.cpp:204:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^~~~~ Muscle/aligngivenpathsw.cpp:205:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^~~~~ Muscle/aligngivenpathsw.cpp:215:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^~~~~ Muscle/aligngivenpathsw.cpp:223:19: warning: unused variable 'uColB' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] #pragma warning(disable:4035) Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/alpha.cpp -o Muscle/alpha.o Muscle/alpha.cpp: In function 'unsigned int GetAlphaSize(ALPHA)': Muscle/alpha.cpp:84:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] switch (Alpha) ^ In file included from Muscle/muscle.h:37, from Muscle/alpha.cpp:1: Muscle/intmath.h: At global scope: Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:162:13: warning: unused variable 'uWindowCenter' [-Wunused-variable] 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] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:146:7: warning: unused variable 'Bits' [-Wunused-variable] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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::ChooseJoin(unsigned int*, unsigned int*, float*, float*)': Muscle/clust.cpp:167:9: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] switch (m_JoinStyle) ^ Muscle/clust.cpp: In member function 'void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)': Muscle/clust.cpp:184:17: warning: unused variable 'uClusterCount' [-Wunused-variable] const unsigned uClusterCount = GetClusterCount(); ^~~~~~~~~~~~~ Muscle/clust.cpp: In member function 'void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)': Muscle/clust.cpp:204:17: warning: unused variable 'uClusterCount' [-Wunused-variable] const unsigned uClusterCount = GetClusterCount(); ^~~~~~~~~~~~~ Muscle/clust.cpp: In member function 'float Clust::ComputeDist(unsigned int, unsigned int)': Muscle/clust.cpp:295:9: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch] switch (m_CentroidStyle) ^ Muscle/clust.cpp: In member function 'float Clust::ComputeDistMAFFT(unsigned int, unsigned int)': Muscle/clust.cpp:360:14: warning: unused variable 'dDistLR' [-Wunused-variable] const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex); ^~~~~~~ Muscle/clust.cpp: In member function 'float Clust::ComputeMetric(unsigned int, unsigned int) const': Muscle/clust.cpp:611:9: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] switch (m_JoinStyle) ^ 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:284:8: warning: variable 'bFound' set but not used [-Wunused-but-set-variable] bool bFound = false; ^~~~~~ Muscle/cluster.cpp:267:9: warning: unused variable 'dMaxDist' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/cluster.cpp: In member function 'void ClusterTree::Create(const DistFunc&)': Muscle/cluster.cpp:308:47: warning: 'uIndexClosest2' may be used uninitialized in this function [-Wmaybe-uninitialized] ClusterNode &Child2 = m_Nodes[uIndexClosest2]; ^ Muscle/cluster.cpp:307:47: warning: 'uIndexClosest1' may be used uninitialized in this function [-Wmaybe-uninitialized] ClusterNode &Child1 = m_Nodes[uIndexClosest1]; ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/diaglist.cpp: In member function 'void DiagList::FromPath(const PWPath&)': Muscle/diaglist.cpp:12:20: warning: 'uStartPosB' may be used uninitialized in this function [-Wmaybe-uninitialized] m_Diags[m_uCount] = d; ~~~~~~~~~~~~~~~~~~^~~ Muscle/diaglist.cpp:52:11: note: 'uStartPosB' was declared here unsigned uStartPosB; ^~~~~~~~~~ Muscle/diaglist.cpp:12:20: warning: 'uStartPosA' may be used uninitialized in this function [-Wmaybe-uninitialized] m_Diags[m_uCount] = d; ~~~~~~~~~~~~~~~~~~^~~ Muscle/diaglist.cpp:51:11: note: 'uStartPosA' was declared here unsigned uStartPosA; ^~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable] const unsigned uSeqCount = msa.GetSeqCount(); ^~~~~~~~~ Muscle/diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:161:17: warning: unused variable 'uLeafCount2' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] #pragma warning(disable:4035) Muscle/domuscle.cpp: In function 'void DoMuscle(MuscleInput*, MuscleOutput*)': Muscle/domuscle.cpp:169:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (g_bClusterOnly) ^~ Muscle/domuscle.cpp:172:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' return; ^~~~~~ Muscle/domuscle.cpp:180:6: warning: unused variable 'PNlength' [-Wunused-variable] int PNlength = (msaInput->inputSeqs).Length(); ^~~~~~~~ In file included from Muscle/domuscle.cpp:9: Muscle/timing.h: At global scope: Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:82:19: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/estring.cpp: In function 'void EstringsToPath(const short int*, const short int*, PWPath&)': Muscle/estring.cpp:424:14: warning: 'cType' may be used uninitialized in this function [-Wmaybe-uninitialized] Edge.cType = cType; ~~~~~~~~~~~^~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:15:11: warning: unused variable 'uSeqCount' [-Wunused-variable] unsigned uSeqCount = 0; ^~~~~~~~~ Muscle/fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:235:11: warning: unused variable 'KD' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:239:15: warning: unused variable 'pName1' [-Wunused-variable] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:223:15: warning: unused variable 'pName1' [-Wunused-variable] 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] static void ListCount(const unsigned char Count[]) ^~~~~~~~~ Muscle/fastdistnuc.cpp:33:17: warning: 'uResidueGroupCount' defined but not used [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:16:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] #pragma warning(disable:4035) Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] #pragma warning(disable:4035) Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] #pragma warning(disable:4035) Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/glbalignla.cpp: In function 'SCORE GlobalAlignLA(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': Muscle/glbalignla.cpp:427:16: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] iTraceBack = (int) uInsertPos - (int) uLengthB; ^~~~~~~~~~~~~~~~ Muscle/glbalignla.cpp:366:24: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] *ptrTraceBack_ij = (int) uInsertPos - (int) j; ^~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/glbalignle.cpp: In function 'SCORE GlobalAlignLE(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': Muscle/glbalignle.cpp:431:16: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] iTraceBack = (int) uInsertPos - (int) uLengthB; ^~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/glbalignns.cpp: In function 'SCORE GlobalAlignNS(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': Muscle/glbalignns.cpp:366:16: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] iTraceBack = (int) uInsertPos - (int) uLengthB; ^~~~~~~~~~~~~~~~ Muscle/glbalignns.cpp:305:24: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] *ptrTraceBack_ij = (int) uInsertPos - (int) j; ^~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/glbalignsp.cpp: In function 'SCORE GlobalAlignSP(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': Muscle/glbalignsp.cpp:366:16: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] iTraceBack = (int) uInsertPos - (int) uLengthB; ^~~~~~~~~~~~~~~~ Muscle/glbalignsp.cpp:305:24: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] *ptrTraceBack_ij = (int) uInsertPos - (int) j; ^~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/glbalignspn.cpp: In function 'SCORE GlobalAlignSPN(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': Muscle/glbalignspn.cpp:401:16: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] iTraceBack = (int) uInsertPos - (int) uLengthB; ^~~~~~~~~~~~~~~~ Muscle/glbalignspn.cpp:340:24: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] *ptrTraceBack_ij = (int) uInsertPos - (int) j; ^~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:177:16: warning: unused variable 'ptrRowA' [-Wunused-variable] const SCORE *ptrRowA = MxRowA[i]; ^~~~~~~ Muscle/glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable] const unsigned uPrefixCountA = uLengthA + 1; ^~~~~~~~~~~~~ Muscle/glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/glbalignss.cpp: In function 'SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)': Muscle/glbalignss.cpp:310:16: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] iTraceBack = (int) uInsertPos - (int) uLengthB; ^~~~~~~~~~~~~~~~ Muscle/glbalignss.cpp:252:24: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] *ptrTraceBack_ij = (int) uInsertPos - (int) j; ^~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/glbalndimer.cpp -o Muscle/glbalndimer.o Muscle/glbalndimer.cpp: In function 'SCORE ScoreProfPosDimer(const ProfPos&, const ProfPos&)': Muscle/glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch] switch (g_PPScore) ^ Muscle/glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_SPN' not handled in switch [-Wswitch] Muscle/glbalndimer.cpp: At global scope: Muscle/glbalndimer.cpp:14:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/globalsosx.cpp -o Muscle/globalsosx.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/globalswin32.cpp -o Muscle/globalswin32.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/gotowt.cpp -o Muscle/gotowt.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:18:17: warning: unused variable 'uSeqLength' [-Wunused-variable] 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:94:17: warning: unused variable 'Path' [-Wunused-variable] const PWPath &Path = Nodes[uNodeIndex].m_Path; ^~~~ Muscle/makerootmsa.cpp: In function 'void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)': Muscle/makerootmsa.cpp:168:17: warning: unused variable 'uTreeNodeCount' [-Wunused-variable] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static void FmtPad(unsigned n) ^~~~~~ Muscle/msa.cpp:407:13: warning: 'void FmtInt0(unsigned int, unsigned int)' defined but not used [-Wunused-function] 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] static void FmtInt(unsigned u, unsigned uWidth) ^~~~~~ Muscle/msa.cpp:385:13: warning: 'void FmtChar(char, unsigned int)' defined but not used [-Wunused-function] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 SetMSAWeightsMuscle(MSA&)': Muscle/msa2.cpp:357:9: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch] switch (Method) ^ Muscle/msa2.cpp: In function 'void MSAAppend(MSA&, const MSA&)': Muscle/msa2.cpp:476:17: warning: unused variable 'uColCountCat' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/nwrec.cpp -o Muscle/nwrec.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] #pragma warning(disable:4035) Muscle/objscore.cpp: In function 'SCORE ObjScore(const MSA&, const unsigned int*, unsigned int, const unsigned int*, unsigned int)': Muscle/objscore.cpp:31:9: warning: enumeration value 'OBJSCORE_Undefined' not handled in switch [-Wswitch] switch (OS) ^ Muscle/objscore.cpp:31:9: warning: enumeration value 'OBJSCORE_SPM' not handled in switch [-Wswitch] In file included from Muscle/objscore.cpp:5: Muscle/timing.h: At global scope: Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 TermGapScore(bool)': Muscle/objscore2.cpp:22:9: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch] switch (g_TermGaps) ^ Muscle/objscore2.cpp: In function 'SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)': Muscle/objscore2.cpp:62:8: warning: unused variable 'scoreGaps' [-Wunused-variable] SCORE scoreGaps = 0; ^~~~~~~~~ Muscle/objscore2.cpp:63:7: warning: unused variable 'bGapping1' [-Wunused-variable] bool bGapping1 = false; ^~~~~~~~~ Muscle/objscore2.cpp:64:7: warning: unused variable 'bGapping2' [-Wunused-variable] bool bGapping2 = false; ^~~~~~~~~ Muscle/objscore2.cpp:67:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable] bool bLeftTermGap = false; ^~~~~~~~~~~~ Muscle/objscore2.cpp:82:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable] bool bRightTermGap = false; ^~~~~~~~~~~~~ Muscle/objscore2.cpp: In function 'SCORE ScoreSeqPairGaps(const MSA&, unsigned int, const MSA&, unsigned int)': Muscle/objscore2.cpp:140:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable] bool bLeftTermGap = false; ^~~~~~~~~~~~ Muscle/objscore2.cpp:155:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable] bool bRightTermGap = false; ^~~~~~~~~~~~~ Muscle/objscore2.cpp: In function 'SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)': Muscle/objscore2.cpp:314:17: warning: unused variable 'uColCount2' [-Wunused-variable] const unsigned uColCount2 = msa2.GetColCount(); ^~~~~~~~~~ Muscle/objscore2.cpp: In function 'SCORE ObjScoreXP(const MSA&, const MSA&)': Muscle/objscore2.cpp:493:17: warning: unused variable 'w' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/params.cpp -o Muscle/params.o Muscle/params.cpp: In function 'void SetPPScore(bool)': Muscle/params.cpp:441:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch] switch (g_PPScore) ^ In file included from Muscle/muscle.h:37, from Muscle/params.cpp:1: Muscle/intmath.h: At global scope: Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:665:9: warning: unused variable 'dEdgeLength' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:125:15: warning: unused variable 'dThisDist' [-Wunused-variable] 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:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable] const unsigned uLeafCount = tree.GetLeafCount(); ^~~~~~~~~~ Muscle/phy3.cpp:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable] double dAllMaxDist = -1e20; ^~~~~~~~~~~ Muscle/phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable] unsigned uMaxFrom = NULL_NEIGHBOR; ^~~~~~~~ Muscle/phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable] unsigned uMaxTo = NULL_NEIGHBOR; ^~~~~~ Muscle/phy3.cpp: In function 'void RootByMidLongestSpan(const Tree&, EdgeInfo**, unsigned int*, unsigned int*, double*, double*)': Muscle/phy3.cpp:263:11: warning: variable 'uMostDistantLeaf' set but not used [-Wunused-but-set-variable] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:60:13: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] if (Col == ColCount) ~~~~^~~~~~~~~~~ Muscle/physeq.cpp:71:12: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] if (Col == ColCount) ~~~~^~~~~~~~~~~ Muscle/physeq.cpp: In member function 'void MSA::ToPhyInterleavedFile(TextFile&) const': Muscle/physeq.cpp:112:13: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] if (Col == ColCount) ~~~~^~~~~~~~~~~ Muscle/physeq.cpp:124:11: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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/clustsetmsa.h:8, from Muscle/profdb.cpp:9: Muscle/msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch] switch(m_Distance) ^ Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch] In file included from Muscle/muscle.h:37, from Muscle/profdb.cpp:1: Muscle/intmath.h: At global scope: Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:131:10: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] if (-1 == PP.m_uResidueGroup) ~~~^~~~~~~~~~~~~~~~~~~~~ Muscle/profilefrommsa.cpp: In function 'unsigned int ResidueGroupFromFCounts(const FCOUNT*)': Muscle/profilefrommsa.cpp:230:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] switch (g_Alpha) ^ Muscle/profilefrommsa.cpp: In function 'ProfPos* ProfileFromMSA(const MSA&)': Muscle/profilefrommsa.cpp:245:17: warning: unused variable 'uSeqCount' [-Wunused-variable] const unsigned uSeqCount = a.GetSeqCount(); ^~~~~~~~~ Muscle/profilefrommsa.cpp:253:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:41:17: warning: unused variable 'uIterCount' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:80:16: warning: unused variable 'LastEdge' [-Wunused-variable] const PWEdge &LastEdge = GetEdge(uEdgeCount - 1); ^~~~~~~~ Muscle/pwpath.cpp: In member function 'void PWPath::FromFile(TextFile&)': Muscle/pwpath.cpp:213:11: warning: unused variable 'uEdgeIndex' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:83:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int i = 0; i < MAX_ALPHA; ++i) ~~^~~~~~~~~~~ Muscle/readmx.cpp:84:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int j = 0; j < MAX_ALPHA; ++j) ~~^~~~~~~~~~~ Muscle/readmx.cpp: In function 'float (* ReadMxFromR(std::vector >, float (*)[32]))[32][32]': Muscle/readmx.cpp:184:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int i = 0; i < MAX_ALPHA; ++i) ~~^~~~~~~~~~~ Muscle/readmx.cpp:185:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:77:13: warning: unused variable 'uNewRight' [-Wunused-variable] unsigned uNewRight = NewTree.GetRight(uNewNodeIndex); ^~~~~~~~~ Muscle/realigndiffse.cpp:80:13: warning: unused variable 'uOldRight' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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/clustsetmsa.h:8, from Muscle/refine.cpp:9: Muscle/msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch] switch(m_Distance) ^ Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch] In file included from Muscle/muscle.h:37, from Muscle/refine.cpp:1: Muscle/intmath.h: At global scope: Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:63:17: warning: unused variable 'uNodeCount' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:22:17: warning: unused variable 'uColCountCat' [-Wunused-variable] const unsigned uColCountCat = uColCount1 + uColCount2; ^~~~~~~~~~~~ Muscle/refinew.cpp: In function 'void RefineW(const MSA&, MSA&)': Muscle/refinew.cpp:125:13: warning: unused variable 'uOutCols' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static SCORE Penalty(unsigned Length, bool Term) ^~~~~~~ Muscle/scoregaps.cpp:37:13: warning: 'void FreeGapInfo(GAPINFO*)' defined but not used [-Wunused-function] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:252:17: warning: unused variable 'uSeqCount' [-Wunused-variable] 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] static SCORE SPColBrute(const MSA &msa, unsigned uColIndex) ^~~~~~~~~~ Muscle/spfast.cpp:14:20: warning: 'const char* GapTypeToStr(int)' defined but not used [-Wunused-function] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:173:6: warning: unused variable 'NotUsed' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] 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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:111:6: warning: unused variable 'i' [-Wunused-variable] int i = fputc(c, m_ptrFile); ^ Muscle/textfile.cpp: In member function 'void TextFile::PutString(const char*)': Muscle/textfile.cpp:124:6: warning: unused variable 'iError' [-Wunused-variable] int iError = fputs(szLine, m_ptrFile); ^~~~~~ Muscle/textfile.cpp: In member function 'TEXTFILEPOS TextFile::GetPos()': Muscle/textfile.cpp:224:6: warning: unused variable 'i' [-Wunused-variable] int i = fgetpos(m_ptrFile, &p); ^ Muscle/textfile.cpp: In member function 'void TextFile::SetPos(TEXTFILEPOS)': Muscle/textfile.cpp:237:6: warning: unused variable 'i' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:21:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ 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:72:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wmaybe-uninitialized] switch (cEdgeType) ^~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:22:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] const unsigned uPrefixCountB = uLengthB + 1; ^~~~~~~~~~~~~ Muscle/tracebacksw.cpp:29:8: warning: unused variable 'scoreMax' [-Wunused-variable] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ 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:47:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wmaybe-uninitialized] switch (cEdgeType) ^~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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/clustsetmsa.h:8, from Muscle/treefrommsa.cpp:5: Muscle/msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch] switch(m_Distance) ^ Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch] Muscle/msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch] In file included from Muscle/muscle.h:37, from Muscle/treefrommsa.cpp:1: Muscle/intmath.h: At global scope: Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] 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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/upgma2.cpp: In function 'void UPGMA2(const DistCalc&, Tree&, LINKAGE)': Muscle/upgma2.cpp:292:15: warning: 'dtNewDist' may be used uninitialized in this function [-Wmaybe-uninitialized] g_Dist[vL] = dtNewDist; ~~~~~~~~~~~^~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ Muscle/writescorefile.cpp: In function 'void WriteScoreFile(const MSA&)': Muscle/writescorefile.cpp:40:9: warning: 'Score' may be used uninitialized in this function [-Wmaybe-uninitialized] dSum += Score; ~~~~~^~~~~~~~ Muscle/writescorefile.cpp:27:11: note: 'Score' was declared here double Score; ^~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RClustalW.cpp -o RClustalW.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RClustalWMain.cpp -o RClustalWMain.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/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] static double ScoreToDouble(SCORE Score) ^~~~~~~~~~~~~ C:/rtools40/mingw64/bin/g++ -std=gnu++11 -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 -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -lpthread -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/enhancerHomologSearch.buildbin-libdir/enhancerHomologSearch/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'enhancerHomologSearch' as enhancerHomologSearch_1.0.1.zip * DONE (enhancerHomologSearch) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'enhancerHomologSearch' successfully unpacked and MD5 sums checked