##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL enhancerHomologSearch
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘enhancerHomologSearch’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/alignment/Alignment.cpp -o ClustalW/alignment/Alignment.o
ClustalW/alignment/Alignment.cpp:819:9: warning: variable 'counter2' set but not used [-Wunused-but-set-variable]
    int counter2 = 2;
        ^
ClustalW/alignment/Alignment.cpp:1715:24: warning: unused variable 'posToAddTo' [-Wunused-variable]
    SeqArray::iterator posToAddTo = sectionToRealign.begin();
                       ^
In file included from ClustalW/alignment/Alignment.cpp:25:
In file included from ClustalW/alignment/Alignment.h:41:
In file included from ClustalW/alignment/Sequence.h:21:
In file included from ClustalW/alignment/../general/userparams.h:8:
In file included from ClustalW/alignment/../general/UserParameters.h:22:
In file included from ClustalW/alignment/../general/utils.h:8:
In file included from ClustalW/alignment/../general/Utility.h:15:
In file included from ClustalW/alignment/../general/clustalw.h:44:
ClustalW/alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/alignment/AlignmentOutput.cpp -o ClustalW/alignment/AlignmentOutput.o
ClustalW/alignment/AlignmentOutput.cpp:2297:16: warning: variable 'slen' set but not used [-Wunused-but-set-variable]
        int j, slen;
               ^
In file included from ClustalW/alignment/AlignmentOutput.cpp:27:
In file included from ClustalW/alignment/AlignmentOutput.h:24:
In file included from ClustalW/alignment/Alignment.h:41:
In file included from ClustalW/alignment/Sequence.h:21:
In file included from ClustalW/alignment/../general/userparams.h:8:
In file included from ClustalW/alignment/../general/UserParameters.h:22:
In file included from ClustalW/alignment/../general/utils.h:8:
In file included from ClustalW/alignment/../general/Utility.h:15:
In file included from ClustalW/alignment/../general/clustalw.h:44:
ClustalW/alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/alignment/ObjectiveScore.cpp -o ClustalW/alignment/ObjectiveScore.o
In file included from ClustalW/alignment/ObjectiveScore.cpp:10:
In file included from ClustalW/alignment/ObjectiveScore.h:14:
In file included from ClustalW/alignment/../general/clustalw.h:44:
ClustalW/alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
In file included from ClustalW/alignment/ObjectiveScore.cpp:10:
ClustalW/alignment/ObjectiveScore.h:40:14: warning: private field 'scale' is not used [-Wunused-private-field]
        long scale;
             ^
ClustalW/alignment/ObjectiveScore.h:41:13: warning: private field 'weightScale' is not used [-Wunused-private-field]
        int weightScale;
            ^
ClustalW/alignment/ObjectiveScore.h:42:13: warning: private field 'sagaGapEx' is not used [-Wunused-private-field]
        int sagaGapEx, sagaGapOp;
            ^
ClustalW/alignment/ObjectiveScore.h:42:24: warning: private field 'sagaGapOp' is not used [-Wunused-private-field]
        int sagaGapEx, sagaGapOp;
                       ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/alignment/Sequence.cpp -o ClustalW/alignment/Sequence.o
In file included from ClustalW/alignment/Sequence.cpp:10:
In file included from ClustalW/alignment/Sequence.h:21:
In file included from ClustalW/alignment/../general/userparams.h:8:
In file included from ClustalW/alignment/../general/UserParameters.h:22:
In file included from ClustalW/alignment/../general/utils.h:8:
In file included from ClustalW/alignment/../general/Utility.h:15:
In file included from ClustalW/alignment/../general/clustalw.h:44:
ClustalW/alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/Clustal.cpp -o ClustalW/Clustal.o
In file included from ClustalW/Clustal.cpp:27:
In file included from ./ClustalW/Clustal.h:16:
In file included from ./ClustalW/general/clustalw.h:44:
./ClustalW/general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/fileInput/ClustalFileParser.cpp -o ClustalW/fileInput/ClustalFileParser.o
In file included from ClustalW/fileInput/ClustalFileParser.cpp:19:
In file included from ClustalW/fileInput/ClustalFileParser.h:10:
In file included from ClustalW/fileInput/FileParser.h:22:
In file included from ClustalW/fileInput/../alignment/Sequence.h:21:
In file included from ClustalW/fileInput/../alignment/../general/userparams.h:8:
In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/fileInput/../alignment/../general/utils.h:8:
In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15:
In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44:
ClustalW/fileInput/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/fileInput/EMBLFileParser.cpp -o ClustalW/fileInput/EMBLFileParser.o
In file included from ClustalW/fileInput/EMBLFileParser.cpp:16:
In file included from ClustalW/fileInput/EMBLFileParser.h:10:
In file included from ClustalW/fileInput/FileParser.h:22:
In file included from ClustalW/fileInput/../alignment/Sequence.h:21:
In file included from ClustalW/fileInput/../alignment/../general/userparams.h:8:
In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/fileInput/../alignment/../general/utils.h:8:
In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15:
In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44:
ClustalW/fileInput/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/fileInput/FileParser.cpp -o ClustalW/fileInput/FileParser.o
ClustalW/fileInput/FileParser.cpp:38:7: warning: unused variable 'n' [-Wunused-variable]
                int n = (*input).inputSeqs.size();
                    ^
In file included from ClustalW/fileInput/FileParser.cpp:14:
In file included from ClustalW/fileInput/FileParser.h:22:
In file included from ClustalW/fileInput/../alignment/Sequence.h:21:
In file included from ClustalW/fileInput/../alignment/../general/userparams.h:8:
In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/fileInput/../alignment/../general/utils.h:8:
In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15:
In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44:
ClustalW/fileInput/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/fileInput/FileReader.cpp -o ClustalW/fileInput/FileReader.o
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.
                ^
In file included from ClustalW/fileInput/FileReader.cpp:29:
In file included from ClustalW/fileInput/FileReader.h:12:
In file included from ClustalW/fileInput/../alignment/Alignment.h:41:
In file included from ClustalW/fileInput/../alignment/Sequence.h:21:
In file included from ClustalW/fileInput/../alignment/../general/userparams.h:8:
In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/fileInput/../alignment/../general/utils.h:8:
In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15:
In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44:
ClustalW/fileInput/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/fileInput/GDEFileParser.cpp -o ClustalW/fileInput/GDEFileParser.o
In file included from ClustalW/fileInput/GDEFileParser.cpp:16:
In file included from ClustalW/fileInput/GDEFileParser.h:10:
In file included from ClustalW/fileInput/FileParser.h:22:
In file included from ClustalW/fileInput/../alignment/Sequence.h:21:
In file included from ClustalW/fileInput/../alignment/../general/userparams.h:8:
In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/fileInput/../alignment/../general/utils.h:8:
In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15:
In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44:
ClustalW/fileInput/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/fileInput/InFileStream.cpp -o ClustalW/fileInput/InFileStream.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/fileInput/MSFFileParser.cpp -o ClustalW/fileInput/MSFFileParser.o
In file included from ClustalW/fileInput/MSFFileParser.cpp:16:
In file included from ClustalW/fileInput/MSFFileParser.h:10:
In file included from ClustalW/fileInput/FileParser.h:22:
In file included from ClustalW/fileInput/../alignment/Sequence.h:21:
In file included from ClustalW/fileInput/../alignment/../general/userparams.h:8:
In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/fileInput/../alignment/../general/utils.h:8:
In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15:
In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44:
ClustalW/fileInput/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/fileInput/PearsonFileParser.cpp -o ClustalW/fileInput/PearsonFileParser.o
In file included from ClustalW/fileInput/PearsonFileParser.cpp:26:
In file included from ClustalW/fileInput/PearsonFileParser.h:14:
In file included from ClustalW/fileInput/FileParser.h:22:
In file included from ClustalW/fileInput/../alignment/Sequence.h:21:
In file included from ClustalW/fileInput/../alignment/../general/userparams.h:8:
In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/fileInput/../alignment/../general/utils.h:8:
In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15:
In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44:
ClustalW/fileInput/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/fileInput/PIRFileParser.cpp -o ClustalW/fileInput/PIRFileParser.o
In file included from ClustalW/fileInput/PIRFileParser.cpp:16:
In file included from ClustalW/fileInput/PIRFileParser.h:10:
In file included from ClustalW/fileInput/FileParser.h:22:
In file included from ClustalW/fileInput/../alignment/Sequence.h:21:
In file included from ClustalW/fileInput/../alignment/../general/userparams.h:8:
In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/fileInput/../alignment/../general/utils.h:8:
In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15:
In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44:
ClustalW/fileInput/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/fileInput/RSFFileParser.cpp -o ClustalW/fileInput/RSFFileParser.o
In file included from ClustalW/fileInput/RSFFileParser.cpp:16:
In file included from ClustalW/fileInput/RSFFileParser.h:10:
In file included from ClustalW/fileInput/FileParser.h:22:
In file included from ClustalW/fileInput/../alignment/Sequence.h:21:
In file included from ClustalW/fileInput/../alignment/../general/userparams.h:8:
In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/fileInput/../alignment/../general/utils.h:8:
In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15:
In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44:
ClustalW/fileInput/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/general/ClustalWResources.cpp -o ClustalW/general/ClustalWResources.o
In file included from ClustalW/general/ClustalWResources.cpp:14:
In file included from ClustalW/general/clustalw.h:44:
ClustalW/general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/general/DebugLog.cpp -o ClustalW/general/DebugLog.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/general/InvalidCombination.cpp -o ClustalW/general/InvalidCombination.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/general/OutputFile.cpp -o ClustalW/general/OutputFile.o
In file included from ClustalW/general/OutputFile.cpp:10:
In file included from ClustalW/general/utils.h:8:
In file included from ClustalW/general/Utility.h:15:
In file included from ClustalW/general/clustalw.h:44:
ClustalW/general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/general/Stats.cpp -o ClustalW/general/Stats.o
In file included from ClustalW/general/Stats.cpp:16:
In file included from ClustalW/general/../alignment/Alignment.h:41:
In file included from ClustalW/general/../alignment/Sequence.h:21:
In file included from ClustalW/general/../alignment/../general/userparams.h:8:
In file included from ClustalW/general/UserParameters.h:22:
In file included from ClustalW/general/utils.h:8:
In file included from ClustalW/general/Utility.h:15:
In file included from ClustalW/general/clustalw.h:44:
ClustalW/general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/general/SymMatrix.cpp -o ClustalW/general/SymMatrix.o
In file included from ClustalW/general/SymMatrix.cpp:10:
ClustalW/general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/general/UserParameters.cpp -o ClustalW/general/UserParameters.o
In file included from ClustalW/general/UserParameters.cpp:24:
In file included from ClustalW/general/UserParameters.h:22:
In file included from ClustalW/general/utils.h:8:
In file included from ClustalW/general/Utility.h:15:
In file included from ClustalW/general/clustalw.h:44:
ClustalW/general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/general/Utility.cpp -o ClustalW/general/Utility.o
ClustalW/general/Utility.cpp:251:8: warning: variable 'n' set but not used [-Wunused-but-set-variable]
   int n;
       ^
In file included from ClustalW/general/Utility.cpp:19:
In file included from ClustalW/general/Utility.h:15:
In file included from ClustalW/general/clustalw.h:44:
ClustalW/general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/general/VectorOutOfRange.cpp -o ClustalW/general/VectorOutOfRange.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/Help.cpp -o ClustalW/Help.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/interface/CommandLineParser.cpp -o ClustalW/interface/CommandLineParser.o
In file included from ClustalW/interface/CommandLineParser.cpp:13:
In file included from ClustalW/interface/CommandLineParser.h:18:
In file included from ClustalW/interface/../Clustal.h:16:
In file included from ./ClustalW/general/clustalw.h:44:
./ClustalW/general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/multipleAlign/Iteration.cpp -o ClustalW/multipleAlign/Iteration.o
ClustalW/multipleAlign/Iteration.cpp:171:9: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    int count;
        ^
In file included from ClustalW/multipleAlign/Iteration.cpp:13:
In file included from ClustalW/multipleAlign/Iteration.h:8:
In file included from ClustalW/multipleAlign/../alignment/Alignment.h:41:
In file included from ClustalW/multipleAlign/../alignment/Sequence.h:21:
In file included from ClustalW/multipleAlign/../alignment/../general/userparams.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/multipleAlign/../alignment/../general/utils.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15:
In file included from ClustalW/multipleAlign/../alignment/../general/clustalw.h:44:
ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/multipleAlign/LowScoreSegProfile.cpp -o ClustalW/multipleAlign/LowScoreSegProfile.o
In file included from ClustalW/multipleAlign/LowScoreSegProfile.cpp:9:
In file included from ClustalW/multipleAlign/LowScoreSegProfile.h:13:
In file included from ClustalW/multipleAlign/../alignment/Alignment.h:41:
In file included from ClustalW/multipleAlign/../alignment/Sequence.h:21:
In file included from ClustalW/multipleAlign/../alignment/../general/userparams.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/multipleAlign/../alignment/../general/utils.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15:
In file included from ClustalW/multipleAlign/../alignment/../general/clustalw.h:44:
ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/multipleAlign/MSA.cpp -o ClustalW/multipleAlign/MSA.o
ClustalW/multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable]
      int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18
          ^
ClustalW/multipleAlign/MSA.cpp:369:18: warning: variable 'entries' set but not used [-Wunused-but-set-variable]
    int sum = 0, entries = 0;
                 ^
In file included from ClustalW/multipleAlign/MSA.cpp:16:
In file included from ClustalW/multipleAlign/MSA.h:10:
In file included from ClustalW/multipleAlign/ProfileBase.h:14:
In file included from ClustalW/multipleAlign/../alignment/Alignment.h:41:
In file included from ClustalW/multipleAlign/../alignment/Sequence.h:21:
In file included from ClustalW/multipleAlign/../alignment/../general/userparams.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/multipleAlign/../alignment/../general/utils.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15:
In file included from ClustalW/multipleAlign/../alignment/../general/clustalw.h:44:
ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/multipleAlign/MyersMillerProfileAlign.cpp -o ClustalW/multipleAlign/MyersMillerProfileAlign.o
In file included from ClustalW/multipleAlign/MyersMillerProfileAlign.cpp:10:
In file included from ClustalW/multipleAlign/MyersMillerProfileAlign.h:11:
In file included from ClustalW/multipleAlign/ProfileAlignAlgorithm.h:10:
In file included from ClustalW/multipleAlign/../alignment/Alignment.h:41:
In file included from ClustalW/multipleAlign/../alignment/Sequence.h:21:
In file included from ClustalW/multipleAlign/../alignment/../general/userparams.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/multipleAlign/../alignment/../general/utils.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15:
In file included from ClustalW/multipleAlign/../alignment/../general/clustalw.h:44:
ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
In file included from ClustalW/multipleAlign/MyersMillerProfileAlign.cpp:10:
ClustalW/multipleAlign/MyersMillerProfileAlign.h:61:13: warning: private field 'matrix' is not used [-Wunused-private-field]
        int matrix[32][32];
            ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/multipleAlign/ProfileBase.cpp -o ClustalW/multipleAlign/ProfileBase.o
In file included from ClustalW/multipleAlign/ProfileBase.cpp:9:
In file included from ClustalW/multipleAlign/ProfileBase.h:14:
In file included from ClustalW/multipleAlign/../alignment/Alignment.h:41:
In file included from ClustalW/multipleAlign/../alignment/Sequence.h:21:
In file included from ClustalW/multipleAlign/../alignment/../general/userparams.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/multipleAlign/../alignment/../general/utils.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15:
In file included from ClustalW/multipleAlign/../alignment/../general/clustalw.h:44:
ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/multipleAlign/ProfileStandard.cpp -o ClustalW/multipleAlign/ProfileStandard.o
In file included from ClustalW/multipleAlign/ProfileStandard.cpp:9:
In file included from ClustalW/multipleAlign/ProfileStandard.h:9:
In file included from ClustalW/multipleAlign/../alignment/Alignment.h:41:
In file included from ClustalW/multipleAlign/../alignment/Sequence.h:21:
In file included from ClustalW/multipleAlign/../alignment/../general/userparams.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/multipleAlign/../alignment/../general/utils.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15:
In file included from ClustalW/multipleAlign/../alignment/../general/clustalw.h:44:
ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/multipleAlign/ProfileWithSub.cpp -o ClustalW/multipleAlign/ProfileWithSub.o
In file included from ClustalW/multipleAlign/ProfileWithSub.cpp:9:
In file included from ClustalW/multipleAlign/ProfileWithSub.h:9:
In file included from ClustalW/multipleAlign/../alignment/Alignment.h:41:
In file included from ClustalW/multipleAlign/../alignment/Sequence.h:21:
In file included from ClustalW/multipleAlign/../alignment/../general/userparams.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/multipleAlign/../alignment/../general/utils.h:8:
In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15:
In file included from ClustalW/multipleAlign/../alignment/../general/clustalw.h:44:
ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/pairwise/FastPairwiseAlign.cpp -o ClustalW/pairwise/FastPairwiseAlign.o
In file included from ClustalW/pairwise/FastPairwiseAlign.cpp:10:
In file included from ClustalW/pairwise/FastPairwiseAlign.h:9:
In file included from ClustalW/pairwise/PairwiseAlignBase.h:10:
In file included from ClustalW/pairwise/../alignment/Alignment.h:41:
In file included from ClustalW/pairwise/../alignment/Sequence.h:21:
In file included from ClustalW/pairwise/../alignment/../general/userparams.h:8:
In file included from ClustalW/pairwise/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/pairwise/../alignment/../general/utils.h:8:
In file included from ClustalW/pairwise/../alignment/../general/Utility.h:15:
In file included from ClustalW/pairwise/../alignment/../general/clustalw.h:44:
ClustalW/pairwise/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/pairwise/FullPairwiseAlign.cpp -o ClustalW/pairwise/FullPairwiseAlign.o
ClustalW/pairwise/FullPairwiseAlign.cpp:229:15: warning: variable 'pos' set but not used [-Wunused-but-set-variable]
    int i, k, pos, toDo;
              ^
In file included from ClustalW/pairwise/FullPairwiseAlign.cpp:9:
In file included from ClustalW/pairwise/FullPairwiseAlign.h:9:
In file included from ClustalW/pairwise/PairwiseAlignBase.h:10:
In file included from ClustalW/pairwise/../alignment/Alignment.h:41:
In file included from ClustalW/pairwise/../alignment/Sequence.h:21:
In file included from ClustalW/pairwise/../alignment/../general/userparams.h:8:
In file included from ClustalW/pairwise/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/pairwise/../alignment/../general/utils.h:8:
In file included from ClustalW/pairwise/../alignment/../general/Utility.h:15:
In file included from ClustalW/pairwise/../alignment/../general/clustalw.h:44:
ClustalW/pairwise/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/substitutionMatrix/SubMatrix.cpp -o ClustalW/substitutionMatrix/SubMatrix.o
ClustalW/substitutionMatrix/SubMatrix.cpp:175:17: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
    short i, j, maxRes;
                ^
ClustalW/substitutionMatrix/SubMatrix.cpp:697:9: warning: variable 'av1' set but not used [-Wunused-but-set-variable]
    int av1, av2, av3, min, max;
        ^
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:1845:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
    int maxRes;
        ^
ClustalW/substitutionMatrix/SubMatrix.cpp:1905:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
    int maxRes;
        ^
In file included from ClustalW/substitutionMatrix/SubMatrix.cpp:15:
In file included from ClustalW/substitutionMatrix/SubMatrix.h:28:
In file included from ClustalW/substitutionMatrix/../general/clustalw.h:44:
ClustalW/substitutionMatrix/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
10 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/tree/AlignmentSteps.cpp -o ClustalW/tree/AlignmentSteps.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/tree/ClusterTree.cpp -o ClustalW/tree/ClusterTree.o
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:967:22: warning: variable 'tempSeed' set but not used [-Wunused-but-set-variable]
        unsigned int tempSeed;
                     ^
In file included from ClustalW/tree/ClusterTree.cpp:9:
In file included from ClustalW/tree/ClusterTree.h:20:
In file included from ClustalW/tree/../alignment/Alignment.h:41:
In file included from ClustalW/tree/../alignment/Sequence.h:21:
In file included from ClustalW/tree/../alignment/../general/userparams.h:8:
In file included from ClustalW/tree/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/tree/../alignment/../general/utils.h:8:
In file included from ClustalW/tree/../alignment/../general/Utility.h:15:
In file included from ClustalW/tree/../alignment/../general/clustalw.h:44:
ClustalW/tree/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
4 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/tree/ClusterTreeOutput.cpp -o ClustalW/tree/ClusterTreeOutput.o
In file included from ClustalW/tree/ClusterTreeOutput.cpp:9:
In file included from ClustalW/tree/ClusterTreeOutput.h:11:
In file included from ClustalW/tree/../alignment/Alignment.h:41:
In file included from ClustalW/tree/../alignment/Sequence.h:21:
In file included from ClustalW/tree/../alignment/../general/userparams.h:8:
In file included from ClustalW/tree/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/tree/../alignment/../general/utils.h:8:
In file included from ClustalW/tree/../alignment/../general/Utility.h:15:
In file included from ClustalW/tree/../alignment/../general/clustalw.h:44:
ClustalW/tree/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/tree/NJTree.cpp -o ClustalW/tree/NJTree.o
In file included from ClustalW/tree/NJTree.cpp:10:
In file included from ClustalW/tree/NJTree.h:11:
In file included from ClustalW/tree/ClusterTreeAlgorithm.h:12:
In file included from ClustalW/tree/../general/clustalw.h:44:
ClustalW/tree/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/tree/RandomGenerator.cpp -o ClustalW/tree/RandomGenerator.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/tree/Tree.cpp -o ClustalW/tree/Tree.o
In file included from ClustalW/tree/Tree.cpp:10:
In file included from ClustalW/tree/Tree.h:13:
In file included from ClustalW/tree/../alignment/Alignment.h:41:
In file included from ClustalW/tree/../alignment/Sequence.h:21:
In file included from ClustalW/tree/../alignment/../general/userparams.h:8:
In file included from ClustalW/tree/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/tree/../alignment/../general/utils.h:8:
In file included from ClustalW/tree/../alignment/../general/Utility.h:15:
In file included from ClustalW/tree/../alignment/../general/clustalw.h:44:
ClustalW/tree/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/tree/TreeInterface.cpp -o ClustalW/tree/TreeInterface.o
In file included from ClustalW/tree/TreeInterface.cpp:15:
In file included from ClustalW/tree/TreeInterface.h:19:
In file included from ClustalW/tree/../alignment/Alignment.h:41:
In file included from ClustalW/tree/../alignment/Sequence.h:21:
In file included from ClustalW/tree/../alignment/../general/userparams.h:8:
In file included from ClustalW/tree/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/tree/../alignment/../general/utils.h:8:
In file included from ClustalW/tree/../alignment/../general/Utility.h:15:
In file included from ClustalW/tree/../alignment/../general/clustalw.h:44:
ClustalW/tree/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/tree/UnRootedClusterTree.cpp -o ClustalW/tree/UnRootedClusterTree.o
In file included from ClustalW/tree/UnRootedClusterTree.cpp:9:
In file included from ClustalW/tree/UnRootedClusterTree.h:8:
In file included from ClustalW/tree/ClusterTree.h:20:
In file included from ClustalW/tree/../alignment/Alignment.h:41:
In file included from ClustalW/tree/../alignment/Sequence.h:21:
In file included from ClustalW/tree/../alignment/../general/userparams.h:8:
In file included from ClustalW/tree/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/tree/../alignment/../general/utils.h:8:
In file included from ClustalW/tree/../alignment/../general/Utility.h:15:
In file included from ClustalW/tree/../alignment/../general/clustalw.h:44:
ClustalW/tree/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/tree/UPGMA/Node.cpp -o ClustalW/tree/UPGMA/Node.o
In file included from ClustalW/tree/UPGMA/Node.cpp:7:
In file included from ClustalW/tree/UPGMA/../../general/clustalw.h:44:
ClustalW/tree/UPGMA/../../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/tree/UPGMA/RootedClusterTree.cpp -o ClustalW/tree/UPGMA/RootedClusterTree.o
In file included from ClustalW/tree/UPGMA/RootedClusterTree.cpp:9:
In file included from ClustalW/tree/UPGMA/RootedClusterTree.h:8:
In file included from ClustalW/tree/UPGMA/../ClusterTree.h:20:
In file included from ClustalW/tree/UPGMA/../../alignment/Alignment.h:41:
In file included from ClustalW/tree/UPGMA/../../alignment/Sequence.h:21:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/userparams.h:8:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/UserParameters.h:22:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/utils.h:8:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/Utility.h:15:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/clustalw.h:44:
ClustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/tree/UPGMA/RootedGuideTree.cpp -o ClustalW/tree/UPGMA/RootedGuideTree.o
In file included from ClustalW/tree/UPGMA/RootedGuideTree.cpp:10:
In file included from ClustalW/tree/UPGMA/RootedGuideTree.h:17:
In file included from ClustalW/tree/UPGMA/../../alignment/Alignment.h:41:
In file included from ClustalW/tree/UPGMA/../../alignment/Sequence.h:21:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/userparams.h:8:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/UserParameters.h:22:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/utils.h:8:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/Utility.h:15:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/clustalw.h:44:
ClustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/tree/UPGMA/RootedTreeOutput.cpp -o ClustalW/tree/UPGMA/RootedTreeOutput.o
In file included from ClustalW/tree/UPGMA/RootedTreeOutput.cpp:9:
In file included from ClustalW/tree/UPGMA/RootedTreeOutput.h:15:
In file included from ClustalW/tree/UPGMA/RootedGuideTree.h:17:
In file included from ClustalW/tree/UPGMA/../../alignment/Alignment.h:41:
In file included from ClustalW/tree/UPGMA/../../alignment/Sequence.h:21:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/userparams.h:8:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/UserParameters.h:22:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/utils.h:8:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/Utility.h:15:
In file included from ClustalW/tree/UPGMA/../../alignment/../general/clustalw.h:44:
ClustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ClustalW/tree/UPGMA/UPGMAAlgorithm.cpp -o ClustalW/tree/UPGMA/UPGMAAlgorithm.o
In file included from ClustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4:
In file included from ClustalW/tree/UPGMA/UPGMAAlgorithm.h:6:
In file included from ClustalW/tree/UPGMA/../../general/clustalw.h:44:
ClustalW/tree/UPGMA/../../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/aligngivenpath.cpp -o Muscle/aligngivenpath.o
In file included from Muscle/aligngivenpath.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
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: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;
                                       ^
Muscle/aligngivenpath.cpp:654:11: warning: variable 'uColIndexA' set but not used [-Wunused-but-set-variable]
        unsigned uColIndexA = 0;
                 ^
Muscle/aligngivenpath.cpp:655:11: warning: variable 'uColIndexB' set but not used [-Wunused-but-set-variable]
        unsigned uColIndexB = 0;
                 ^
In file included from Muscle/aligngivenpath.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
10 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/aligngivenpathsw.cpp -o Muscle/aligngivenpathsw.o
In file included from Muscle/aligngivenpathsw.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
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: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/aligngivenpathsw.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/aligntwomsas.cpp -o Muscle/aligntwomsas.o
In file included from Muscle/aligntwomsas.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/aligntwomsas.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/aligntwoprofs.cpp -o Muscle/aligntwoprofs.o
In file included from Muscle/aligntwoprofs.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/aligntwoprofs.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/aln.cpp -o Muscle/aln.o
In file included from Muscle/aln.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/aln.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/alpha.cpp -o Muscle/alpha.o
In file included from Muscle/alpha.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/alpha.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/anchors.cpp -o Muscle/anchors.o
In file included from Muscle/anchors.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/anchors.cpp:162:13: warning: unused variable 'uWindowCenter' [-Wunused-variable]
                        unsigned uWindowCenter = uBestColIndex + uWindowLength/2;
                                 ^
In file included from Muscle/anchors.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/anchors.cpp:53:13: warning: unused function 'FindBestColsGrade' [-Wunused-function]
static void FindBestColsGrade(const SCORE Score[], unsigned uCount,
            ^
Muscle/anchors.cpp:105:13: warning: unused function 'ListBestCols' [-Wunused-function]
static void ListBestCols(const MSA &msa, const SCORE Score[], const SCORE SmoothScore[],
            ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/bittraceback.cpp -o Muscle/bittraceback.o
In file included from Muscle/bittraceback.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/bittraceback.cpp:146:7: warning: unused variable 'Bits' [-Wunused-variable]
        char Bits = TraceBack[uLengthA][uLengthB];
             ^
In file included from Muscle/bittraceback.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/bittraceback.cpp:15:20: warning: unused function 'BitsToStr' [-Wunused-function]
static const char *BitsToStr(char Bits)
                   ^
4 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/blosum62.cpp -o Muscle/blosum62.o
In file included from Muscle/blosum62.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/blosum62.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/blosumla.cpp -o Muscle/blosumla.o
In file included from Muscle/blosumla.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/blosumla.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/blosumla.cpp:7:14: warning: unused variable 'Blosum62LA' [-Wunused-variable]
static float Blosum62LA[20][20] =
             ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/clust.cpp -o Muscle/clust.o
In file included from Muscle/clust.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/clust.cpp:186:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
        const unsigned uClusterCount = GetClusterCount();
                       ^
Muscle/clust.cpp:206:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
        const unsigned uClusterCount = GetClusterCount();
                       ^
Muscle/clust.cpp:365:14: warning: unused variable 'dDistLR' [-Wunused-variable]
        const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex);
                    ^
In file included from Muscle/clust.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/cluster.cpp -o Muscle/cluster.o
In file included from Muscle/cluster.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
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/cluster.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/cluster.cpp:10:21: warning: unused function 'Max' [-Wunused-function]
static inline float Max(float d1, float d2)
                    ^
Muscle/cluster.cpp:15:21: warning: unused function 'Mean' [-Wunused-function]
static inline float Mean(float d1, float d2)
                    ^
6 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/clwwt.cpp -o Muscle/clwwt.o
In file included from Muscle/clwwt.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/clwwt.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/color.cpp -o Muscle/color.o
In file included from Muscle/color.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/color.cpp:7:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        +4, -2, +0, -2, -1,  -2, +0, -2, -1, -1,  -1, -1, -2, -1, -1,  -1, +1, +0, +0, -3,  -1, -2, -1,  // A
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:8:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -2, +6, -3, +6, +2,  -3, -1, -1, -3, -1,  -4, -3, +1, -1, +0,  -2, +0, -1, -3, -4,  -1, -3, +2,  // B
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:9:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        +0, -3, +9, -3, -4,  -2, -3, -3, -1, -3,  -1, -1, -3, -3, -3,  -3, -1, -1, -1, -2,  -1, -2, -4,  // C
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:10:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -2, +6, -3, +6, +2,  -3, -1, -1, -3, -1,  -4, -3, +1, -1, +0,  -2, +0, -1, -3, -4,  -1, -3, +2,  // D
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:11:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -1, +2, -4, +2, +5,  -3, -2, +0, -3, +1,  -3, -2, +0, -1, +2,  +0, +0, -1, -2, -3,  -1, -2, +5,  // E
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:13:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -2, -3, -2, -3, -3,  +6, -3, -1, +0, -3,  +0, +0, -3, -4, -3,  -3, -2, -2, -1, +1,  -1, +3, -3,  // F
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:14:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        +0, -1, -3, -1, -2,  -3, +6, -2, -4, -2,  -4, -3, +0, -2, -2,  -2, +0, -2, -3, -2,  -1, -3, -2,  // G
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:15:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -2, -1, -3, -1, +0,  -1, -2, +8, -3, -1,  -3, -2, +1, -2, +0,  +0, -1, -2, -3, -2,  -1, +2, +0,  // H
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:16:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -1, -3, -1, -3, -3,  +0, -4, -3, +4, -3,  +2, +1, -3, -3, -3,  -3, -2, -1, +3, -3,  -1, -1, -3,  // I
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:17:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -1, -1, -3, -1, +1,  -3, -2, -1, -3, +5,  -2, -1, +0, -1, +1,  +2, +0, -1, -2, -3,  -1, -2, +1,  // K
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:19:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -1, -4, -1, -4, -3,  +0, -4, -3, +2, -2,  +4, +2, -3, -3, -2,  -2, -2, -1, +1, -2,  -1, -1, -3,  // L
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:20:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -1, -3, -1, -3, -2,  +0, -3, -2, +1, -1,  +2, +5, -2, -2, +0,  -1, -1, -1, +1, -1,  -1, -1, -2,  // M
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:21:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -2, +1, -3, +1, +0,  -3, +0, +1, -3, +0,  -3, -2, +6, -2, +0,  +0, +1, +0, -3, -4,  -1, -2, +0,  // N
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:22:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -1, -1, -3, -1, -1,  -4, -2, -2, -3, -1,  -3, -2, -2, +7, -1,  -2, -1, -1, -2, -4,  -1, -3, -1,  // P
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:23:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -1, +0, -3, +0, +2,  -3, -2, +0, -3, +1,  -2, +0, +0, -1, +5,  +1, +0, -1, -2, -2,  -1, -1, +2,  // Q
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:25:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -1, -2, -3, -2, +0,  -3, -2, +0, -3, +2,  -2, -1, +0, -2, +1,  +5, -1, -1, -3, -3,  -1, -2, +0,  // R
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:26:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        +1, +0, -1, +0, +0,  -2, +0, -1, -2, +0,  -2, -1, +1, -1, +0,  -1, +4, +1, -2, -3,  -1, -2, +0,  // S
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:27:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        +0, -1, -1, -1, -1,  -2, -2, -2, -1, -1,  -1, -1, +0, -1, -1,  -1, +1, +5, +0, -2,  -1, -2, -1,  // T
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:28:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        +0, -3, -1, -3, -2,  -1, -3, -3, +3, -2,  +1, +1, -3, -2, -2,  -3, -2, +0, +4, -3,  -1, -1, -2,  // V
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:29:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -3, -4, -2, -4, -3,  +1, -2, -2, -3, -3,  -2, -1, -4, -4, -2,  -3, -3, -2, -3,+11,  -1, +2, -3,  // W
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:31:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -1, -1, -1, -1, -1,  -1, -1, -1, -1, -1,  -1, -1, -1, -1, -1,  -1, -1, -1, -1, -1,  -1, -1, -1,  // X
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:32:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -2, -3, -2, -3, -2,  +3, -3, +2, -1, -2,  -1, -1, -2, -3, -1,  -2, -2, -2, -1, +2,  -1, +7, -2,  // Y
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:33:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        -1, +2, -4, +2, +5,  -3, -2, +0, -3, +1,  -3, -2, +0, -1, +2,  +0, +0, -1, -2, -3,  -1, -2, +5,  // Z
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
Muscle/color.cpp:126:11: warning: variable 'uCharCount' set but not used [-Wunused-but-set-variable]
        unsigned uCharCount = 0;
                 ^
In file included from Muscle/color.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/color.cpp:72:12: warning: unused function 'BlosumScore' [-Wunused-function]
static int BlosumScore(char c1, char c2)
           ^
27 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/cons.cpp -o Muscle/cons.o
In file included from Muscle/cons.cpp:7:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/cons.cpp:7:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/diaglist.cpp -o Muscle/diaglist.o
In file included from Muscle/diaglist.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/diaglist.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/diffobjscore.cpp -o Muscle/diffobjscore.o
In file included from Muscle/diffobjscore.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
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/diffobjscore.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
4 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/diffpaths.cpp -o Muscle/diffpaths.o
In file included from Muscle/diffpaths.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/diffpaths.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/difftrees.cpp -o Muscle/difftrees.o
In file included from Muscle/difftrees.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/difftrees.cpp:161:17: warning: unused variable 'uLeafCount2' [-Wunused-variable]
        const unsigned uLeafCount2 = Tree2.GetLeafCount();
                       ^
Muscle/difftrees.cpp:296:11: warning: variable 'uDiffCount' set but not used [-Wunused-but-set-variable]
        unsigned uDiffCount = 0;
                 ^
In file included from Muscle/difftrees.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
4 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/difftreese.cpp -o Muscle/difftreese.o
In file included from Muscle/difftreese.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/difftreese.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/distcalc.cpp -o Muscle/distcalc.o
In file included from Muscle/distcalc.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/distcalc.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/distfunc.cpp -o Muscle/distfunc.o
In file included from Muscle/distfunc.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/distfunc.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/distpwkimura.cpp -o Muscle/distpwkimura.o
In file included from Muscle/distpwkimura.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/distpwkimura.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/domuscle.cpp -o Muscle/domuscle.o
In file included from Muscle/domuscle.cpp:1:
In file included from ./RMuscle.h:4:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/domuscle.cpp:180:6: warning: unused variable 'PNlength' [-Wunused-variable]
        int PNlength = (msaInput->inputSeqs).Length();
            ^
In file included from Muscle/domuscle.cpp:1:
In file included from ./RMuscle.h:4:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/dosp.cpp -o Muscle/dosp.o
In file included from Muscle/dosp.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/dosp.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/dpreglist.cpp -o Muscle/dpreglist.o
In file included from Muscle/dpreglist.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/dpreglist.cpp:82:19: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable]
                        const unsigned uDiagLengthMinusCaps = uEndVertexA - uStartVertexA - 1;
                                       ^
In file included from Muscle/dpreglist.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/drawtree.cpp -o Muscle/drawtree.o
In file included from Muscle/drawtree.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/drawtree.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/edgelist.cpp -o Muscle/edgelist.o
In file included from Muscle/edgelist.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/edgelist.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/enumopts.cpp -o Muscle/enumopts.o
In file included from Muscle/enumopts.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:12:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(ALPHA, Amino)
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:190:1: note: expanded from here
"Amino"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:13:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(ALPHA, DNA)
^~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:193:1: note: expanded from here
"DNA"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:14:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(ALPHA, RNA)
^~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:196:1: note: expanded from here
"RNA"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:15:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(ALPHA)
^~~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^~~~
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:18:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQTYPE, Protein)
^~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:200:1: note: expanded from here
"Protein"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:19:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQTYPE, DNA)
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:203:1: note: expanded from here
"DNA"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:20:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQTYPE, RNA)
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:206:1: note: expanded from here
"RNA"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:21:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQTYPE, Auto)
^~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:209:1: note: expanded from here
"Auto"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:22:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(SEQTYPE)
^~~~~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^~~~
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:25:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(ROOT, Pseudo)
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:213:1: note: expanded from here
"Pseudo"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:26:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(ROOT, MidLongestSpan)
^~~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:216:1: note: expanded from here
"MidLongestSpan"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:27:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(ROOT, MinAvgLeafDist)
^~~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:219:1: note: expanded from here
"MinAvgLeafDist"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:28:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(ROOT)
^~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^~~~
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:31:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(CLUSTER, UPGMA)
^~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:223:1: note: expanded from here
"UPGMA"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:32:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(CLUSTER, UPGMAMax)
^~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:226:1: note: expanded from here
"UPGMAMax"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:33:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(CLUSTER, UPGMAMin)
^~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:229:1: note: expanded from here
"UPGMAMin"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:34:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(CLUSTER, UPGMB)
^~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:232:1: note: expanded from here
"UPGMB"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:35:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(CLUSTER, NeighborJoining)
^~~~~~~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:235:1: note: expanded from here
"NeighborJoining"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:36:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(CLUSTER)
^~~~~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^~~~
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:39:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(JOIN, NearestNeighbor)
^~~~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:239:1: note: expanded from here
"NearestNeighbor"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:40:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(JOIN, NeighborJoining)
^~~~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:242:1: note: expanded from here
"NeighborJoining"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:41:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(JOIN)
^~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^~~~
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:44:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(LINKAGE, Min)
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:246:1: note: expanded from here
"Min"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:45:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(LINKAGE, Avg)
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:249:1: note: expanded from here
"Avg"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:46:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(LINKAGE, Max)
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:252:1: note: expanded from here
"Max"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:47:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(LINKAGE, NeighborJoining)
^~~~~~~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:255:1: note: expanded from here
"NeighborJoining"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:48:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(LINKAGE, Biased)
^~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:258:1: note: expanded from here
"Biased"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:49:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(LINKAGE)
^~~~~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^~~~
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:52:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, Kmer6_6)
^~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:262:1: note: expanded from here
"Kmer6_6"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:53:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, Kmer20_3)
^~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:265:1: note: expanded from here
"Kmer20_3"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:54:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, Kmer20_4)
^~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:268:1: note: expanded from here
"Kmer20_4"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:55:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, Kbit20_3)
^~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:271:1: note: expanded from here
"Kbit20_3"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:56:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, Kmer4_6)
^~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:274:1: note: expanded from here
"Kmer4_6"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:57:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, PctIdKimura)
^~~~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:277:1: note: expanded from here
"PctIdKimura"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:58:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, PctIdLog)
^~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:280:1: note: expanded from here
"PctIdLog"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:59:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, PWKimura)
^~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:283:1: note: expanded from here
"PWKimura"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:60:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, PWScoreDist)
^~~~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:286:1: note: expanded from here
"PWScoreDist"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:61:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, ScoreDist)
^~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:289:1: note: expanded from here
"ScoreDist"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:62:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(DISTANCE, Edit)
^~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:292:1: note: expanded from here
"Edit"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:63:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(DISTANCE)
^~~~~~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^~~~
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:66:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(PPSCORE, LE)
^~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:296:1: note: expanded from here
"LE"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:67:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(PPSCORE, SP)
^~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:299:1: note: expanded from here
"SP"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:68:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(PPSCORE, SV)
^~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:302:1: note: expanded from here
"SV"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:69:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(PPSCORE, SPN)
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:305:1: note: expanded from here
"SPN"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:70:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(PPSCORE)
^~~~~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^~~~
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:73:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQWEIGHT, None)
^~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:309:1: note: expanded from here
"None"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:74:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQWEIGHT, Henikoff)
^~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:312:1: note: expanded from here
"Henikoff"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:75:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQWEIGHT, HenikoffPB)
^~~~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:315:1: note: expanded from here
"HenikoffPB"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:76:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQWEIGHT, GSC)
^~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:318:1: note: expanded from here
"GSC"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:77:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQWEIGHT, ClustalW)
^~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:321:1: note: expanded from here
"ClustalW"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:78:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(SEQWEIGHT, ThreeWay)
^~~~~~~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:324:1: note: expanded from here
"ThreeWay"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:79:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(SEQWEIGHT)
^~~~~~~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^~~~
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:82:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(OBJSCORE, SP)                         // Sum of Pairs of sequences
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:328:1: note: expanded from here
"SP"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:83:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(OBJSCORE, DP)                         // Dynamic Programming score
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:3:1: note: expanded from here
"DP"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:84:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(OBJSCORE, XP)                         // Cross Pairs = sum of pairs between two MSAs
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:6:1: note: expanded from here
"XP"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:85:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(OBJSCORE, PS)                         // sum of Prof-Seq score for all seqs in MSA
^~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:9:1: note: expanded from here
"PS"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:86:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(OBJSCORE, SPF)                        // sum of pairs, fast approximation
^~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:12:1: note: expanded from here
"SPF"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:87:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(OBJSCORE, SPM)                        // sp if <= 100 seqs, spf otherwise
^~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:15:1: note: expanded from here
"SPM"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:88:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(OBJSCORE)
^~~~~~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^~~~
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:91:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(TERMGAPS, Full)
^~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:19:1: note: expanded from here
"Full"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:92:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(TERMGAPS, Half)
^~~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:22:1: note: expanded from here
"Half"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:93:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
c(TERMGAPS, Ext)
^~~~~~~~~~~~~~~~
{
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
#define c(t, x)         #x, t##_##x,
                        ^~~~~~~~~~~
<scratch space>:25:1: note: expanded from here
"Ext"
^
In file included from Muscle/enumopts.cpp:8:
./Muscle/enums.h:94:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
e(TERMGAPS)
^~~~~~~~~~~
{
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
#define e(t)            0, 0 };
                        ^~~~
In file included from Muscle/enumopts.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
65 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/enumtostr.cpp -o Muscle/enumtostr.o
In file included from Muscle/enumtostr.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/enumtostr.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/estring.cpp -o Muscle/estring.o
In file included from Muscle/estring.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/estring.cpp:397:8: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        if (nB > 0)
                            ^~~~~~
Muscle/estring.cpp:409:11: note: uninitialized use occurs here
                switch (cType)
                        ^~~~~
Muscle/estring.cpp:397:4: note: remove the 'if' if its condition is always true
                        if (nB > 0)
                        ^~~~~~~~~~~
Muscle/estring.cpp:395:12: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                else if (nA < 0)
                         ^~~~~~
Muscle/estring.cpp:409:11: note: uninitialized use occurs here
                switch (cType)
                        ^~~~~
Muscle/estring.cpp:395:8: note: remove the 'if' if its condition is always true
                else if (nA < 0)
                     ^~~~~~~~~~~
Muscle/estring.cpp:386:13: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        else if (nB < 0)
                                 ^~~~~~
Muscle/estring.cpp:409:11: note: uninitialized use occurs here
                switch (cType)
                        ^~~~~
Muscle/estring.cpp:386:9: note: remove the 'if' if its condition is always true
                        else if (nB < 0)
                             ^~~~~~~~~~~
Muscle/estring.cpp:377:13: note: initialize the variable 'cType' to silence this warning
                char cType;
                          ^
                           = '\0'
In file included from Muscle/estring.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/estring.cpp:464:13: warning: unused function 'CanMultiplyEstrings' [-Wunused-function]
static bool CanMultiplyEstrings(const short es1[], const short es2[])
            ^
6 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/fasta.cpp -o Muscle/fasta.o
In file included from Muscle/fasta.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
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/fasta.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
4 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/fasta2.cpp -o Muscle/fasta2.o
In file included from Muscle/fasta2.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/fasta2.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/fastclust.cpp -o Muscle/fastclust.o
In file included from Muscle/fastclust.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/fastclust.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/fastdist.cpp -o Muscle/fastdist.o
In file included from Muscle/fastdist.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/fastdist.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/fastdistjones.cpp -o Muscle/fastdistjones.o
In file included from Muscle/fastdistjones.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/fastdistjones.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/fastdistkbit.cpp -o Muscle/fastdistkbit.o
In file included from Muscle/fastdistkbit.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/fastdistkbit.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/fastdistkmer.cpp -o Muscle/fastdistkmer.o
In file included from Muscle/fastdistkmer.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/fastdistkmer.cpp:235:11: warning: unused variable 'KD' [-Wunused-variable]
                        double KD = KimuraDist(EstimatedPctId);
                               ^
In file included from Muscle/fastdistkmer.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/fastdistmafft.cpp -o Muscle/fastdistmafft.o
In file included from Muscle/fastdistmafft.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/fastdistmafft.cpp:239:15: warning: unused variable 'pName1' [-Wunused-variable]
                const char *pName1 = s1.GetName();
                            ^
In file included from Muscle/fastdistmafft.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/fastdistmafft.cpp:104:13: warning: unused function 'ListCount' [-Wunused-function]
static void ListCount(const unsigned char Count[])
            ^
4 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/fastdistnuc.cpp -o Muscle/fastdistnuc.o
In file included from Muscle/fastdistnuc.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/fastdistnuc.cpp:223:15: warning: unused variable 'pName1' [-Wunused-variable]
                const char *pName1 = s1.GetName();
                            ^
In file included from Muscle/fastdistnuc.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/fastdistnuc.cpp:33:17: warning: unused variable 'uResidueGroupCount' [-Wunused-variable]
static unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]);
                ^
Muscle/fastdistnuc.cpp:85:13: warning: unused function 'ListCount' [-Wunused-function]
static void ListCount(const unsigned char Count[])
            ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/fastscorepath2.cpp -o Muscle/fastscorepath2.o
In file included from Muscle/fastscorepath2.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/fastscorepath2.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/finddiags.cpp -o Muscle/finddiags.o
In file included from Muscle/finddiags.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/finddiags.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/finddiags.cpp:11:14: warning: unused function 'TupleToStr' [-Wunused-function]
static char *TupleToStr(int t)
             ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/finddiagsn.cpp -o Muscle/finddiagsn.o
In file included from Muscle/finddiagsn.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/finddiagsn.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/finddiagsn.cpp:12:14: warning: unused function 'TupleToStr' [-Wunused-function]
static char *TupleToStr(int t)
             ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/glbalign.cpp -o Muscle/glbalign.o
In file included from Muscle/glbalign.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/glbalign.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/glbalign352.cpp -o Muscle/glbalign352.o
In file included from Muscle/glbalign352.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/glbalign352.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/glbaligndiag.cpp -o Muscle/glbaligndiag.o
In file included from Muscle/glbaligndiag.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/glbaligndiag.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/glbalignla.cpp -o Muscle/glbalignla.o
In file included from Muscle/glbalignla.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/glbalignla.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/glbalignle.cpp -o Muscle/glbalignle.o
In file included from Muscle/glbalignle.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/glbalignle.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/glbalignns.cpp -o Muscle/glbalignns.o
In file included from Muscle/glbalignns.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/glbalignns.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/glbalignsimple.cpp -o Muscle/glbalignsimple.o
In file included from Muscle/glbalignsimple.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/glbalignsimple.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/glbalignsimple.cpp:28:13: warning: unused function 'ListTB' [-Wunused-function]
static void ListTB(const char *TBM_, const ProfPos *PA, const ProfPos *PB,
            ^
Muscle/glbalignsimple.cpp:52:13: warning: unused function 'ListDP' [-Wunused-function]
static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
            ^
4 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/glbalignsp.cpp -o Muscle/glbalignsp.o
In file included from Muscle/glbalignsp.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/glbalignsp.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/glbalignspn.cpp -o Muscle/glbalignspn.o
In file included from Muscle/glbalignspn.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/glbalignspn.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/glbalignss.cpp -o Muscle/glbalignss.o
In file included from Muscle/glbalignss.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
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;
                       ^
In file included from Muscle/glbalignss.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/glbalignss.cpp:11:14: warning: unused function 'Subst' [-Wunused-function]
static SCORE Subst(const Seq &seqA, const Seq &seqB, unsigned i, unsigned j)
             ^
6 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/glbalndimer.cpp -o Muscle/glbalndimer.o
In file included from Muscle/glbalndimer.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/glbalndimer.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/glbalndimer.cpp:14:20: warning: unused function 'LocalScoreToStr' [-Wunused-function]
static const char *LocalScoreToStr(SCORE s)
                   ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/globals.cpp -o Muscle/globals.o
In file included from Muscle/globals.cpp:6:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/globals.cpp:6:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/globalslinux.cpp -o Muscle/globalslinux.o
In file included from Muscle/globalslinux.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/globalslinux.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/globalsosx.cpp -o Muscle/globalsosx.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/globalsother.cpp -o Muscle/globalsother.o
In file included from Muscle/globalsother.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/globalsother.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/globalswin32.cpp -o Muscle/globalswin32.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/gonnet.cpp -o Muscle/gonnet.o
In file included from Muscle/gonnet.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/gonnet.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/gonnet.cpp:137:14: warning: unused variable 'Gonnet160' [-Wunused-variable]
static SCORE Gonnet160[20][20] =
             ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/gotowt.cpp -o Muscle/gotowt.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/henikoffweight.cpp -o Muscle/henikoffweight.o
In file included from Muscle/henikoffweight.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/henikoffweight.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/henikoffweightpb.cpp -o Muscle/henikoffweightpb.o
In file included from Muscle/henikoffweightpb.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/henikoffweightpb.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/html.cpp -o Muscle/html.o
In file included from Muscle/html.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/html.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/hydro.cpp -o Muscle/hydro.o
In file included from Muscle/hydro.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/hydro.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/intmath.cpp -o Muscle/intmath.o
In file included from Muscle/intmath.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/intmath.cpp:304:12: warning: variable 'uNumberGreater' set but not used [-Wunused-but-set-variable]
                unsigned uNumberGreater = 0;
                         ^
Muscle/intmath.cpp:328:12: warning: variable 'uNumberGreater' set but not used [-Wunused-but-set-variable]
                unsigned uNumberGreater = 0;
                         ^
In file included from Muscle/intmath.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
4 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/local.cpp -o Muscle/local.o
In file included from Muscle/local.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/local.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/main.cpp -o Muscle/main.o
In file included from Muscle/main.cpp:3:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/main.cpp:3:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/makerootmsa.cpp -o Muscle/makerootmsa.o
In file included from Muscle/makerootmsa.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/makerootmsa.cpp:18:17: warning: unused variable 'uSeqLength' [-Wunused-variable]
        const unsigned uSeqLength = s.Length();
                       ^
Muscle/makerootmsa.cpp:94:17: warning: unused variable 'Path' [-Wunused-variable]
                const PWPath &Path = Nodes[uNodeIndex].m_Path;
                              ^
Muscle/makerootmsa.cpp:168:17: warning: unused variable 'uTreeNodeCount' [-Wunused-variable]
        const unsigned uTreeNodeCount = GuideTree.GetNodeCount();
                       ^
In file included from Muscle/makerootmsa.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/makerootmsa.cpp:12:13: warning: unused function 'PathSeq' [-Wunused-function]
static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut)
            ^
6 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/makerootmsab.cpp -o Muscle/makerootmsab.o
In file included from Muscle/makerootmsab.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/makerootmsab.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/maketree.cpp -o Muscle/maketree.o
In file included from Muscle/maketree.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/maketree.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/mhack.cpp -o Muscle/mhack.o
In file included from Muscle/mhack.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/mhack.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/mpam200.cpp -o Muscle/mpam200.o
In file included from Muscle/mpam200.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/mpam200.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/msa.cpp -o Muscle/msa.o
In file included from Muscle/msa.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/msa.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/msa.cpp:385:13: warning: unused function 'FmtChar' [-Wunused-function]
static void FmtChar(char c, unsigned uWidth)
            ^
Muscle/msa.cpp:392:13: warning: unused function 'FmtInt' [-Wunused-function]
static void FmtInt(unsigned u, unsigned uWidth)
            ^
Muscle/msa.cpp:407:13: warning: unused function 'FmtInt0' [-Wunused-function]
static void FmtInt0(unsigned u, unsigned uWidth)
            ^
Muscle/msa.cpp:419:13: warning: unused function 'FmtPad' [-Wunused-function]
static void FmtPad(unsigned n)
            ^
6 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/msa2.cpp -o Muscle/msa2.o
In file included from Muscle/msa2.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/msa2.cpp:479:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
        const unsigned uColCountCat = uColCount1 + uColCount2;
                       ^
In file included from Muscle/msa2.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/msadistkimura.cpp -o Muscle/msadistkimura.o
In file included from Muscle/msadistkimura.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/msadistkimura.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/msf.cpp -o Muscle/msf.o
In file included from Muscle/msf.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/msf.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/msf.cpp:24:20: warning: unused function 'strfind' [-Wunused-function]
static const char *strfind(const char *s, const char *t)
                   ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/muscle.cpp -o Muscle/muscle.o
In file included from Muscle/muscle.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/muscle.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/muscleout.cpp -o Muscle/muscleout.o
In file included from Muscle/muscleout.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/muscleout.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/nucmx.cpp -o Muscle/nucmx.o
In file included from Muscle/nucmx.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/nucmx.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/nwdasimple.cpp -o Muscle/nwdasimple.o
In file included from Muscle/nwdasimple.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/nwdasimple.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/nwdasimple2.cpp -o Muscle/nwdasimple2.o
In file included from Muscle/nwdasimple2.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/nwdasimple2.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/nwdasmall.cpp -o Muscle/nwdasmall.o
In file included from Muscle/nwdasmall.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/nwdasmall.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/nwrec.cpp -o Muscle/nwrec.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/nwsmall.cpp -o Muscle/nwsmall.o
In file included from Muscle/nwsmall.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/nwsmall.cpp:390:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
        default:
        ^~~~~~~
Muscle/nwsmall.cpp:394:14: note: uninitialized use occurs here
        TB[i][j] |= Bit;
                    ^~~
Muscle/nwsmall.cpp:378:10: note: initialize the variable 'Bit' to silence this warning
        char Bit;
                ^
                 = '\0'
Muscle/nwsmall.cpp:408:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
        default:
        ^~~~~~~
Muscle/nwsmall.cpp:412:14: note: uninitialized use occurs here
        TB[i][j] |= Bit;
                    ^~~
Muscle/nwsmall.cpp:399:10: note: initialize the variable 'Bit' to silence this warning
        char Bit;
                ^
                 = '\0'
Muscle/nwsmall.cpp:426:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
        default:
        ^~~~~~~
Muscle/nwsmall.cpp:430:14: note: uninitialized use occurs here
        TB[i][j] |= Bit;
                    ^~~
Muscle/nwsmall.cpp:417:10: note: initialize the variable 'Bit' to silence this warning
        char Bit;
                ^
                 = '\0'
In file included from Muscle/nwsmall.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/nwsmall.cpp:397:20: warning: unused function 'SetBitTBD' [-Wunused-function]
static inline void SetBitTBD(char **TB, unsigned i, unsigned j, char c)
                   ^
Muscle/nwsmall.cpp:415:20: warning: unused function 'SetBitTBI' [-Wunused-function]
static inline void SetBitTBI(char **TB, unsigned i, unsigned j, char c)
                   ^
7 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/objscore.cpp -o Muscle/objscore.o
In file included from Muscle/objscore.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/objscore.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/objscore2.cpp -o Muscle/objscore2.o
In file included from Muscle/objscore2.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/objscore2.cpp:65:8: warning: unused variable 'scoreGaps' [-Wunused-variable]
        SCORE scoreGaps = 0;
              ^
Muscle/objscore2.cpp:66:7: warning: unused variable 'bGapping1' [-Wunused-variable]
        bool bGapping1 = false;
             ^
Muscle/objscore2.cpp:67:7: warning: unused variable 'bGapping2' [-Wunused-variable]
        bool bGapping2 = false;
             ^
Muscle/objscore2.cpp:70:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
        bool bLeftTermGap = false;
             ^
Muscle/objscore2.cpp:85:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
        bool bRightTermGap = false;
             ^
Muscle/objscore2.cpp:143:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
        bool bLeftTermGap = false;
             ^
Muscle/objscore2.cpp:158:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
        bool bRightTermGap = false;
             ^
Muscle/objscore2.cpp:253:11: warning: variable 'uPairCount' set but not used [-Wunused-but-set-variable]
        unsigned uPairCount = 0;
                 ^
Muscle/objscore2.cpp:317:17: warning: unused variable 'uColCount2' [-Wunused-variable]
        const unsigned uColCount2 = msa2.GetColCount();
                       ^
Muscle/objscore2.cpp:496:17: warning: unused variable 'w' [-Wunused-variable]
                        const WEIGHT w = w1*w2;
                                     ^
In file included from Muscle/objscore2.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
12 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/objscoreda.cpp -o Muscle/objscoreda.o
In file included from Muscle/objscoreda.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/objscoreda.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/onexception.cpp -o Muscle/onexception.o
In file included from Muscle/onexception.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/onexception.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/options.cpp -o Muscle/options.o
In file included from Muscle/options.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/options.cpp:19:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "in",                           0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:20:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "in1",                          0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:21:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "in2",                          0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:22:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "out",                          0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:23:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "MaxIters",                     0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:24:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "MaxHours",                     0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:25:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "GapOpen",                      0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:26:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "GapOpen2",                     0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:27:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "GapExtend",            0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:28:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "GapExtend2",           0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:29:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "GapAmbig",                     0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:30:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Center",                       0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:31:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "SmoothScoreCeil",      0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:32:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "MinBestColScore",      0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:33:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "MinSmoothScore",       0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:34:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "ObjScore",                     0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:35:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "SmoothWindow",         0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:36:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "RefineWindow",         0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:37:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "FromWindow",           0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:38:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "ToWindow",                     0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:39:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "SaveWindow",           0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:40:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "WindowOffset",         0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:41:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "FirstWindow",          0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:42:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "AnchorSpacing",        0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:43:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Log",                          0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:44:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "LogA",                         0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:45:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "MaxTrees",                     0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:46:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "SUEFF",                        0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:47:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Distance",                     0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:48:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Distance1",            0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:49:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Distance2",            0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:50:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Weight",                       0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:51:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Weight1",                      0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:52:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Weight2",                      0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:53:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Cluster",                      0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:54:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Cluster1",                     0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:55:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Cluster2",                     0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:56:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Root1",                        0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:57:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Root2",                        0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:58:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Tree1",                        0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:59:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Tree2",                        0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:60:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "UseTree",                      0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:61:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "UseTree_NoWarn",       0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:62:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "DiagLength",           0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:63:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "DiagMargin",           0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:64:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "DiagBreak",            0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:65:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Hydro",                        0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:66:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "HydroFactor",          0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:67:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "SPScore",                      0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:68:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "SeqType",                      0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:69:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "MaxMB",                        0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:70:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "ComputeWeights",       0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:71:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "MaxSubFam",            0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:72:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "ScoreFile",            0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:73:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "TermGaps",                     0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:74:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "FASTAOut",                     0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:75:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "CLWOut",                       0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:76:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "CLWStrictOut",         0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~
        {                        }
Muscle/options.cpp:77:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "HTMLOut",                      0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:78:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "MSFOut",                       0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:79:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "PHYIOut",                      0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:80:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "PHYSOut",                      0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:81:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Matrix",                       0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:82:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "DistMx1",                      0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:83:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "DistMx2",                      0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:84:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Weight",                       0,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                }
Muscle/options.cpp:90:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "LE",                                   false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:91:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "SP",                                   false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:92:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "SV",                                   false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:93:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "SPN",                                  false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:94:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Core",                                 false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:95:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "NoCore",                               false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:96:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Diags1",                               false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:97:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Diags2",                               false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:98:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Diags",                                false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:99:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Quiet",                                false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:100:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "MSF",                                  false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:101:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Verbose",                              false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:102:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Anchors",                              false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:103:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "NoAnchors",                    false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                    }
Muscle/options.cpp:104:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Refine",                               false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:105:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "RefineW",                              false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:106:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "SW",                                   false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:107:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Profile",                              false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:108:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "PPScore",                              false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:109:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "ClusterOnly",                  false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                    }
Muscle/options.cpp:110:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Brenner",                              false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:111:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Dimer",                                false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:112:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "clw",                                  false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:113:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "clwstrict",                    false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                    }
Muscle/options.cpp:114:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "HTML",                                 false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:115:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Version",                              false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:116:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Stable",                               false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:117:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "Group",                                false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:118:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "FASTA",                                false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:119:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "ProfDB",                               false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:120:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "PAS",                                  false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:121:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "PHYI",                                 false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:122:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "PHYS",                                 false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:123:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "TomHydro",                             false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
Muscle/options.cpp:124:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        "MakeTree",                             false,
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                            }
In file included from Muscle/options.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
103 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/outweights.cpp -o Muscle/outweights.o
In file included from Muscle/outweights.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/outweights.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/pam200mafft.cpp -o Muscle/pam200mafft.o
In file included from Muscle/pam200mafft.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/pam200mafft.cpp:9:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   408,    20,    54,    52,  -182,   179,   -68,   109,   -35,   -47,    39,   106,   206,   -14,   -12,   257,   293,   191,  -306,  -219,     0,     0,     0, // A
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   {                                                                                                                                                            }
Muscle/pam200mafft.cpp:10:5: warning: suggest braces around initialization of subobject [-Wmissing-braces]
    20,  1190,  -228,  -295,    94,     6,    63,  -131,  -184,  -176,  -112,   -29,  -122,  -195,    49,   185,    13,   -49,   199,   333,     0,     0,     0, // C
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    {                                                                                                                                                           }
Muscle/pam200mafft.cpp:11:5: warning: suggest braces around initialization of subobject [-Wmissing-braces]
    54,  -228,   645,   516,  -399,   168,    98,  -225,    75,  -341,  -235,   352,  -149,   142,   -44,    65,     7,  -147,  -418,  -128,     0,     0,     0, // D
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    {                                                                                                                                                           }
Muscle/pam200mafft.cpp:12:5: warning: suggest braces around initialization of subobject [-Wmissing-braces]
    52,  -295,   516,   630,  -460,   145,    45,  -225,   195,  -307,  -222,   186,  -121,   299,    54,   -10,   -36,  -130,  -366,  -285,     0,     0,     0, // E
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    {                                                                                                                                                           }
Muscle/pam200mafft.cpp:13:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
  -182,    94,  -399,  -460,   908,  -387,    82,   100,  -423,   340,    87,  -216,  -160,  -274,  -307,   -31,  -153,    51,    19,   604,     0,     0,     0, // F
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  {                                                                                                                                                             }
Muscle/pam200mafft.cpp:14:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   179,     6,   168,   145,  -387,   682,   -94,  -196,   -14,  -304,  -226,    99,   -57,   -48,   117,   175,    41,   -73,   -38,  -329,     0,     0,     0, // G
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   {                                                                                                                                                            }
Muscle/pam200mafft.cpp:15:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   -68,    63,    98,    45,    82,   -94,   786,  -185,   164,   -72,  -132,   258,    86,   388,   277,    55,   -15,  -197,  -181,   488,     0,     0,     0, // H
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   {                                                                                                                                                            }
Muscle/pam200mafft.cpp:16:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   109,  -131,  -225,  -225,   100,  -196,  -185,   574,  -204,   308,   411,   -94,   -95,  -202,  -188,     1,   182,   489,  -254,  -133,     0,     0,     0, // I
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   {                                                                                                                                                            }
Muscle/pam200mafft.cpp:17:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   -35,  -184,    75,   195,  -423,   -14,   164,  -204,   652,  -229,   -98,   206,   -66,   335,   486,    22,    39,  -207,  -196,  -244,     0,     0,     0, // K
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   {                                                                                                                                                            }
Muscle/pam200mafft.cpp:18:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   -47,  -176,  -341,  -307,   340,  -304,   -72,   308,  -229,   611,   389,  -203,    73,   -66,  -150,   -49,   -21,   259,   -46,    -9,     0,     0,     0, // L
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   {                                                                                                                                                            }
Muscle/pam200mafft.cpp:19:5: warning: suggest braces around initialization of subobject [-Wmissing-braces]
    39,  -112,  -235,  -222,    87,  -226,  -132,   411,   -98,   389,   776,  -111,   -78,  -104,  -109,   -29,   149,   351,  -209,  -162,     0,     0,     0, // M
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    {                                                                                                                                                           }
Muscle/pam200mafft.cpp:20:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   106,   -29,   352,   186,  -216,    99,   258,   -94,   206,  -203,  -111,   536,    -1,   108,    93,   260,   188,   -98,  -359,    12,     0,     0,     0, // N
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   {                                                                                                                                                            }
Muscle/pam200mafft.cpp:21:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   206,  -122,  -149,  -121,  -160,   -57,    86,   -95,   -66,    73,   -78,    -1,   756,   142,    25,   241,   159,   -55,  -353,  -206,     0,     0,     0, // P
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   {                                                                                                                                                            }
Muscle/pam200mafft.cpp:22:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   -14,  -195,   142,   299,  -274,   -48,   388,  -202,   335,   -66,  -104,   108,   142,   655,   321,     7,   -15,  -175,  -223,   -53,     0,     0,     0, // Q
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   {                                                                                                                                                            }
Muscle/pam200mafft.cpp:23:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   -12,    49,   -44,    54,  -307,   117,   277,  -188,   486,  -150,  -109,    93,    25,   321,   626,    48,    16,  -181,   124,  -113,     0,     0,     0, // R
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   {                                                                                                                                                            }
Muscle/pam200mafft.cpp:24:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   257,   185,    65,   -10,   -31,   175,    55,     1,    22,   -49,   -29,   260,   241,     7,    48,   373,   279,    28,  -193,   -35,     0,     0,     0, // S
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   {                                                                                                                                                            }
Muscle/pam200mafft.cpp:25:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   293,    13,     7,   -36,  -153,    41,   -15,   182,    39,   -21,   149,   188,   159,   -15,    16,   279,   442,   163,  -323,  -170,     0,     0,     0, // T
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   {                                                                                                                                                            }
Muscle/pam200mafft.cpp:26:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
   191,   -49,  -147,  -130,    51,   -73,  -197,   489,  -207,   259,   351,   -98,   -55,  -175,  -181,    28,   163,   525,  -225,  -177,     0,     0,     0, // V
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   {                                                                                                                                                            }
Muscle/pam200mafft.cpp:27:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
  -306,   199,  -418,  -366,    19,   -38,  -181,  -254,  -196,   -46,  -209,  -359,  -353,  -223,   124,  -193,  -323,  -225,  1495,    83,     0,     0,     0, // W
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  {                                                                                                                                                             }
Muscle/pam200mafft.cpp:28:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
  -219,   333,  -128,  -285,   604,  -329,   488,  -133,  -244,    -9,  -162,    12,  -206,   -53,  -113,   -35,  -170,  -177,    83,   999,     0,     0,     0, // Y
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  {                                                                                                                                                             }
Muscle/pam200mafft.cpp:29:6: warning: suggest braces around initialization of subobject [-Wmissing-braces]
     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0, // B
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     {                                                                                                                                                          }
Muscle/pam200mafft.cpp:30:6: warning: suggest braces around initialization of subobject [-Wmissing-braces]
     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0, // Z
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     {                                                                                                                                                          }
Muscle/pam200mafft.cpp:31:6: warning: suggest braces around initialization of subobject [-Wmissing-braces]
     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0, // X
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     {                                                                                                                                                          }
In file included from Muscle/pam200mafft.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/pam200mafft.cpp:6:14: warning: unused variable 'PAM200' [-Wunused-variable]
static float PAM200[23][23] =
             ^
26 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/params.cpp -o Muscle/params.o
In file included from Muscle/params.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/params.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/phy.cpp -o Muscle/phy.o
In file included from Muscle/phy.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/phy.cpp:665:9: warning: unused variable 'dEdgeLength' [-Wunused-variable]
        double dEdgeLength = GetEdgeLength(uNode1, uNode2);
               ^
In file included from Muscle/phy.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/phy2.cpp -o Muscle/phy2.o
In file included from Muscle/phy2.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/phy2.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/phy3.cpp -o Muscle/phy3.o
In file included from Muscle/phy3.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/phy3.cpp:125:15: warning: unused variable 'dThisDist' [-Wunused-variable]
        const double dThisDist = tree.GetEdgeLength(uNode1, uNode2);
                     ^
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:263:11: warning: variable 'uMostDistantLeaf' set but not used [-Wunused-but-set-variable]
        unsigned uMostDistantLeaf = NULL_NEIGHBOR;
                 ^
In file included from Muscle/phy3.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/phy3.cpp:45:13: warning: unused function 'ListEIs' [-Wunused-function]
static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount)
            ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/phy4.cpp -o Muscle/phy4.o
In file included from Muscle/phy4.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/phy4.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/phyfromclust.cpp -o Muscle/phyfromclust.o
In file included from Muscle/phyfromclust.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/phyfromclust.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/phyfromfile.cpp -o Muscle/phyfromfile.o
In file included from Muscle/phyfromfile.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/phyfromfile.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/physeq.cpp -o Muscle/physeq.o
In file included from Muscle/physeq.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/physeq.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/phytofile.cpp -o Muscle/phytofile.o
In file included from Muscle/phytofile.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/phytofile.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/posgap.cpp -o Muscle/posgap.o
In file included from Muscle/posgap.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/posgap.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/ppscore.cpp -o Muscle/ppscore.o
In file included from Muscle/ppscore.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/ppscore.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/profdb.cpp -o Muscle/profdb.o
In file included from Muscle/profdb.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/profdb.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/profile.cpp -o Muscle/profile.o
In file included from Muscle/profile.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/profile.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/profilefrommsa.cpp -o Muscle/profilefrommsa.o
In file included from Muscle/profilefrommsa.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/profilefrommsa.cpp:248:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
        const unsigned uSeqCount = a.GetSeqCount();
                       ^
Muscle/profilefrommsa.cpp:256:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable]
        unsigned uHydrophobicRunLength = 0;
                 ^
In file included from Muscle/profilefrommsa.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/profilefrommsa.cpp:15:20: warning: unused function 'LocalScoreToStr' [-Wunused-function]
static const char *LocalScoreToStr(SCORE s)
                   ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/progalign.cpp -o Muscle/progalign.o
In file included from Muscle/progalign.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/progalign.cpp:41:17: warning: unused variable 'uIterCount' [-Wunused-variable]
        const unsigned uIterCount = uSeqCount - 1;
                       ^
In file included from Muscle/progalign.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/progress.cpp -o Muscle/progress.o
In file included from Muscle/progress.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/progress.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/progressivealign.cpp -o Muscle/progressivealign.o
In file included from Muscle/progressivealign.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/progressivealign.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/pwpath.cpp -o Muscle/pwpath.o
In file included from Muscle/pwpath.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/pwpath.cpp:80:16: warning: unused variable 'LastEdge' [-Wunused-variable]
        const PWEdge &LastEdge = GetEdge(uEdgeCount - 1);
                      ^
Muscle/pwpath.cpp:81:11: warning: variable 'uStartA' set but not used [-Wunused-but-set-variable]
        unsigned uStartA = FirstEdge.uPrefixLengthA;
                 ^
Muscle/pwpath.cpp:82:11: warning: variable 'uStartB' set but not used [-Wunused-but-set-variable]
        unsigned uStartB = FirstEdge.uPrefixLengthB;
                 ^
Muscle/pwpath.cpp:213:11: warning: unused variable 'uEdgeIndex' [-Wunused-variable]
        unsigned uEdgeIndex = 0;
                 ^
In file included from Muscle/pwpath.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
6 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/readmx.cpp -o Muscle/readmx.o
In file included from Muscle/readmx.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/readmx.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/readmx.cpp:30:17: warning: unused function 'MxCharToLetter' [-Wunused-function]
static unsigned MxCharToLetter(char c)
                ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/realigndiffs.cpp -o Muscle/realigndiffs.o
In file included from Muscle/realigndiffs.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/realigndiffs.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/realigndiffse.cpp -o Muscle/realigndiffse.o
In file included from Muscle/realigndiffse.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
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/realigndiffse.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
4 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/refine.cpp -o Muscle/refine.o
In file included from Muscle/refine.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/refine.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/refinehoriz.cpp -o Muscle/refinehoriz.o
In file included from Muscle/refinehoriz.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/refinehoriz.cpp:260:4: warning: variable 'bRight' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
                        default:
                        ^~~~~~~
Muscle/refinehoriz.cpp:263:56: note: uninitialized use occurs here
                        RefineHeightParts(msaIn, tree, Internals, bReverse, bRight,
                                                                            ^~~~~~
Muscle/refinehoriz.cpp:251:15: note: initialize the variable 'bRight' to silence this warning
                        bool bRight;
                                   ^
                                    = false
In file included from Muscle/refinehoriz.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/refinesubfams.cpp -o Muscle/refinesubfams.o
In file included from Muscle/refinesubfams.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/refinesubfams.cpp:63:17: warning: unused variable 'uNodeCount' [-Wunused-variable]
        const unsigned uNodeCount = tree.GetNodeCount();
                       ^
In file included from Muscle/refinesubfams.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/refinetree.cpp -o Muscle/refinetree.o
In file included from Muscle/refinetree.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/refinetree.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/refinetreee.cpp -o Muscle/refinetreee.o
In file included from Muscle/refinetreee.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/refinetreee.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/refinevert.cpp -o Muscle/refinevert.o
In file included from Muscle/refinevert.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/refinevert.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/refinew.cpp -o Muscle/refinew.o
In file included from Muscle/refinew.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/refinew.cpp:23:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
        const unsigned uColCountCat = uColCount1 + uColCount2;
                       ^
Muscle/refinew.cpp:128:13: warning: unused variable 'uOutCols' [-Wunused-variable]
                        unsigned uOutCols = msaOut.GetColCount();
                                 ^
In file included from Muscle/refinew.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
4 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/savebest.cpp -o Muscle/savebest.o
In file included from Muscle/savebest.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/savebest.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/scoredist.cpp -o Muscle/scoredist.o
In file included from Muscle/scoredist.cpp:3:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/scoredist.cpp:3:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/scoredist.cpp:17:21: warning: unused variable 'Dayhoff_CalibrationFactor' [-Wunused-const-variable]
static const double Dayhoff_CalibrationFactor = 1.3370;
                    ^
Muscle/scoredist.cpp:19:21: warning: unused variable 'MV_CalibrationFactor' [-Wunused-const-variable]
static const double MV_CalibrationFactor = 1.1775;
                    ^
4 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/scoregaps.cpp -o Muscle/scoregaps.o
In file included from Muscle/scoregaps.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/scoregaps.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/scoregaps.cpp:37:13: warning: unused function 'FreeGapInfo' [-Wunused-function]
static void FreeGapInfo(GAPINFO *GI)
            ^
Muscle/scoregaps.cpp:80:14: warning: unused function 'Penalty' [-Wunused-function]
static SCORE Penalty(unsigned Length, bool Term)
             ^
4 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/scorehistory.cpp -o Muscle/scorehistory.o
In file included from Muscle/scorehistory.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/scorehistory.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/scorepp.cpp -o Muscle/scorepp.o
In file included from Muscle/scorepp.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/scorepp.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/seq.cpp -o Muscle/seq.o
In file included from Muscle/seq.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/seq.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/seqvect.cpp -o Muscle/seqvect.o
In file included from Muscle/seqvect.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/seqvect.cpp:201:17: warning: binding dereferenced null pointer to reference has undefined behavior [-Wnull-dereference]
        return (Seq &) *((Seq *) 0);
                       ^~~~~~~~~~~~
In file included from Muscle/seqvect.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/seqvect.cpp:6:14: warning: unused variable 'MAX_FASTA_LINE' [-Wunused-const-variable]
const size_t MAX_FASTA_LINE = 16000;
             ^
4 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/setblosumweights.cpp -o Muscle/setblosumweights.o
In file included from Muscle/setblosumweights.cpp:42:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/setblosumweights.cpp:42:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/setgscweights.cpp -o Muscle/setgscweights.o
In file included from Muscle/setgscweights.cpp:104:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/setgscweights.cpp:104:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/setnewhandler.cpp -o Muscle/setnewhandler.o
In file included from Muscle/setnewhandler.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/setnewhandler.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/spfast.cpp -o Muscle/spfast.o
In file included from Muscle/spfast.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/spfast.cpp:252:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
        const unsigned uSeqCount = msa.GetSeqCount();
                       ^
In file included from Muscle/spfast.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/spfast.cpp:14:20: warning: unused function 'GapTypeToStr' [-Wunused-function]
static const char *GapTypeToStr(int GapType)
                   ^
Muscle/spfast.cpp:59:14: warning: unused function 'SPColBrute' [-Wunused-function]
static SCORE SPColBrute(const MSA &msa, unsigned uColIndex)
             ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/sptest.cpp -o Muscle/sptest.o
In file included from Muscle/sptest.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/sptest.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/stabilize.cpp -o Muscle/stabilize.o
In file included from Muscle/stabilize.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/stabilize.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/subfam.cpp -o Muscle/subfam.o
In file included from Muscle/subfam.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/subfam.cpp:173:6: warning: unused variable 'NotUsed' [-Wunused-variable]
        int NotUsed = system(CmdLine);
            ^
In file included from Muscle/subfam.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/subfams.cpp -o Muscle/subfams.o
In file included from Muscle/subfams.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/subfams.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/subfams.cpp:10:13: warning: unused function 'GetMostDistantPair' [-Wunused-function]
static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2)
            ^
Muscle/subfams.cpp:40:13: warning: unused function 'InitializeSingleSource' [-Wunused-function]
static void InitializeSingleSource(DistFunc &DF, unsigned uIndex)
            ^
Muscle/subfams.cpp:52:13: warning: unused function 'Relax' [-Wunused-function]
static void Relax(DistFunc &DF, unsigned u, unsigned v)
            ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/sw.cpp -o Muscle/sw.o
In file included from Muscle/sw.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/sw.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/sw.cpp:20:13: warning: unused function 'ListDP' [-Wunused-function]
static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
            ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/termgaps.cpp -o Muscle/termgaps.o
In file included from Muscle/termgaps.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/termgaps.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/textfile.cpp -o Muscle/textfile.o
In file included from Muscle/textfile.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/textfile.cpp:107:6: warning: unused variable 'i' [-Wunused-variable]
        int i = fputc(c, m_ptrFile);
            ^
Muscle/textfile.cpp:120:6: warning: unused variable 'iError' [-Wunused-variable]
        int iError = fputs(szLine, m_ptrFile);
            ^
In file included from Muscle/textfile.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
4 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/threewaywt.cpp -o Muscle/threewaywt.o
In file included from Muscle/threewaywt.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/threewaywt.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/tomhydro.cpp -o Muscle/tomhydro.o
In file included from Muscle/tomhydro.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/tomhydro.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/traceback.cpp -o Muscle/traceback.o
In file included from Muscle/traceback.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/traceback.cpp:21:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
        const unsigned uPrefixCountB = uLengthB + 1;
                       ^
Muscle/traceback.cpp:195:3: warning: variable 'cPrevEdgeType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
                default:
                ^~~~~~~
Muscle/traceback.cpp:202:15: note: uninitialized use occurs here
                cEdgeType = cPrevEdgeType;
                            ^~~~~~~~~~~~~
Muscle/traceback.cpp:186:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        else if (EQ(Score, scoreSI))
                                 ^~~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b)        (fabs(a-b) < 0.1)
                        ^~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:202:15: note: uninitialized use occurs here
                cEdgeType = cPrevEdgeType;
                            ^~~~~~~~~~~~~
Muscle/traceback.cpp:186:9: note: remove the 'if' if its condition is always true
                        else if (EQ(Score, scoreSI))
                             ^~~~~~~~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:150:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        else if (EQ(Score, scoreSD))
                                 ^~~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b)        (fabs(a-b) < 0.1)
                        ^~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:202:15: note: uninitialized use occurs here
                cEdgeType = cPrevEdgeType;
                            ^~~~~~~~~~~~~
Muscle/traceback.cpp:150:9: note: remove the 'if' if its condition is always true
                        else if (EQ(Score, scoreSD))
                             ^~~~~~~~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:112:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        else if (EQ(scoreSM, Score))
                                 ^~~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b)        (fabs(a-b) < 0.1)
                        ^~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:202:15: note: uninitialized use occurs here
                cEdgeType = cPrevEdgeType;
                            ^~~~~~~~~~~~~
Muscle/traceback.cpp:112:9: note: remove the 'if' if its condition is always true
                        else if (EQ(scoreSM, Score))
                             ^~~~~~~~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:68:21: note: initialize the variable 'cPrevEdgeType' to silence this warning
                char cPrevEdgeType;
                                  ^
                                   = '\0'
In file included from Muscle/traceback.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
7 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/tracebackopt.cpp -o Muscle/tracebackopt.o
In file included from Muscle/tracebackopt.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/tracebackopt.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/tracebacksw.cpp -o Muscle/tracebacksw.o
In file included from Muscle/tracebacksw.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
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);
              ^
Muscle/tracebacksw.cpp:175:3: warning: variable 'cPrevEdgeType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
                default:
                ^~~~~~~
Muscle/tracebacksw.cpp:182:15: note: uninitialized use occurs here
                cEdgeType = cPrevEdgeType;
                            ^~~~~~~~~~~~~
Muscle/tracebacksw.cpp:166:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        else if (EQ(Score, scoreSI))
                                 ^~~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b)        (fabs(a-b) < 0.1)
                        ^~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:182:15: note: uninitialized use occurs here
                cEdgeType = cPrevEdgeType;
                            ^~~~~~~~~~~~~
Muscle/tracebacksw.cpp:166:9: note: remove the 'if' if its condition is always true
                        else if (EQ(Score, scoreSI))
                             ^~~~~~~~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:130:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        else if (EQ(Score, scoreSD))
                                 ^~~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b)        (fabs(a-b) < 0.1)
                        ^~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:182:15: note: uninitialized use occurs here
                cEdgeType = cPrevEdgeType;
                            ^~~~~~~~~~~~~
Muscle/tracebacksw.cpp:130:9: note: remove the 'if' if its condition is always true
                        else if (EQ(Score, scoreSD))
                             ^~~~~~~~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:92:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        else if (EQ(scoreMatch, Score))
                                 ^~~~~~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b)        (fabs(a-b) < 0.1)
                        ^~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:182:15: note: uninitialized use occurs here
                cEdgeType = cPrevEdgeType;
                            ^~~~~~~~~~~~~
Muscle/tracebacksw.cpp:92:9: note: remove the 'if' if its condition is always true
                        else if (EQ(scoreMatch, Score))
                             ^~~~~~~~~~~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:43:21: note: initialize the variable 'cPrevEdgeType' to silence this warning
                char cPrevEdgeType;
                                  ^
                                   = '\0'
In file included from Muscle/tracebacksw.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/treefrommsa.cpp -o Muscle/treefrommsa.o
In file included from Muscle/treefrommsa.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/treefrommsa.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/typetostr.cpp -o Muscle/typetostr.o
In file included from Muscle/typetostr.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/typetostr.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/upgma2.cpp -o Muscle/upgma2.o
In file included from Muscle/upgma2.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/upgma2.cpp:272:4: warning: variable 'dtNewDist' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
                        default:
                        ^~~~~~~
Muscle/upgma2.cpp:292:17: note: uninitialized use occurs here
                        g_Dist[vL] = dtNewDist;
                                     ^~~~~~~~~
Muscle/upgma2.cpp:252:20: note: initialize the variable 'dtNewDist' to silence this warning
                        dist_t dtNewDist;
                                        ^
                                         = 0.0
Muscle/upgma2.cpp:366:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                        0,  2, 14, 14, 20,
                        ^~~~~~~~~~~~~~~~~
                        {                }
Muscle/upgma2.cpp:367:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                        2,  0, 14, 14, 20,
                        ^~~~~~~~~~~~~~~~~
                        {                }
Muscle/upgma2.cpp:368:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                        14, 14,  0,  4, 20,
                        ^~~~~~~~~~~~~~~~~~
                        {                 }
Muscle/upgma2.cpp:369:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                        14, 14,  4,  0, 20,
                        ^~~~~~~~~~~~~~~~~~
                        {                 }
Muscle/upgma2.cpp:370:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                        20, 20, 20, 20,  0,
                        ^~~~~~~~~~~~~~~~~~
                        {                 }
In file included from Muscle/upgma2.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
Muscle/upgma2.cpp:68:13: warning: unused function 'ListState' [-Wunused-function]
static void ListState()
            ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/usage.cpp -o Muscle/usage.o
In file included from Muscle/usage.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/usage.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/validateids.cpp -o Muscle/validateids.o
In file included from Muscle/validateids.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/validateids.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/vtml2.cpp -o Muscle/vtml2.o
In file included from Muscle/vtml2.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from Muscle/vtml2.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c Muscle/writescorefile.cpp -o Muscle/writescorefile.o
In file included from Muscle/writescorefile.cpp:1:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
Muscle/writescorefile.cpp:37:4: warning: variable 'Score' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
                        default:
                        ^~~~~~~
Muscle/writescorefile.cpp:40:12: note: uninitialized use occurs here
                        dSum += Score;
                                ^~~~~
Muscle/writescorefile.cpp:27:16: note: initialize the variable 'Score' to silence this warning
                        double Score;
                                    ^
                                     = 0.0
In file included from Muscle/writescorefile.cpp:1:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c RClustalW.cpp -o RClustalW.o
In file included from RClustalW.cpp:2:
In file included from ./RClustalWMain.h:6:
In file included from ./ClustalW/general/clustalw.h:44:
./ClustalW/general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c RClustalWMain.cpp -o RClustalWMain.o
In file included from RClustalWMain.cpp:5:
In file included from ./ClustalW/alignment/Alignment.h:41:
In file included from ./ClustalW/alignment/Sequence.h:21:
In file included from ./ClustalW/alignment/../general/userparams.h:8:
In file included from ./ClustalW/alignment/../general/UserParameters.h:22:
In file included from ./ClustalW/alignment/../general/utils.h:8:
In file included from ./ClustalW/alignment/../general/Utility.h:15:
In file included from ./ClustalW/alignment/../general/clustalw.h:44:
./ClustalW/alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
        int firstSeq, numSeqsInSub;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c RMuscle.cpp -o RMuscle.o
In file included from RMuscle.cpp:1:
In file included from ./RMuscle.h:4:
./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from RMuscle.cpp:1:
In file included from ./RMuscle.h:4:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ushuffle.c -o ushuffle.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC  -falign-functions=64 -Wall -g -O2   -c ushuffler.cpp -o ushuffler.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o enhancerHomologSearch.so ClustalW/alignment/Alignment.o ClustalW/alignment/AlignmentOutput.o ClustalW/alignment/ObjectiveScore.o ClustalW/alignment/Sequence.o ClustalW/Clustal.o ClustalW/fileInput/ClustalFileParser.o ClustalW/fileInput/EMBLFileParser.o ClustalW/fileInput/FileParser.o ClustalW/fileInput/FileReader.o ClustalW/fileInput/GDEFileParser.o ClustalW/fileInput/InFileStream.o ClustalW/fileInput/MSFFileParser.o ClustalW/fileInput/PearsonFileParser.o ClustalW/fileInput/PIRFileParser.o ClustalW/fileInput/RSFFileParser.o ClustalW/general/ClustalWResources.o ClustalW/general/DebugLog.o ClustalW/general/InvalidCombination.o ClustalW/general/OutputFile.o ClustalW/general/Stats.o ClustalW/general/SymMatrix.o ClustalW/general/UserParameters.o ClustalW/general/Utility.o ClustalW/general/VectorOutOfRange.o ClustalW/Help.o ClustalW/interface/CommandLineParser.o ClustalW/multipleAlign/Iteration.o ClustalW/multipleAlign/LowScoreSegProfile.o ClustalW/multipleAlign/MSA.o ClustalW/multipleAlign/MyersMillerProfileAlign.o ClustalW/multipleAlign/ProfileBase.o ClustalW/multipleAlign/ProfileStandard.o ClustalW/multipleAlign/ProfileWithSub.o ClustalW/pairwise/FastPairwiseAlign.o ClustalW/pairwise/FullPairwiseAlign.o ClustalW/substitutionMatrix/SubMatrix.o ClustalW/tree/AlignmentSteps.o ClustalW/tree/ClusterTree.o ClustalW/tree/ClusterTreeOutput.o ClustalW/tree/NJTree.o ClustalW/tree/RandomGenerator.o ClustalW/tree/Tree.o ClustalW/tree/TreeInterface.o ClustalW/tree/UnRootedClusterTree.o ClustalW/tree/UPGMA/Node.o ClustalW/tree/UPGMA/RootedClusterTree.o ClustalW/tree/UPGMA/RootedGuideTree.o ClustalW/tree/UPGMA/RootedTreeOutput.o ClustalW/tree/UPGMA/UPGMAAlgorithm.o Muscle/aligngivenpath.o Muscle/aligngivenpathsw.o Muscle/aligntwomsas.o Muscle/aligntwoprofs.o Muscle/aln.o Muscle/alpha.o Muscle/anchors.o Muscle/bittraceback.o Muscle/blosum62.o Muscle/blosumla.o Muscle/clust.o Muscle/cluster.o Muscle/clwwt.o Muscle/color.o Muscle/cons.o Muscle/diaglist.o Muscle/diffobjscore.o Muscle/diffpaths.o Muscle/difftrees.o Muscle/difftreese.o Muscle/distcalc.o Muscle/distfunc.o Muscle/distpwkimura.o Muscle/domuscle.o Muscle/dosp.o Muscle/dpreglist.o Muscle/drawtree.o Muscle/edgelist.o Muscle/enumopts.o Muscle/enumtostr.o Muscle/estring.o Muscle/fasta.o Muscle/fasta2.o Muscle/fastclust.o Muscle/fastdist.o Muscle/fastdistjones.o Muscle/fastdistkbit.o Muscle/fastdistkmer.o Muscle/fastdistmafft.o Muscle/fastdistnuc.o Muscle/fastscorepath2.o Muscle/finddiags.o Muscle/finddiagsn.o Muscle/glbalign.o Muscle/glbalign352.o Muscle/glbaligndiag.o Muscle/glbalignla.o Muscle/glbalignle.o Muscle/glbalignns.o Muscle/glbalignsimple.o Muscle/glbalignsp.o Muscle/glbalignspn.o Muscle/glbalignss.o Muscle/glbalndimer.o Muscle/globals.o Muscle/globalslinux.o Muscle/globalsosx.o Muscle/globalsother.o Muscle/globalswin32.o Muscle/gonnet.o Muscle/gotowt.o Muscle/henikoffweight.o Muscle/henikoffweightpb.o Muscle/html.o Muscle/hydro.o Muscle/intmath.o Muscle/local.o Muscle/main.o Muscle/makerootmsa.o Muscle/makerootmsab.o Muscle/maketree.o Muscle/mhack.o Muscle/mpam200.o Muscle/msa.o Muscle/msa2.o Muscle/msadistkimura.o Muscle/msf.o Muscle/muscle.o Muscle/muscleout.o Muscle/nucmx.o Muscle/nwdasimple.o Muscle/nwdasimple2.o Muscle/nwdasmall.o Muscle/nwrec.o Muscle/nwsmall.o Muscle/objscore.o Muscle/objscore2.o Muscle/objscoreda.o Muscle/onexception.o Muscle/options.o Muscle/outweights.o Muscle/pam200mafft.o Muscle/params.o Muscle/phy.o Muscle/phy2.o Muscle/phy3.o Muscle/phy4.o Muscle/phyfromclust.o Muscle/phyfromfile.o Muscle/physeq.o Muscle/phytofile.o Muscle/posgap.o Muscle/ppscore.o Muscle/profdb.o Muscle/profile.o Muscle/profilefrommsa.o Muscle/progalign.o Muscle/progress.o Muscle/progressivealign.o Muscle/pwpath.o Muscle/readmx.o Muscle/realigndiffs.o Muscle/realigndiffse.o Muscle/refine.o Muscle/refinehoriz.o Muscle/refinesubfams.o Muscle/refinetree.o Muscle/refinetreee.o Muscle/refinevert.o Muscle/refinew.o Muscle/savebest.o Muscle/scoredist.o Muscle/scoregaps.o Muscle/scorehistory.o Muscle/scorepp.o Muscle/seq.o Muscle/seqvect.o Muscle/setblosumweights.o Muscle/setgscweights.o Muscle/setnewhandler.o Muscle/spfast.o Muscle/sptest.o Muscle/stabilize.o Muscle/subfam.o Muscle/subfams.o Muscle/sw.o Muscle/termgaps.o Muscle/textfile.o Muscle/threewaywt.o Muscle/tomhydro.o Muscle/traceback.o Muscle/tracebackopt.o Muscle/tracebacksw.o Muscle/treefrommsa.o Muscle/typetostr.o Muscle/upgma2.o Muscle/usage.o Muscle/validateids.o Muscle/vtml2.o Muscle/writescorefile.o RClustalW.o RClustalWMain.o RcppExports.o RMuscle.o ushuffle.o ushuffler.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-enhancerHomologSearch/00new/enhancerHomologSearch/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (enhancerHomologSearch)