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###
### Running command:
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### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL enhancerHomologSearch
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'enhancerHomologSearch' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/alignment/Alignment.cpp -o ClustalW/alignment/Alignment.o
ClustalW/alignment/Alignment.cpp: In member function 'bool clustalw::Alignment::keepPortionOfSeqArray(int, int)':
ClustalW/alignment/Alignment.cpp:1715:24: warning: variable 'posToAddTo' set but not used [-Wunused-but-set-variable]
1715 | SeqArray::iterator posToAddTo = sectionToRealign.begin();
| ^~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/alignment/AlignmentOutput.cpp -o ClustalW/alignment/AlignmentOutput.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/alignment/ObjectiveScore.cpp -o ClustalW/alignment/ObjectiveScore.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/alignment/Sequence.cpp -o ClustalW/alignment/Sequence.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/Clustal.cpp -o ClustalW/Clustal.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/ClustalFileParser.cpp -o ClustalW/fileInput/ClustalFileParser.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/EMBLFileParser.cpp -o ClustalW/fileInput/EMBLFileParser.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/FileParser.cpp -o ClustalW/fileInput/FileParser.o
ClustalW/fileInput/FileParser.cpp: In member function 'std::vector<clustalw::Sequence> clustalw::FileParser::getSeqRangeR(int, int, std::string*, ClustalWInput*)':
ClustalW/fileInput/FileParser.cpp:38:21: warning: unused variable 'n' [-Wunused-variable]
38 | int n = (*input).inputSeqs.size();
| ^
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/FileReader.cpp -o ClustalW/fileInput/FileReader.o
ClustalW/fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readCharacterSeqs(clustalw::Alignment*, int, std::string*, ClustalWInput*)':
ClustalW/fileInput/FileReader.cpp:421:17: warning: variable 'maxAlnLength' set but not used [-Wunused-but-set-variable]
421 | int maxAlnLength; // Get values from the Alignment object.
| ^~~~~~~~~~~~
ClustalW/fileInput/FileReader.cpp:357:54: warning: 'this' pointer is null [-Wnonnull]
357 | seqRangeVector = fileParser->getSeqRangeR(1, noSeqs, offendingSeq, input);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ClustalW/fileInput/FileReader.h:16,
from ClustalW/fileInput/FileReader.cpp:29:
ClustalW/fileInput/FileParser.h:44:26: note: in a call to non-static member function 'std::vector<clustalw::Sequence> clustalw::FileParser::getSeqRangeR(int, int, std::string*, ClustalWInput*)'
44 | vector<Sequence> getSeqRangeR(int firstSeq, int num, string *offendingSeq, ClustalWInput *input);
| ^~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/GDEFileParser.cpp -o ClustalW/fileInput/GDEFileParser.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/InFileStream.cpp -o ClustalW/fileInput/InFileStream.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/MSFFileParser.cpp -o ClustalW/fileInput/MSFFileParser.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/PearsonFileParser.cpp -o ClustalW/fileInput/PearsonFileParser.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/PIRFileParser.cpp -o ClustalW/fileInput/PIRFileParser.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/fileInput/RSFFileParser.cpp -o ClustalW/fileInput/RSFFileParser.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/ClustalWResources.cpp -o ClustalW/general/ClustalWResources.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/DebugLog.cpp -o ClustalW/general/DebugLog.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/InvalidCombination.cpp -o ClustalW/general/InvalidCombination.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/OutputFile.cpp -o ClustalW/general/OutputFile.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/Stats.cpp -o ClustalW/general/Stats.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/SymMatrix.cpp -o ClustalW/general/SymMatrix.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/UserParameters.cpp -o ClustalW/general/UserParameters.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/Utility.cpp -o ClustalW/general/Utility.o
ClustalW/general/Utility.cpp: In member function 'bool clustalw::Utility::lineType(char*, const char*)':
ClustalW/general/Utility.cpp:251:8: warning: variable 'n' set but not used [-Wunused-but-set-variable]
251 | int n;
| ^
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/general/VectorOutOfRange.cpp -o ClustalW/general/VectorOutOfRange.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/Help.cpp -o ClustalW/Help.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/interface/CommandLineParser.cpp -o ClustalW/interface/CommandLineParser.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/multipleAlign/Iteration.cpp -o ClustalW/multipleAlign/Iteration.o
ClustalW/multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)':
ClustalW/multipleAlign/Iteration.cpp:171:9: warning: variable 'count' set but not used [-Wunused-but-set-variable]
171 | int count;
| ^~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/multipleAlign/LowScoreSegProfile.cpp -o ClustalW/multipleAlign/LowScoreSegProfile.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/multipleAlign/MSA.cpp -o ClustalW/multipleAlign/MSA.o
ClustalW/multipleAlign/MSA.cpp: In member function 'int clustalw::MSA::multiSeqAlign(clustalw::Alignment*, clustalw::DistMatrix*, std::vector<int>*, clustalw::AlignmentSteps*, int)':
ClustalW/multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable]
340 | int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18
| ^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/multipleAlign/MyersMillerProfileAlign.cpp -o ClustalW/multipleAlign/MyersMillerProfileAlign.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/multipleAlign/ProfileBase.cpp -o ClustalW/multipleAlign/ProfileBase.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/multipleAlign/ProfileStandard.cpp -o ClustalW/multipleAlign/ProfileStandard.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/multipleAlign/ProfileWithSub.cpp -o ClustalW/multipleAlign/ProfileWithSub.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/pairwise/FastPairwiseAlign.cpp -o ClustalW/pairwise/FastPairwiseAlign.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/pairwise/FullPairwiseAlign.cpp -o ClustalW/pairwise/FullPairwiseAlign.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/substitutionMatrix/SubMatrix.cpp -o ClustalW/substitutionMatrix/SubMatrix.o
ClustalW/substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeriesFromR(Rcpp::NumericMatrix, clustalw::Matrix&, clustalw::Xref&)':
ClustalW/substitutionMatrix/SubMatrix.cpp:1305:10: warning: unused variable 'inline1' [-Wunused-variable]
1305 | char inline1[1024];
| ^~~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp:1307:9: warning: unused variable 'nmat' [-Wunused-variable]
1307 | int nmat;
| ^~~~
ClustalW/substitutionMatrix/SubMatrix.cpp:1308:9: warning: unused variable 'n' [-Wunused-variable]
1308 | int n, llimit, ulimit;
| ^
ClustalW/substitutionMatrix/SubMatrix.cpp:1308:12: warning: unused variable 'llimit' [-Wunused-variable]
1308 | int n, llimit, ulimit;
| ^~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp:1308:20: warning: unused variable 'ulimit' [-Wunused-variable]
1308 | int n, llimit, ulimit;
| ^~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readUserMatrixFromR(Rcpp::NumericMatrix, clustalw::Matrix&, clustalw::Xref&)':
ClustalW/substitutionMatrix/SubMatrix.cpp:1361:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
1361 | for (j = 0; j < curline.length(); j++) {
| ~~^~~~~~~~~~~~~~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForHistogram(int (*)[32])':
ClustalW/substitutionMatrix/SubMatrix.cpp:1845:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
1845 | int maxRes;
| ^~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForLowScoreSeg(int (*)[32])':
ClustalW/substitutionMatrix/SubMatrix.cpp:1905:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
1905 | int maxRes;
| ^~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeries(const char*, clustalw::Matrix&, clustalw::Xref&)':
ClustalW/substitutionMatrix/SubMatrix.cpp:1128:19: warning: 'n' may be used uninitialized [-Wmaybe-uninitialized]
1128 | return (maxRes);
| ^
ClustalW/substitutionMatrix/SubMatrix.cpp:1023:9: note: 'n' was declared here
1023 | int n, llimit, ulimit;
| ^
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/AlignmentSteps.cpp -o ClustalW/tree/AlignmentSteps.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/ClusterTree.cpp -o ClustalW/tree/ClusterTree.o
ClustalW/tree/ClusterTree.cpp: In member function 'void clustalw::ClusterTree::calcPercIdentity(std::ofstream*, clustalw::Alignment*)':
ClustalW/tree/ClusterTree.cpp:580:9: warning: variable 'rs' set but not used [-Wunused-but-set-variable]
580 | int rs = 0, rl = 0;
| ^~
ClustalW/tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable]
580 | int rs = 0, rl = 0;
| ^~
ClustalW/tree/ClusterTree.cpp: In member function 'void clustalw::ClusterTree::promptForBoolSeedAndNumTrials()':
ClustalW/tree/ClusterTree.cpp:967:22: warning: variable 'tempSeed' set but not used [-Wunused-but-set-variable]
967 | unsigned int tempSeed;
| ^~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/ClusterTreeOutput.cpp -o ClustalW/tree/ClusterTreeOutput.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/NJTree.cpp -o ClustalW/tree/NJTree.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/RandomGenerator.cpp -o ClustalW/tree/RandomGenerator.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/Tree.cpp -o ClustalW/tree/Tree.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/TreeInterface.cpp -o ClustalW/tree/TreeInterface.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/UnRootedClusterTree.cpp -o ClustalW/tree/UnRootedClusterTree.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/UPGMA/Node.cpp -o ClustalW/tree/UPGMA/Node.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/UPGMA/RootedClusterTree.cpp -o ClustalW/tree/UPGMA/RootedClusterTree.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/UPGMA/RootedGuideTree.cpp -o ClustalW/tree/UPGMA/RootedGuideTree.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/UPGMA/RootedTreeOutput.cpp -o ClustalW/tree/UPGMA/RootedTreeOutput.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClustalW/tree/UPGMA/UPGMAAlgorithm.cpp -o ClustalW/tree/UPGMA/UPGMAAlgorithm.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/aligngivenpath.cpp -o Muscle/aligngivenpath.o
Muscle/aligngivenpath.cpp: In function 'void AppendTplInserts(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)':
Muscle/aligngivenpath.cpp:186:24: warning: unused variable 'uLengthA' [-Wunused-variable]
186 | const unsigned uLengthA = msaA.GetColCount();
| ^~~~~~~~
Muscle/aligngivenpath.cpp:187:24: warning: unused variable 'uLengthB' [-Wunused-variable]
187 | const unsigned uLengthB = msaB.GetColCount();
| ^~~~~~~~
Muscle/aligngivenpath.cpp: In function 'void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)':
Muscle/aligngivenpath.cpp:335:40: warning: unused variable 'uColA' [-Wunused-variable]
335 | const unsigned uColA = uPrefixLengthA - 1;
| ^~~~~
Muscle/aligngivenpath.cpp:336:40: warning: unused variable 'uColB' [-Wunused-variable]
336 | const unsigned uColB = uPrefixLengthB - 1;
| ^~~~~
Muscle/aligngivenpath.cpp:346:40: warning: unused variable 'uColA' [-Wunused-variable]
346 | const unsigned uColA = uPrefixLengthA - 1;
| ^~~~~
Muscle/aligngivenpath.cpp:354:40: warning: unused variable 'uColB' [-Wunused-variable]
354 | const unsigned uColB = uPrefixLengthB - 1;
| ^~~~~
In file included from Muscle/muscle.h:37,
from Muscle/aligngivenpath.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/aligngivenpathsw.cpp -o Muscle/aligngivenpathsw.o
Muscle/aligngivenpathsw.cpp: In function 'void AppendUnalignedTerminals(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)':
Muscle/aligngivenpathsw.cpp:58:24: warning: unused variable 'uLengthA' [-Wunused-variable]
58 | const unsigned uLengthA = msaA.GetColCount();
| ^~~~~~~~
Muscle/aligngivenpathsw.cpp:59:24: warning: unused variable 'uLengthB' [-Wunused-variable]
59 | const unsigned uLengthB = msaB.GetColCount();
| ^~~~~~~~
Muscle/aligngivenpathsw.cpp: In function 'void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)':
Muscle/aligngivenpathsw.cpp:204:40: warning: unused variable 'uColA' [-Wunused-variable]
204 | const unsigned uColA = uPrefixLengthA - 1;
| ^~~~~
Muscle/aligngivenpathsw.cpp:205:40: warning: unused variable 'uColB' [-Wunused-variable]
205 | const unsigned uColB = uPrefixLengthB - 1;
| ^~~~~
Muscle/aligngivenpathsw.cpp:215:40: warning: unused variable 'uColA' [-Wunused-variable]
215 | const unsigned uColA = uPrefixLengthA - 1;
| ^~~~~
Muscle/aligngivenpathsw.cpp:223:40: warning: unused variable 'uColB' [-Wunused-variable]
223 | const unsigned uColB = uPrefixLengthB - 1;
| ^~~~~
In file included from Muscle/muscle.h:37,
from Muscle/aligngivenpathsw.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/aligntwomsas.cpp -o Muscle/aligntwomsas.o
In file included from Muscle/aligntwomsas.cpp:6:
Muscle/timing.h:5: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
5 | #pragma warning(disable:4035)
|
Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
24 | static double TicksToSecs(TICKS t)
| ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
from Muscle/aligntwomsas.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/aligntwoprofs.cpp -o Muscle/aligntwoprofs.o
In file included from Muscle/muscle.h:37,
from Muscle/aligntwoprofs.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/aln.cpp -o Muscle/aln.o
In file included from Muscle/muscle.h:37,
from Muscle/aln.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/alpha.cpp -o Muscle/alpha.o
In file included from Muscle/muscle.h:37,
from Muscle/alpha.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/anchors.cpp -o Muscle/anchors.o
Muscle/anchors.cpp: In function 'void MergeBestCols(const SCORE*, const unsigned int*, unsigned int, unsigned int, unsigned int*, unsigned int*)':
Muscle/anchors.cpp:162:34: warning: unused variable 'uWindowCenter' [-Wunused-variable]
162 | unsigned uWindowCenter = uBestColIndex + uWindowLength/2;
| ^~~~~~~~~~~~~
Muscle/anchors.cpp: At global scope:
Muscle/anchors.cpp:105:13: warning: 'void ListBestCols(const MSA&, const SCORE*, const SCORE*, unsigned int*, unsigned int)' defined but not used [-Wunused-function]
105 | static void ListBestCols(const MSA &msa, const SCORE Score[], const SCORE SmoothScore[],
| ^~~~~~~~~~~~
Muscle/anchors.cpp:53:13: warning: 'void FindBestColsGrade(const SCORE*, unsigned int, double, unsigned int*, unsigned int*)' defined but not used [-Wunused-function]
53 | static void FindBestColsGrade(const SCORE Score[], unsigned uCount,
| ^~~~~~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
from Muscle/anchors.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/bittraceback.cpp -o Muscle/bittraceback.o
Muscle/bittraceback.cpp: In function 'void BitTraceBack(char**, unsigned int, unsigned int, char, PWPath&)':
Muscle/bittraceback.cpp:146:14: warning: unused variable 'Bits' [-Wunused-variable]
146 | char Bits = TraceBack[uLengthA][uLengthB];
| ^~~~
Muscle/bittraceback.cpp: At global scope:
Muscle/bittraceback.cpp:15:20: warning: 'const char* BitsToStr(char)' defined but not used [-Wunused-function]
15 | static const char *BitsToStr(char Bits)
| ^~~~~~~~~
In file included from Muscle/muscle.h:37,
from Muscle/bittraceback.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/blosum62.cpp -o Muscle/blosum62.o
In file included from Muscle/muscle.h:37,
from Muscle/blosum62.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/blosumla.cpp -o Muscle/blosumla.o
Muscle/blosumla.cpp:7:14: warning: 'Blosum62LA' defined but not used [-Wunused-variable]
7 | static float Blosum62LA[20][20] =
| ^~~~~~~~~~
In file included from Muscle/muscle.h:37,
from Muscle/blosumla.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/clust.cpp -o Muscle/clust.o
Muscle/clust.cpp: In member function 'void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)':
Muscle/clust.cpp:186:24: warning: unused variable 'uClusterCount' [-Wunused-variable]
186 | const unsigned uClusterCount = GetClusterCount();
| ^~~~~~~~~~~~~
Muscle/clust.cpp: In member function 'void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)':
Muscle/clust.cpp:206:24: warning: unused variable 'uClusterCount' [-Wunused-variable]
206 | const unsigned uClusterCount = GetClusterCount();
| ^~~~~~~~~~~~~
Muscle/clust.cpp: In member function 'float Clust::ComputeDistMAFFT(unsigned int, unsigned int)':
Muscle/clust.cpp:365:21: warning: unused variable 'dDistLR' [-Wunused-variable]
365 | const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex);
| ^~~~~~~
In file included from Muscle/muscle.h:37,
from Muscle/clust.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/cluster.cpp -o Muscle/cluster.o
Muscle/cluster.cpp: In member function 'void ClusterTree::Create(const DistFunc&)':
Muscle/cluster.cpp:284:22: warning: variable 'bFound' set but not used [-Wunused-but-set-variable]
284 | bool bFound = false;
| ^~~~~~
Muscle/cluster.cpp:267:16: warning: unused variable 'dMaxDist' [-Wunused-variable]
267 | double dMaxDist = 0.0;
| ^~~~~~~~
In file included from Muscle/muscle.h:37,
from Muscle/cluster.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/cluster.cpp: In member function 'void ClusterTree::Create(const DistFunc&)':
Muscle/cluster.cpp:308:47: warning: 'uIndexClosest2' may be used uninitialized [-Wmaybe-uninitialized]
308 | ClusterNode &Child2 = m_Nodes[uIndexClosest2];
| ^~~~~~~~~~~~~~
Muscle/cluster.cpp:283:26: note: 'uIndexClosest2' was declared here
283 | unsigned uIndexClosest2;
| ^~~~~~~~~~~~~~
Muscle/cluster.cpp:307:47: warning: 'uIndexClosest1' may be used uninitialized [-Wmaybe-uninitialized]
307 | ClusterNode &Child1 = m_Nodes[uIndexClosest1];
| ^~~~~~~~~~~~~~
Muscle/cluster.cpp:282:26: note: 'uIndexClosest1' was declared here
282 | unsigned uIndexClosest1;
| ^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/clwwt.cpp -o Muscle/clwwt.o
In file included from Muscle/muscle.h:37,
from Muscle/clwwt.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/color.cpp -o Muscle/color.o
Muscle/color.cpp:72:12: warning: 'int BlosumScore(char, char)' defined but not used [-Wunused-function]
72 | static int BlosumScore(char c1, char c2)
| ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
from Muscle/color.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/cons.cpp -o Muscle/cons.o
In file included from Muscle/muscle.h:37,
from Muscle/cons.cpp:7:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/diaglist.cpp -o Muscle/diaglist.o
In file included from Muscle/muscle.h:37,
from Muscle/diaglist.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/diaglist.cpp: In member function 'void DiagList::FromPath(const PWPath&)':
Muscle/diaglist.cpp:51:18: warning: 'uStartPosA' is used uninitialized [-Wuninitialized]
51 | unsigned uStartPosA;
| ^~~~~~~~~~
Muscle/diaglist.cpp:52:18: warning: 'uStartPosB' is used uninitialized [-Wuninitialized]
52 | unsigned uStartPosB;
| ^~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/diffobjscore.cpp -o Muscle/diffobjscore.o
Muscle/diffobjscore.cpp: In function 'SCORE ScoreLetters(const MSA&, const unsigned int*, unsigned int)':
Muscle/diffobjscore.cpp:76:24: warning: unused variable 'uSeqCount' [-Wunused-variable]
76 | const unsigned uSeqCount = msa.GetSeqCount();
| ^~~~~~~~~
Muscle/diffobjscore.cpp:77:24: warning: unused variable 'uColCount' [-Wunused-variable]
77 | const unsigned uColCount = msa.GetColCount();
| ^~~~~~~~~
In file included from Muscle/muscle.h:37,
from Muscle/diffobjscore.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/diffpaths.cpp -o Muscle/diffpaths.o
In file included from Muscle/muscle.h:37,
from Muscle/diffpaths.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/difftrees.cpp -o Muscle/difftrees.o
Muscle/difftrees.cpp: In function 'void DiffTrees(const Tree&, const Tree&, Tree&, unsigned int*)':
Muscle/difftrees.cpp:161:24: warning: unused variable 'uLeafCount2' [-Wunused-variable]
161 | const unsigned uLeafCount2 = Tree2.GetLeafCount();
| ^~~~~~~~~~~
In file included from Muscle/muscle.h:37,
from Muscle/difftrees.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/difftreese.cpp -o Muscle/difftreese.o
In file included from Muscle/muscle.h:37,
from Muscle/difftreese.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/distcalc.cpp -o Muscle/distcalc.o
In file included from Muscle/muscle.h:37,
from Muscle/distcalc.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/distfunc.cpp -o Muscle/distfunc.o
In file included from Muscle/muscle.h:37,
from Muscle/distfunc.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/distpwkimura.cpp -o Muscle/distpwkimura.o
In file included from Muscle/muscle.h:37,
from Muscle/distpwkimura.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/domuscle.cpp -o Muscle/domuscle.o
In file included from Muscle/domuscle.cpp:9:
Muscle/timing.h:5: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
5 | #pragma warning(disable:4035)
|
Muscle/domuscle.cpp: In function 'void DoMuscle(MuscleInput*, MuscleOutput*)':
Muscle/domuscle.cpp:169:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
169 | if (g_bClusterOnly)
| ^~
Muscle/domuscle.cpp:172:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
172 | return;
| ^~~~~~
Muscle/domuscle.cpp:180:13: warning: unused variable 'PNlength' [-Wunused-variable]
180 | int PNlength = (msaInput->inputSeqs).Length();
| ^~~~~~~~
Muscle/timing.h: At global scope:
Muscle/timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
24 | static double TicksToSecs(TICKS t)
| ^~~~~~~~~~~
In file included from ./Muscle/muscle.h:37,
from ./RMuscle.h:4,
from Muscle/domuscle.cpp:1:
./Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/dosp.cpp -o Muscle/dosp.o
In file included from Muscle/muscle.h:37,
from Muscle/dosp.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/dpreglist.cpp -o Muscle/dpreglist.o
Muscle/dpreglist.cpp: In function 'void DiagListToDPRegionList(const DiagList&, DPRegionList&, unsigned int, unsigned int)':
Muscle/dpreglist.cpp:82:40: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable]
82 | const unsigned uDiagLengthMinusCaps = uEndVertexA - uStartVertexA - 1;
| ^~~~~~~~~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
from Muscle/dpreglist.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/drawtree.cpp -o Muscle/drawtree.o
In file included from Muscle/muscle.h:37,
from Muscle/drawtree.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/edgelist.cpp -o Muscle/edgelist.o
In file included from Muscle/muscle.h:37,
from Muscle/edgelist.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/enumopts.cpp -o Muscle/enumopts.o
In file included from Muscle/muscle.h:37,
from Muscle/enumopts.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/enumtostr.cpp -o Muscle/enumtostr.o
In file included from Muscle/muscle.h:37,
from Muscle/enumtostr.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/estring.cpp -o Muscle/estring.o
Muscle/estring.cpp:464:13: warning: 'bool CanMultiplyEstrings(const short int*, const short int*)' defined but not used [-Wunused-function]
464 | static bool CanMultiplyEstrings(const short es1[], const short es2[])
| ^~~~~~~~~~~~~~~~~~~
In file included from Muscle/muscle.h:37,
from Muscle/estring.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/estring.cpp: In function 'void EstringsToPath(const short int*, const short int*, PWPath&)':
Muscle/estring.cpp:409:17: warning: 'cType' may be used uninitialized [-Wmaybe-uninitialized]
409 | switch (cType)
| ^~~~~~
Muscle/estring.cpp:377:22: note: 'cType' was declared here
377 | char cType;
| ^~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/fasta.cpp -o Muscle/fasta.o
Muscle/fasta.cpp: In member function 'void MSA::FromFASTAFile(TextFile&)':
Muscle/fasta.cpp:15:18: warning: unused variable 'uSeqCount' [-Wunused-variable]
15 | unsigned uSeqCount = 0;
| ^~~~~~~~~
Muscle/fasta.cpp:16:18: warning: unused variable 'uColCount' [-Wunused-variable]
16 | unsigned uColCount = uInsane;
| ^~~~~~~~~
In file included from Muscle/muscle.h:37,
from Muscle/fasta.cpp:1:
Muscle/intmath.h: At global scope:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/fasta2.cpp -o Muscle/fasta2.o
In file included from Muscle/muscle.h:37,
from Muscle/fasta2.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/fastclust.cpp -o Muscle/fastclust.o
In file included from Muscle/muscle.h:37,
from Muscle/fastclust.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/fastdist.cpp -o Muscle/fastdist.o
In file included from Muscle/muscle.h:37,
from Muscle/fastdist.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/fastdistjones.cpp -o Muscle/fastdistjones.o
In file included from Muscle/muscle.h:37,
from Muscle/fastdistjones.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/fastdistkbit.cpp -o Muscle/fastdistkbit.o
In file included from Muscle/muscle.h:37,
from Muscle/fastdistkbit.cpp:1:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -I. -I"./ClustalW" -I"./Muscle" -pthread -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Muscle/fastdistkmer.cpp -o Muscle/fastdistkmer.o
Muscle/fastdistkmer.cpp:79:23: error: reference to 'byte' is ambiguous
79 | void CountKmers(const byte s[], unsigned uSeqLength, byte KmerCounts[])
| ^~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_algobase.h:61,
from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\vector:60,
from Muscle/muscle.h:1,
from Muscle/fastdistkmer.cpp:1:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
In file included from Muscle/muscle.h:36:
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp:79:54: error: reference to 'byte' is ambiguous
79 | void CountKmers(const byte s[], unsigned uSeqLength, byte KmerCounts[])
| ^~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp:79:54: error: 'byte' has not been declared
79 | void CountKmers(const byte s[], unsigned uSeqLength, byte KmerCounts[])
| ^~~~
Muscle/fastdistkmer.cpp: In function 'void CountKmers(const int*, unsigned int, int*)':
Muscle/fastdistkmer.cpp:84:49: error: reference to 'byte' is ambiguous
84 | memset(KmerCounts, 0, TABLE_SIZE*sizeof(byte));
| ^~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp:86:15: error: reference to 'byte' is ambiguous
86 | const byte *ptrKmerStart = s;
| ^~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp:87:15: error: reference to 'byte' is ambiguous
87 | const byte *ptrKmerEnd = s + 4;
| ^~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp:88:15: error: reference to 'byte' is ambiguous
88 | const byte *ptrSeqEnd = s + uSeqLength;
| ^~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp:106:21: error: 'ptrKmerEnd' was not declared in this scope
106 | if (ptrKmerEnd == ptrSeqEnd)
| ^~~~~~~~~~
Muscle/fastdistkmer.cpp:106:35: error: 'ptrSeqEnd' was not declared in this scope
106 | if (ptrKmerEnd == ptrSeqEnd)
| ^~~~~~~~~
Muscle/fastdistkmer.cpp:113:24: error: 'ptrKmerStart' was not declared in this scope
113 | c3 = (*ptrKmerStart++) * N_3;
| ^~~~~~~~~~~~
Muscle/fastdistkmer.cpp:115:26: error: 'ptrKmerEnd' was not declared in this scope
115 | Kmer += *ptrKmerEnd++;
| ^~~~~~~~~~
Muscle/fastdistkmer.cpp: At global scope:
Muscle/fastdistkmer.cpp:119:32: error: reference to 'byte' is ambiguous
119 | unsigned CommonKmerCount(const byte Seq[], unsigned uSeqLength,
| ^~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp:120:9: error: reference to 'byte' is ambiguous
120 | const byte KmerCounts1[], const byte Seq2[], unsigned uSeqLength2)
| ^~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp:120:35: error: reference to 'byte' is ambiguous
120 | const byte KmerCounts1[], const byte Seq2[], unsigned uSeqLength2)
| ^~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp: In function 'unsigned int CommonKmerCount(const int*, unsigned int, const int*, const int*, unsigned int)':
Muscle/fastdistkmer.cpp:122:9: error: reference to 'byte' is ambiguous
122 | byte KmerCounts2[TABLE_SIZE];
| ^~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp:123:39: error: 'KmerCounts2' was not declared in this scope; did you mean 'KmerCounts1'?
123 | CountKmers(Seq2, uSeqLength2, KmerCounts2);
| ^~~~~~~~~~~
| KmerCounts1
Muscle/fastdistkmer.cpp:125:15: error: reference to 'byte' is ambiguous
125 | const byte *ptrKmerStart = Seq;
| ^~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp:126:15: error: reference to 'byte' is ambiguous
126 | const byte *ptrKmerEnd = Seq + 4;
| ^~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp:127:15: error: reference to 'byte' is ambiguous
127 | const byte *ptrSeqEnd = Seq + uSeqLength;
| ^~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp:141:23: error: reference to 'byte' is ambiguous
141 | const byte Count1 = KmerCounts1[Kmer];
| ^~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp:142:23: error: reference to 'byte' is ambiguous
142 | const byte Count2 = KmerCounts2[Kmer];
| ^~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp:144:37: error: 'Count1' was not declared in this scope
144 | uCommonCount += MIN(Count1, Count2);
| ^~~~~~
Muscle/fastdistkmer.cpp:52:28: note: in definition of macro 'MIN'
52 | #define MIN(x, y) (((x) < (y)) ? (x) : (y))
| ^
Muscle/fastdistkmer.cpp:144:45: error: 'Count2' was not declared in this scope
144 | uCommonCount += MIN(Count1, Count2);
| ^~~~~~
Muscle/fastdistkmer.cpp:52:34: note: in definition of macro 'MIN'
52 | #define MIN(x, y) (((x) < (y)) ? (x) : (y))
| ^
Muscle/fastdistkmer.cpp:149:21: error: 'ptrKmerEnd' was not declared in this scope
149 | if (ptrKmerEnd == ptrSeqEnd)
| ^~~~~~~~~~
Muscle/fastdistkmer.cpp:149:35: error: 'ptrSeqEnd' was not declared in this scope
149 | if (ptrKmerEnd == ptrSeqEnd)
| ^~~~~~~~~
Muscle/fastdistkmer.cpp:156:24: error: 'ptrKmerStart' was not declared in this scope
156 | c3 = (*ptrKmerStart++) * N_3;
| ^~~~~~~~~~~~
Muscle/fastdistkmer.cpp:158:26: error: 'ptrKmerEnd' was not declared in this scope
158 | Kmer += *ptrKmerEnd++;
| ^~~~~~~~~~
Muscle/fastdistkmer.cpp: At global scope:
Muscle/fastdistkmer.cpp:163:40: error: reference to 'byte' is ambiguous
163 | static void SeqToLetters(const Seq &s, byte Letters[])
| ^~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp:163:40: error: 'byte' has not been declared
163 | static void SeqToLetters(const Seq &s, byte Letters[])
| ^~~~
Muscle/fastdistkmer.cpp: In function 'void FastDistKmer(const SeqVect&, DistFunc&)':
Muscle/fastdistkmer.cpp:180:9: error: reference to 'byte' is ambiguous
180 | byte KmerCounts[TABLE_SIZE];
| ^~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp:207:9: error: reference to 'byte' is ambiguous
207 | byte *Seq1Letters = new byte[uMaxLength];
| ^~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp:207:15: error: 'Seq1Letters' was not declared in this scope; did you mean 'SeqToLetters'?
207 | byte *Seq1Letters = new byte[uMaxLength];
| ^~~~~~~~~~~
| SeqToLetters
Muscle/fastdistkmer.cpp:207:33: error: reference to 'byte' is ambiguous
207 | byte *Seq1Letters = new byte[uMaxLength];
| ^~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp:208:9: error: reference to 'byte' is ambiguous
208 | byte *Seq2Letters = new byte[uMaxLength];
| ^~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp:208:15: error: 'Seq2Letters' was not declared in this scope; did you mean 'SeqToLetters'?
208 | byte *Seq2Letters = new byte[uMaxLength];
| ^~~~~~~~~~~
| SeqToLetters
Muscle/fastdistkmer.cpp:208:33: error: reference to 'byte' is ambiguous
208 | byte *Seq2Letters = new byte[uMaxLength];
| ^~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\cpp_type_traits.h:406:30: note: candidates are: 'enum class std::byte'
406 | enum class byte : unsigned char;
| ^~~~
Muscle/types.h:4:23: note: 'typedef unsigned char byte'
4 | typedef unsigned char byte;
| ^~~~
Muscle/fastdistkmer.cpp:216:54: error: 'KmerCounts' was not declared in this scope
216 | CountKmers(Seq1Letters, uSeqLength1, KmerCounts);
| ^~~~~~~~~~
Muscle/fastdistkmer.cpp:235:32: warning: unused variable 'KD' [-Wunused-variable]
235 | double KD = KimuraDist(EstimatedPctId);
| ^~
Muscle/fastdistkmer.cpp:245:18: error: type '<type error>' argument given to 'delete', expected pointer
245 | delete[] Seq1Letters;
| ^~~~~~~~~~~
Muscle/fastdistkmer.cpp:246:18: error: type '<type error>' argument given to 'delete', expected pointer
246 | delete[] Seq2Letters;
| ^~~~~~~~~~~
Muscle/fastdistkmer.cpp: At global scope:
Muscle/fastdistkmer.cpp:163:13: warning: 'void SeqToLetters(const Seq&, int*)' defined but not used [-Wunused-function]
163 | static void SeqToLetters(const Seq &s, byte Letters[])
| ^~~~~~~~~~~~
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
make: *** [F:/biocbuild/bbs-3.17-bioc/R/etc/x64/Makeconf:272: Muscle/fastdistkmer.o] Error 1
ERROR: compilation failed for package 'enhancerHomologSearch'
* removing 'F:/biocbuild/bbs-3.17-bioc/R/library/enhancerHomologSearch'