##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf enhancerHomologSearch.buildbin-libdir && mkdir enhancerHomologSearch.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh enhancerHomologSearch_1.17.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R enhancerHomologSearch.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=enhancerHomologSearch.buildbin-libdir enhancerHomologSearch_1.17.0.tar.gz'
>>>>>>>
* installing *source* package ‘enhancerHomologSearch’ ...
** this is package ‘enhancerHomologSearch’ version ‘1.17.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
819 | int counter2 = 2;
| ^
ClustalW/alignment/Alignment.cpp:1715:24: warning: unused variable 'posToAddTo' [-Wunused-variable]
1715 | 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]
292 | int firstSeq, numSeqsInSub;
| ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
2297 | 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]
292 | int firstSeq, numSeqsInSub;
| ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
38 | int n = (*input).inputSeqs.size();
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
421 | int maxAlnLength; // Get values from the Alignment object.
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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/../alignment/../general/UserParameters.h:22:
In file included from ClustalW/general/../alignment/../general/utils.h:8:
In file included from ClustalW/general/../alignment/../general/Utility.h:15:
In file included from ClustalW/general/../alignment/../general/clustalw.h:44:
ClustalW/general/../alignment/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
251 | 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]
292 | int firstSeq, numSeqsInSub;
| ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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/interface/../general/clustalw.h:44:
ClustalW/interface/../general/SymMatrix.h:292:13: warning: private field 'firstSeq' is not used [-Wunused-private-field]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
171 | 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]
292 | int firstSeq, numSeqsInSub;
| ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
340 | 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]
369 | int sum = 0, entries = 0;
| ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
292 | 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]
61 | int matrix[32][32];
| ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
229 | 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]
292 | int firstSeq, numSeqsInSub;
| ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
175 | short i, j, maxRes;
| ^
ClustalW/substitutionMatrix/SubMatrix.cpp:697:9: warning: variable 'av1' set but not used [-Wunused-but-set-variable]
697 | int av1, av2, av3, min, max;
| ^
ClustalW/substitutionMatrix/SubMatrix.cpp:1305:10: warning: unused variable 'inline1' [-Wunused-variable]
1305 | char inline1[1024];
| ^~~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp:1307:9: warning: unused variable 'nmat' [-Wunused-variable]
1307 | int nmat;
| ^~~~
ClustalW/substitutionMatrix/SubMatrix.cpp:1308:9: warning: unused variable 'n' [-Wunused-variable]
1308 | int n, llimit, ulimit;
| ^
ClustalW/substitutionMatrix/SubMatrix.cpp:1308:12: warning: unused variable 'llimit' [-Wunused-variable]
1308 | int n, llimit, ulimit;
| ^~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp:1308:20: warning: unused variable 'ulimit' [-Wunused-variable]
1308 | int n, llimit, ulimit;
| ^~~~~~
ClustalW/substitutionMatrix/SubMatrix.cpp:1845:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
1845 | int maxRes;
| ^
ClustalW/substitutionMatrix/SubMatrix.cpp:1905:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
1905 | int maxRes;
| ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
580 | int rs = 0, rl = 0;
| ^
ClustalW/tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable]
580 | int rs = 0, rl = 0;
| ^
ClustalW/tree/ClusterTree.cpp:967:22: warning: variable 'tempSeed' set but not used [-Wunused-but-set-variable]
967 | 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]
292 | int firstSeq, numSeqsInSub;
| ^
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/aligngivenpath.cpp:186:17: warning: unused variable 'uLengthA' [-Wunused-variable]
186 | const unsigned uLengthA = msaA.GetColCount();
| ^~~~~~~~
Muscle/aligngivenpath.cpp:187:17: warning: unused variable 'uLengthB' [-Wunused-variable]
187 | const unsigned uLengthB = msaB.GetColCount();
| ^~~~~~~~
Muscle/aligngivenpath.cpp:335:19: warning: unused variable 'uColA' [-Wunused-variable]
335 | const unsigned uColA = uPrefixLengthA - 1;
| ^~~~~
Muscle/aligngivenpath.cpp:336:19: warning: unused variable 'uColB' [-Wunused-variable]
336 | const unsigned uColB = uPrefixLengthB - 1;
| ^~~~~
Muscle/aligngivenpath.cpp:346:19: warning: unused variable 'uColA' [-Wunused-variable]
346 | const unsigned uColA = uPrefixLengthA - 1;
| ^~~~~
Muscle/aligngivenpath.cpp:354:19: warning: unused variable 'uColB' [-Wunused-variable]
354 | const unsigned uColB = uPrefixLengthB - 1;
| ^~~~~
Muscle/aligngivenpath.cpp:654:11: warning: variable 'uColIndexA' set but not used [-Wunused-but-set-variable]
654 | unsigned uColIndexA = 0;
| ^
Muscle/aligngivenpath.cpp:655:11: warning: variable 'uColIndexB' set but not used [-Wunused-but-set-variable]
655 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/aligngivenpathsw.cpp:58:17: warning: unused variable 'uLengthA' [-Wunused-variable]
58 | const unsigned uLengthA = msaA.GetColCount();
| ^~~~~~~~
Muscle/aligngivenpathsw.cpp:59:17: warning: unused variable 'uLengthB' [-Wunused-variable]
59 | const unsigned uLengthB = msaB.GetColCount();
| ^~~~~~~~
Muscle/aligngivenpathsw.cpp:204:19: warning: unused variable 'uColA' [-Wunused-variable]
204 | const unsigned uColA = uPrefixLengthA - 1;
| ^~~~~
Muscle/aligngivenpathsw.cpp:205:19: warning: unused variable 'uColB' [-Wunused-variable]
205 | const unsigned uColB = uPrefixLengthB - 1;
| ^~~~~
Muscle/aligngivenpathsw.cpp:215:19: warning: unused variable 'uColA' [-Wunused-variable]
215 | const unsigned uColA = uPrefixLengthA - 1;
| ^~~~~
Muscle/aligngivenpathsw.cpp:223:19: warning: unused variable 'uColB' [-Wunused-variable]
223 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
7 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/anchors.cpp:162:13: warning: unused variable 'uWindowCenter' [-Wunused-variable]
162 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/anchors.cpp:53:13: warning: unused function 'FindBestColsGrade' [-Wunused-function]
53 | static void FindBestColsGrade(const SCORE Score[], unsigned uCount,
| ^~~~~~~~~~~~~~~~~
Muscle/anchors.cpp:105:13: warning: unused function 'ListBestCols' [-Wunused-function]
105 | static void ListBestCols(const MSA &msa, const SCORE Score[], const SCORE SmoothScore[],
| ^~~~~~~~~~~~
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/bittraceback.cpp:146:7: warning: unused variable 'Bits' [-Wunused-variable]
146 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/bittraceback.cpp:15:20: warning: unused function 'BitsToStr' [-Wunused-function]
15 | static const char *BitsToStr(char Bits)
| ^~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/blosumla.cpp:7:14: warning: unused variable 'Blosum62LA' [-Wunused-variable]
7 | static float Blosum62LA[20][20] =
| ^~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/clust.cpp:186:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
186 | const unsigned uClusterCount = GetClusterCount();
| ^~~~~~~~~~~~~
Muscle/clust.cpp:206:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
206 | const unsigned uClusterCount = GetClusterCount();
| ^~~~~~~~~~~~~
Muscle/clust.cpp:365:14: warning: unused variable 'dDistLR' [-Wunused-variable]
365 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/cluster.cpp:284:8: warning: variable 'bFound' set but not used [-Wunused-but-set-variable]
284 | bool bFound = false;
| ^
Muscle/cluster.cpp:267:9: warning: unused variable 'dMaxDist' [-Wunused-variable]
267 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/cluster.cpp:10:21: warning: unused function 'Max' [-Wunused-function]
10 | static inline float Max(float d1, float d2)
| ^~~
Muscle/cluster.cpp:15:21: warning: unused function 'Mean' [-Wunused-function]
15 | static inline float Mean(float d1, float d2)
| ^~~~
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/color.cpp:7:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
7 | +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]
8 | -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]
9 | +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]
10 | -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]
11 | -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]
13 | -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]
14 | +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]
15 | -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]
16 | -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]
17 | -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]
19 | -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]
20 | -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]
21 | -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]
22 | -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]
23 | -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]
25 | -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]
26 | +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]
27 | +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]
28 | +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]
29 | -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]
31 | -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]
32 | -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]
33 | -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]
126 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/color.cpp:72:12: warning: unused function 'BlosumScore' [-Wunused-function]
72 | static int BlosumScore(char c1, char c2)
| ^~~~~~~~~~~
26 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/diffobjscore.cpp:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
76 | const unsigned uSeqCount = msa.GetSeqCount();
| ^~~~~~~~~
Muscle/diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable]
77 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/difftrees.cpp:161:17: warning: unused variable 'uLeafCount2' [-Wunused-variable]
161 | const unsigned uLeafCount2 = Tree2.GetLeafCount();
| ^~~~~~~~~~~
Muscle/difftrees.cpp:296:11: warning: variable 'uDiffCount' set but not used [-Wunused-but-set-variable]
296 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/domuscle.cpp:180:6: warning: unused variable 'PNlength' [-Wunused-variable]
180 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/dpreglist.cpp:82:19: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable]
82 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:8:
Muscle/enums.h:12:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
12 | c(ALPHA, Amino)
| ^~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:128:1: note: expanded from here
128 | "Amino"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:13:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
13 | c(ALPHA, DNA)
| ^~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:131:1: note: expanded from here
131 | "DNA"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:14:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
14 | c(ALPHA, RNA)
| ^~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:134:1: note: expanded from here
134 | "RNA"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:15:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
15 | e(ALPHA)
| ^~~~~~~~
| {
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
18 | c(SEQTYPE, Protein)
| ^~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:138:1: note: expanded from here
138 | "Protein"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:19:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
19 | c(SEQTYPE, DNA)
| ^~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:141:1: note: expanded from here
141 | "DNA"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:20:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
20 | c(SEQTYPE, RNA)
| ^~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:144:1: note: expanded from here
144 | "RNA"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:21:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
21 | c(SEQTYPE, Auto)
| ^~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:147:1: note: expanded from here
147 | "Auto"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:22:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
22 | e(SEQTYPE)
| ^~~~~~~~~~
| {
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
25 | c(ROOT, Pseudo)
| ^~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:151:1: note: expanded from here
151 | "Pseudo"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:26:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
26 | c(ROOT, MidLongestSpan)
| ^~~~~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:154:1: note: expanded from here
154 | "MidLongestSpan"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:27:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
27 | c(ROOT, MinAvgLeafDist)
| ^~~~~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:157:1: note: expanded from here
157 | "MinAvgLeafDist"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:28:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
28 | e(ROOT)
| ^~~~~~~
| {
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
31 | c(CLUSTER, UPGMA)
| ^~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:161:1: note: expanded from here
161 | "UPGMA"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:32:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
32 | c(CLUSTER, UPGMAMax)
| ^~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:164:1: note: expanded from here
164 | "UPGMAMax"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:33:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
33 | c(CLUSTER, UPGMAMin)
| ^~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:167:1: note: expanded from here
167 | "UPGMAMin"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:34:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
34 | c(CLUSTER, UPGMB)
| ^~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:170:1: note: expanded from here
170 | "UPGMB"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:35:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
35 | c(CLUSTER, NeighborJoining)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:173:1: note: expanded from here
173 | "NeighborJoining"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:36:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
36 | e(CLUSTER)
| ^~~~~~~~~~
| {
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
39 | c(JOIN, NearestNeighbor)
| ^~~~~~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:177:1: note: expanded from here
177 | "NearestNeighbor"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:40:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
40 | c(JOIN, NeighborJoining)
| ^~~~~~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:180:1: note: expanded from here
180 | "NeighborJoining"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:41:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
41 | e(JOIN)
| ^~~~~~~
| {
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
44 | c(LINKAGE, Min)
| ^~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:184:1: note: expanded from here
184 | "Min"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:45:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
45 | c(LINKAGE, Avg)
| ^~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:187:1: note: expanded from here
187 | "Avg"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:46:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
46 | c(LINKAGE, Max)
| ^~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:190:1: note: expanded from here
190 | "Max"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:47:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
47 | c(LINKAGE, NeighborJoining)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:193:1: note: expanded from here
193 | "NeighborJoining"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:48:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
48 | c(LINKAGE, Biased)
| ^~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:196:1: note: expanded from here
196 | "Biased"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:49:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
49 | e(LINKAGE)
| ^~~~~~~~~~
| {
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
52 | c(DISTANCE, Kmer6_6)
| ^~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:200:1: note: expanded from here
200 | "Kmer6_6"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:53:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
53 | c(DISTANCE, Kmer20_3)
| ^~~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:203:1: note: expanded from here
203 | "Kmer20_3"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:54:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
54 | c(DISTANCE, Kmer20_4)
| ^~~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:206:1: note: expanded from here
206 | "Kmer20_4"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:55:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
55 | c(DISTANCE, Kbit20_3)
| ^~~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:209:1: note: expanded from here
209 | "Kbit20_3"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:56:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
56 | c(DISTANCE, Kmer4_6)
| ^~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:212:1: note: expanded from here
212 | "Kmer4_6"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:57:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
57 | c(DISTANCE, PctIdKimura)
| ^~~~~~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:215:1: note: expanded from here
215 | "PctIdKimura"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:58:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
58 | c(DISTANCE, PctIdLog)
| ^~~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:218:1: note: expanded from here
218 | "PctIdLog"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:59:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
59 | c(DISTANCE, PWKimura)
| ^~~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:221:1: note: expanded from here
221 | "PWKimura"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:60:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
60 | c(DISTANCE, PWScoreDist)
| ^~~~~~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:224:1: note: expanded from here
224 | "PWScoreDist"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:61:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
61 | c(DISTANCE, ScoreDist)
| ^~~~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:227:1: note: expanded from here
227 | "ScoreDist"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:62:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
62 | c(DISTANCE, Edit)
| ^~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:230:1: note: expanded from here
230 | "Edit"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:63:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
63 | e(DISTANCE)
| ^~~~~~~~~~~
| {
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
66 | c(PPSCORE, LE)
| ^~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:234:1: note: expanded from here
234 | "LE"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:67:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
67 | c(PPSCORE, SP)
| ^~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:237:1: note: expanded from here
237 | "SP"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:68:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
68 | c(PPSCORE, SV)
| ^~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:240:1: note: expanded from here
240 | "SV"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:69:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
69 | c(PPSCORE, SPN)
| ^~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:243:1: note: expanded from here
243 | "SPN"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:70:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
70 | e(PPSCORE)
| ^~~~~~~~~~
| {
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
73 | c(SEQWEIGHT, None)
| ^~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:247:1: note: expanded from here
247 | "None"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:74:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
74 | c(SEQWEIGHT, Henikoff)
| ^~~~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:250:1: note: expanded from here
250 | "Henikoff"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:75:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
75 | c(SEQWEIGHT, HenikoffPB)
| ^~~~~~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:253:1: note: expanded from here
253 | "HenikoffPB"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:76:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
76 | c(SEQWEIGHT, GSC)
| ^~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:256:1: note: expanded from here
256 | "GSC"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:77:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
77 | c(SEQWEIGHT, ClustalW)
| ^~~~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:259:1: note: expanded from here
259 | "ClustalW"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:78:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
78 | c(SEQWEIGHT, ThreeWay)
| ^~~~~~~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:262:1: note: expanded from here
262 | "ThreeWay"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:79:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
79 | e(SEQWEIGHT)
| ^~~~~~~~~~~~
| {
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
82 | c(OBJSCORE, SP) // Sum of Pairs of sequences
| ^~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:266:1: note: expanded from here
266 | "SP"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:83:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
83 | c(OBJSCORE, DP) // Dynamic Programming score
| ^~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:269:1: note: expanded from here
269 | "DP"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:84:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
84 | c(OBJSCORE, XP) // Cross Pairs = sum of pairs between two MSAs
| ^~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:272:1: note: expanded from here
272 | "XP"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:85:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
85 | c(OBJSCORE, PS) // sum of Prof-Seq score for all seqs in MSA
| ^~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:275:1: note: expanded from here
275 | "PS"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:86:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
86 | c(OBJSCORE, SPF) // sum of pairs, fast approximation
| ^~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:278:1: note: expanded from here
278 | "SPF"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:87:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
87 | c(OBJSCORE, SPM) // sp if <= 100 seqs, spf otherwise
| ^~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:281:1: note: expanded from here
281 | "SPM"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:88:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
88 | e(OBJSCORE)
| ^~~~~~~~~~~
| {
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
91 | c(TERMGAPS, Full)
| ^~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:285:1: note: expanded from here
285 | "Full"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:92:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
92 | c(TERMGAPS, Half)
| ^~~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:288:1: note: expanded from here
288 | "Half"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:93:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
93 | c(TERMGAPS, Ext)
| ^~~~~~~~~~~~~~~~
| {
Muscle/enumopts.cpp:5:18: note: expanded from macro 'c'
5 | #define c(t, x) #x, t##_##x,
| ^~~~~~~~~~~
<scratch space>:291:1: note: expanded from here
291 | "Ext"
| ^
In file included from Muscle/enumopts.cpp:8:
Muscle/enums.h:94:1: warning: suggest braces around initialization of subobject [-Wmissing-braces]
94 | e(TERMGAPS)
| ^~~~~~~~~~~
| {
Muscle/enumopts.cpp:6:15: note: expanded from macro 'e'
6 | #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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
64 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/estring.cpp:397:8: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
397 | if (nB > 0)
| ^~~~~~
Muscle/estring.cpp:409:11: note: uninitialized use occurs here
409 | switch (cType)
| ^~~~~
Muscle/estring.cpp:397:4: note: remove the 'if' if its condition is always true
397 | if (nB > 0)
| ^~~~~~~~~~~
398 | {
399 | cType = 'I';
400 | ++nA;
401 | --nB;
402 | }
|
403 | else
| ~~~~
404 | assert(false);
| ~~~~~~~~~~~~~
Muscle/estring.cpp:395:12: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
395 | else if (nA < 0)
| ^~~~~~
Muscle/estring.cpp:409:11: note: uninitialized use occurs here
409 | switch (cType)
| ^~~~~
Muscle/estring.cpp:395:8: note: remove the 'if' if its condition is always true
395 | else if (nA < 0)
| ^~~~~~~~~~~
396 | {
397 | if (nB > 0)
398 | {
399 | cType = 'I';
400 | ++nA;
401 | --nB;
402 | }
403 | else
404 | assert(false);
405 | }
|
406 | else
| ~~~~
407 | assert(false);
| ~~~~~~~~~~~~~
Muscle/estring.cpp:386:13: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
386 | else if (nB < 0)
| ^~~~~~
Muscle/estring.cpp:409:11: note: uninitialized use occurs here
409 | switch (cType)
| ^~~~~
Muscle/estring.cpp:386:9: note: remove the 'if' if its condition is always true
386 | else if (nB < 0)
| ^~~~~~~~~~~
387 | {
388 | cType = 'D';
389 | --nA;
390 | ++nB;
391 | }
|
392 | else
| ~~~~
393 | assert(false);
| ~~~~~~~~~~~~~
Muscle/estring.cpp:377:13: note: initialize the variable 'cType' to silence this warning
377 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/estring.cpp:464:13: warning: unused function 'CanMultiplyEstrings' [-Wunused-function]
464 | static bool CanMultiplyEstrings(const short es1[], const short es2[])
| ^~~~~~~~~~~~~~~~~~~
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/fasta.cpp:15:11: warning: unused variable 'uSeqCount' [-Wunused-variable]
15 | unsigned uSeqCount = 0;
| ^~~~~~~~~
Muscle/fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable]
16 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/fastdistkmer.cpp:235:11: warning: unused variable 'KD' [-Wunused-variable]
235 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/fastdistmafft.cpp:239:15: warning: unused variable 'pName1' [-Wunused-variable]
239 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/fastdistmafft.cpp:104:13: warning: unused function 'ListCount' [-Wunused-function]
104 | static void ListCount(const unsigned char Count[])
| ^~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/fastdistnuc.cpp:223:15: warning: unused variable 'pName1' [-Wunused-variable]
223 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/fastdistnuc.cpp:33:17: warning: unused variable 'uResidueGroupCount' [-Wunused-variable]
33 | static unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]);
| ^~~~~~~~~~~~~~~~~~
Muscle/fastdistnuc.cpp:85:13: warning: unused function 'ListCount' [-Wunused-function]
85 | static void ListCount(const unsigned char Count[])
| ^~~~~~~~~
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/finddiags.cpp:11:14: warning: unused function 'TupleToStr' [-Wunused-function]
11 | static char *TupleToStr(int t)
| ^~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/finddiagsn.cpp:12:14: warning: unused function 'TupleToStr' [-Wunused-function]
12 | static char *TupleToStr(int t)
| ^~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/glbalignsimple.cpp:28:13: warning: unused function 'ListTB' [-Wunused-function]
28 | static void ListTB(const char *TBM_, const ProfPos *PA, const ProfPos *PB,
| ^~~~~~
Muscle/glbalignsimple.cpp:52:13: warning: unused function 'ListDP' [-Wunused-function]
52 | static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
| ^~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/glbalignss.cpp:177:16: warning: unused variable 'ptrRowA' [-Wunused-variable]
177 | const SCORE *ptrRowA = MxRowA[i];
| ^~~~~~~
Muscle/glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable]
119 | const unsigned uPrefixCountA = uLengthA + 1;
| ^~~~~~~~~~~~~
Muscle/glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
120 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/glbalignss.cpp:11:14: warning: unused function 'Subst' [-Wunused-function]
11 | static SCORE Subst(const Seq &seqA, const Seq &seqB, unsigned i, unsigned j)
| ^~~~~
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/glbalndimer.cpp:14:20: warning: unused function 'LocalScoreToStr' [-Wunused-function]
14 | static const char *LocalScoreToStr(SCORE s)
| ^~~~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/gonnet.cpp:137:14: warning: unused variable 'Gonnet160' [-Wunused-variable]
137 | static SCORE Gonnet160[20][20] =
| ^~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/intmath.cpp:304:12: warning: variable 'uNumberGreater' set but not used [-Wunused-but-set-variable]
304 | unsigned uNumberGreater = 0;
| ^
Muscle/intmath.cpp:328:12: warning: variable 'uNumberGreater' set but not used [-Wunused-but-set-variable]
328 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/makerootmsa.cpp:18:17: warning: unused variable 'uSeqLength' [-Wunused-variable]
18 | const unsigned uSeqLength = s.Length();
| ^~~~~~~~~~
Muscle/makerootmsa.cpp:94:17: warning: unused variable 'Path' [-Wunused-variable]
94 | const PWPath &Path = Nodes[uNodeIndex].m_Path;
| ^~~~
Muscle/makerootmsa.cpp:168:17: warning: unused variable 'uTreeNodeCount' [-Wunused-variable]
168 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/makerootmsa.cpp:12:13: warning: unused function 'PathSeq' [-Wunused-function]
12 | static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut)
| ^~~~~~~
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/msa.cpp:385:13: warning: unused function 'FmtChar' [-Wunused-function]
385 | static void FmtChar(char c, unsigned uWidth)
| ^~~~~~~
Muscle/msa.cpp:392:13: warning: unused function 'FmtInt' [-Wunused-function]
392 | static void FmtInt(unsigned u, unsigned uWidth)
| ^~~~~~
Muscle/msa.cpp:407:13: warning: unused function 'FmtInt0' [-Wunused-function]
407 | static void FmtInt0(unsigned u, unsigned uWidth)
| ^~~~~~~
Muscle/msa.cpp:419:13: warning: unused function 'FmtPad' [-Wunused-function]
419 | static void FmtPad(unsigned n)
| ^~~~~~
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/msa2.cpp:479:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
479 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/msf.cpp:24:20: warning: unused function 'strfind' [-Wunused-function]
24 | static const char *strfind(const char *s, const char *t)
| ^~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/nwsmall.cpp:390:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
390 | default:
| ^~~~~~~
Muscle/nwsmall.cpp:394:14: note: uninitialized use occurs here
394 | TB[i][j] |= Bit;
| ^~~
Muscle/nwsmall.cpp:378:10: note: initialize the variable 'Bit' to silence this warning
378 | char Bit;
| ^
| = '\0'
Muscle/nwsmall.cpp:408:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
408 | default:
| ^~~~~~~
Muscle/nwsmall.cpp:412:14: note: uninitialized use occurs here
412 | TB[i][j] |= Bit;
| ^~~
Muscle/nwsmall.cpp:399:10: note: initialize the variable 'Bit' to silence this warning
399 | char Bit;
| ^
| = '\0'
Muscle/nwsmall.cpp:426:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
426 | default:
| ^~~~~~~
Muscle/nwsmall.cpp:430:14: note: uninitialized use occurs here
430 | TB[i][j] |= Bit;
| ^~~
Muscle/nwsmall.cpp:417:10: note: initialize the variable 'Bit' to silence this warning
417 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/nwsmall.cpp:397:20: warning: unused function 'SetBitTBD' [-Wunused-function]
397 | static inline void SetBitTBD(char **TB, unsigned i, unsigned j, char c)
| ^~~~~~~~~
Muscle/nwsmall.cpp:415:20: warning: unused function 'SetBitTBI' [-Wunused-function]
415 | static inline void SetBitTBI(char **TB, unsigned i, unsigned j, char c)
| ^~~~~~~~~
6 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/objscore2.cpp:65:8: warning: unused variable 'scoreGaps' [-Wunused-variable]
65 | SCORE scoreGaps = 0;
| ^~~~~~~~~
Muscle/objscore2.cpp:66:7: warning: unused variable 'bGapping1' [-Wunused-variable]
66 | bool bGapping1 = false;
| ^~~~~~~~~
Muscle/objscore2.cpp:67:7: warning: unused variable 'bGapping2' [-Wunused-variable]
67 | bool bGapping2 = false;
| ^~~~~~~~~
Muscle/objscore2.cpp:70:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
70 | bool bLeftTermGap = false;
| ^
Muscle/objscore2.cpp:85:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
85 | bool bRightTermGap = false;
| ^
Muscle/objscore2.cpp:143:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
143 | bool bLeftTermGap = false;
| ^
Muscle/objscore2.cpp:158:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
158 | bool bRightTermGap = false;
| ^
Muscle/objscore2.cpp:253:11: warning: variable 'uPairCount' set but not used [-Wunused-but-set-variable]
253 | unsigned uPairCount = 0;
| ^
Muscle/objscore2.cpp:317:17: warning: unused variable 'uColCount2' [-Wunused-variable]
317 | const unsigned uColCount2 = msa2.GetColCount();
| ^~~~~~~~~~
Muscle/objscore2.cpp:496:17: warning: unused variable 'w' [-Wunused-variable]
496 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
11 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/options.cpp:19:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
19 | "in", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:20:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
20 | "in1", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:21:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
21 | "in2", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:22:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
22 | "out", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:23:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
23 | "MaxIters", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:24:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
24 | "MaxHours", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:25:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
25 | "GapOpen", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:26:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
26 | "GapOpen2", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:27:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
27 | "GapExtend", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:28:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
28 | "GapExtend2", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:29:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
29 | "GapAmbig", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:30:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
30 | "Center", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:31:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
31 | "SmoothScoreCeil", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:32:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
32 | "MinBestColScore", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:33:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
33 | "MinSmoothScore", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:34:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
34 | "ObjScore", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:35:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
35 | "SmoothWindow", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:36:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
36 | "RefineWindow", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:37:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
37 | "FromWindow", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:38:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
38 | "ToWindow", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:39:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
39 | "SaveWindow", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:40:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
40 | "WindowOffset", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:41:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
41 | "FirstWindow", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:42:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
42 | "AnchorSpacing", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:43:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
43 | "Log", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:44:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
44 | "LogA", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:45:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
45 | "MaxTrees", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:46:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
46 | "SUEFF", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:47:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
47 | "Distance", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:48:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
48 | "Distance1", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:49:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
49 | "Distance2", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:50:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
50 | "Weight", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:51:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
51 | "Weight1", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:52:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
52 | "Weight2", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:53:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
53 | "Cluster", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:54:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
54 | "Cluster1", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:55:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
55 | "Cluster2", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:56:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
56 | "Root1", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:57:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
57 | "Root2", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:58:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
58 | "Tree1", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:59:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
59 | "Tree2", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:60:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
60 | "UseTree", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:61:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
61 | "UseTree_NoWarn", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:62:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
62 | "DiagLength", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:63:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
63 | "DiagMargin", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:64:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
64 | "DiagBreak", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:65:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
65 | "Hydro", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:66:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
66 | "HydroFactor", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:67:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
67 | "SPScore", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:68:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
68 | "SeqType", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:69:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
69 | "MaxMB", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:70:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
70 | "ComputeWeights", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:71:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
71 | "MaxSubFam", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:72:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
72 | "ScoreFile", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:73:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
73 | "TermGaps", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:74:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
74 | "FASTAOut", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:75:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
75 | "CLWOut", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:76:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
76 | "CLWStrictOut", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:77:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
77 | "HTMLOut", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:78:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
78 | "MSFOut", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:79:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
79 | "PHYIOut", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:80:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
80 | "PHYSOut", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:81:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
81 | "Matrix", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:82:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
82 | "DistMx1", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:83:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
83 | "DistMx2", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:84:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
84 | "Weight", 0,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:90:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
90 | "LE", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:91:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
91 | "SP", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:92:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
92 | "SV", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:93:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
93 | "SPN", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:94:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
94 | "Core", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:95:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
95 | "NoCore", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:96:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
96 | "Diags1", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:97:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
97 | "Diags2", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:98:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
98 | "Diags", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:99:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
99 | "Quiet", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:100:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
100 | "MSF", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:101:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
101 | "Verbose", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:102:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
102 | "Anchors", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:103:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
103 | "NoAnchors", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:104:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
104 | "Refine", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:105:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
105 | "RefineW", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:106:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
106 | "SW", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:107:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
107 | "Profile", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:108:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
108 | "PPScore", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:109:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
109 | "ClusterOnly", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:110:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
110 | "Brenner", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:111:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
111 | "Dimer", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:112:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
112 | "clw", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:113:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
113 | "clwstrict", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:114:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
114 | "HTML", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:115:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
115 | "Version", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:116:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
116 | "Stable", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:117:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
117 | "Group", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:118:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
118 | "FASTA", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:119:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
119 | "ProfDB", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:120:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
120 | "PAS", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:121:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
121 | "PHYI", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:122:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
122 | "PHYS", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:123:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
123 | "TomHydro", false,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| { }
Muscle/options.cpp:124:2: warning: suggest braces around initialization of subobject [-Wmissing-braces]
124 | "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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
102 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/pam200mafft.cpp:9:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
9 | 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]
10 | 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]
11 | 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]
12 | 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]
13 | -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]
14 | 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]
15 | -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]
16 | 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]
17 | -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]
18 | -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]
19 | 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]
20 | 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]
21 | 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]
22 | -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]
23 | -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]
24 | 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]
25 | 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]
26 | 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]
27 | -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]
28 | -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]
29 | 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]
30 | 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]
31 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/pam200mafft.cpp:6:14: warning: unused variable 'PAM200' [-Wunused-variable]
6 | static float PAM200[23][23] =
| ^~~~~~
25 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/phy.cpp:665:9: warning: unused variable 'dEdgeLength' [-Wunused-variable]
665 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/phy3.cpp:125:15: warning: unused variable 'dThisDist' [-Wunused-variable]
125 | const double dThisDist = tree.GetEdgeLength(uNode1, uNode2);
| ^~~~~~~~~
Muscle/phy3.cpp:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable]
167 | const unsigned uLeafCount = tree.GetLeafCount();
| ^~~~~~~~~~
Muscle/phy3.cpp:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable]
190 | double dAllMaxDist = -1e20;
| ^~~~~~~~~~~
Muscle/phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable]
191 | unsigned uMaxFrom = NULL_NEIGHBOR;
| ^~~~~~~~
Muscle/phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable]
192 | unsigned uMaxTo = NULL_NEIGHBOR;
| ^~~~~~
Muscle/phy3.cpp:263:11: warning: variable 'uMostDistantLeaf' set but not used [-Wunused-but-set-variable]
263 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/phy3.cpp:45:13: warning: unused function 'ListEIs' [-Wunused-function]
45 | static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount)
| ^~~~~~~
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/profilefrommsa.cpp:248:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
248 | const unsigned uSeqCount = a.GetSeqCount();
| ^~~~~~~~~
Muscle/profilefrommsa.cpp:256:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable]
256 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/profilefrommsa.cpp:15:20: warning: unused function 'LocalScoreToStr' [-Wunused-function]
15 | static const char *LocalScoreToStr(SCORE s)
| ^~~~~~~~~~~~~~~
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/progalign.cpp:41:17: warning: unused variable 'uIterCount' [-Wunused-variable]
41 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/pwpath.cpp:80:16: warning: unused variable 'LastEdge' [-Wunused-variable]
80 | const PWEdge &LastEdge = GetEdge(uEdgeCount - 1);
| ^~~~~~~~
Muscle/pwpath.cpp:81:11: warning: variable 'uStartA' set but not used [-Wunused-but-set-variable]
81 | unsigned uStartA = FirstEdge.uPrefixLengthA;
| ^
Muscle/pwpath.cpp:82:11: warning: variable 'uStartB' set but not used [-Wunused-but-set-variable]
82 | unsigned uStartB = FirstEdge.uPrefixLengthB;
| ^
Muscle/pwpath.cpp:213:11: warning: unused variable 'uEdgeIndex' [-Wunused-variable]
213 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/readmx.cpp:30:17: warning: unused function 'MxCharToLetter' [-Wunused-function]
30 | static unsigned MxCharToLetter(char c)
| ^~~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/realigndiffse.cpp:77:13: warning: unused variable 'uNewRight' [-Wunused-variable]
77 | unsigned uNewRight = NewTree.GetRight(uNewNodeIndex);
| ^~~~~~~~~
Muscle/realigndiffse.cpp:80:13: warning: unused variable 'uOldRight' [-Wunused-variable]
80 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/refinehoriz.cpp:260:4: warning: variable 'bRight' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
260 | default:
| ^~~~~~~
Muscle/refinehoriz.cpp:263:56: note: uninitialized use occurs here
263 | RefineHeightParts(msaIn, tree, Internals, bReverse, bRight,
| ^~~~~~
Muscle/refinehoriz.cpp:251:15: note: initialize the variable 'bRight' to silence this warning
251 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/refinesubfams.cpp:63:17: warning: unused variable 'uNodeCount' [-Wunused-variable]
63 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/refinew.cpp:23:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
23 | const unsigned uColCountCat = uColCount1 + uColCount2;
| ^~~~~~~~~~~~
Muscle/refinew.cpp:128:13: warning: unused variable 'uOutCols' [-Wunused-variable]
128 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/scoredist.cpp:17:21: warning: unused variable 'Dayhoff_CalibrationFactor' [-Wunused-const-variable]
17 | static const double Dayhoff_CalibrationFactor = 1.3370;
| ^~~~~~~~~~~~~~~~~~~~~~~~~
Muscle/scoredist.cpp:19:21: warning: unused variable 'MV_CalibrationFactor' [-Wunused-const-variable]
19 | static const double MV_CalibrationFactor = 1.1775;
| ^~~~~~~~~~~~~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/scoregaps.cpp:37:13: warning: unused function 'FreeGapInfo' [-Wunused-function]
37 | static void FreeGapInfo(GAPINFO *GI)
| ^~~~~~~~~~~
Muscle/scoregaps.cpp:80:14: warning: unused function 'Penalty' [-Wunused-function]
80 | static SCORE Penalty(unsigned Length, bool Term)
| ^~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/seqvect.cpp:201:17: warning: binding dereferenced null pointer to reference has undefined behavior [-Wnull-dereference]
201 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/seqvect.cpp:6:14: warning: unused variable 'MAX_FASTA_LINE' [-Wunused-const-variable]
6 | const size_t MAX_FASTA_LINE = 16000;
| ^~~~~~~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/spfast.cpp:252:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
252 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/spfast.cpp:14:20: warning: unused function 'GapTypeToStr' [-Wunused-function]
14 | static const char *GapTypeToStr(int GapType)
| ^~~~~~~~~~~~
Muscle/spfast.cpp:59:14: warning: unused function 'SPColBrute' [-Wunused-function]
59 | static SCORE SPColBrute(const MSA &msa, unsigned uColIndex)
| ^~~~~~~~~~
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/subfam.cpp:173:6: warning: unused variable 'NotUsed' [-Wunused-variable]
173 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/subfams.cpp:10:13: warning: unused function 'GetMostDistantPair' [-Wunused-function]
10 | static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2)
| ^~~~~~~~~~~~~~~~~~
Muscle/subfams.cpp:40:13: warning: unused function 'InitializeSingleSource' [-Wunused-function]
40 | static void InitializeSingleSource(DistFunc &DF, unsigned uIndex)
| ^~~~~~~~~~~~~~~~~~~~~~
Muscle/subfams.cpp:52:13: warning: unused function 'Relax' [-Wunused-function]
52 | static void Relax(DistFunc &DF, unsigned u, unsigned v)
| ^~~~~
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/sw.cpp:20:13: warning: unused function 'ListDP' [-Wunused-function]
20 | static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
| ^~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/textfile.cpp:107:6: warning: unused variable 'i' [-Wunused-variable]
107 | int i = fputc(c, m_ptrFile);
| ^
Muscle/textfile.cpp:120:6: warning: unused variable 'iError' [-Wunused-variable]
120 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/traceback.cpp:21:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
21 | const unsigned uPrefixCountB = uLengthB + 1;
| ^~~~~~~~~~~~~
Muscle/traceback.cpp:195:3: warning: variable 'cPrevEdgeType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
195 | default:
| ^~~~~~~
Muscle/traceback.cpp:202:15: note: uninitialized use occurs here
202 | cEdgeType = cPrevEdgeType;
| ^~~~~~~~~~~~~
Muscle/traceback.cpp:186:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
186 | else if (EQ(Score, scoreSI))
| ^~~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:8:18: note: expanded from macro 'EQ'
8 | #define EQ(a, b) (fabs(a-b) < 0.1)
| ^~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:202:15: note: uninitialized use occurs here
202 | cEdgeType = cPrevEdgeType;
| ^~~~~~~~~~~~~
Muscle/traceback.cpp:186:9: note: remove the 'if' if its condition is always true
186 | else if (EQ(Score, scoreSI))
| ^~~~~~~~~~~~~~~~~~~~~~~
187 | cPrevEdgeType = 'S';
| ~
188 | else
| ~~~~
189 | Quit("TraceBack: failed to match I");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:150:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
150 | else if (EQ(Score, scoreSD))
| ^~~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:8:18: note: expanded from macro 'EQ'
8 | #define EQ(a, b) (fabs(a-b) < 0.1)
| ^~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:202:15: note: uninitialized use occurs here
202 | cEdgeType = cPrevEdgeType;
| ^~~~~~~~~~~~~
Muscle/traceback.cpp:150:9: note: remove the 'if' if its condition is always true
150 | else if (EQ(Score, scoreSD))
| ^~~~~~~~~~~~~~~~~~~~~~~
151 | cPrevEdgeType = 'S';
| ~
152 | else
| ~~~~
153 | Quit("TraceBack: failed to match D");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:112:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
112 | else if (EQ(scoreSM, Score))
| ^~~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:8:18: note: expanded from macro 'EQ'
8 | #define EQ(a, b) (fabs(a-b) < 0.1)
| ^~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:202:15: note: uninitialized use occurs here
202 | cEdgeType = cPrevEdgeType;
| ^~~~~~~~~~~~~
Muscle/traceback.cpp:112:9: note: remove the 'if' if its condition is always true
112 | else if (EQ(scoreSM, Score))
| ^~~~~~~~~~~~~~~~~~~~~~~
113 | cPrevEdgeType = 'S';
| ~
114 | else
| ~~~~
115 | Quit("TraceBack: failed to match M score=%g M=%g D=%g I=%g S=%g",
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
116 | Score, scoreMM, scoreDM, scoreIM, scoreSM);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Muscle/traceback.cpp:68:21: note: initialize the variable 'cPrevEdgeType' to silence this warning
68 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
6 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/tracebacksw.cpp:22:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
22 | const unsigned uPrefixCountB = uLengthB + 1;
| ^~~~~~~~~~~~~
Muscle/tracebacksw.cpp:29:8: warning: unused variable 'scoreMax' [-Wunused-variable]
29 | SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB);
| ^~~~~~~~
Muscle/tracebacksw.cpp:175:3: warning: variable 'cPrevEdgeType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
175 | default:
| ^~~~~~~
Muscle/tracebacksw.cpp:182:15: note: uninitialized use occurs here
182 | cEdgeType = cPrevEdgeType;
| ^~~~~~~~~~~~~
Muscle/tracebacksw.cpp:166:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
166 | else if (EQ(Score, scoreSI))
| ^~~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:8:18: note: expanded from macro 'EQ'
8 | #define EQ(a, b) (fabs(a-b) < 0.1)
| ^~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:182:15: note: uninitialized use occurs here
182 | cEdgeType = cPrevEdgeType;
| ^~~~~~~~~~~~~
Muscle/tracebacksw.cpp:166:9: note: remove the 'if' if its condition is always true
166 | else if (EQ(Score, scoreSI))
| ^~~~~~~~~~~~~~~~~~~~~~~
167 | cPrevEdgeType = 'S';
| ~
168 | else
| ~~~~
169 | Quit("TraceBack2: failed to match I");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:130:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
130 | else if (EQ(Score, scoreSD))
| ^~~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:8:18: note: expanded from macro 'EQ'
8 | #define EQ(a, b) (fabs(a-b) < 0.1)
| ^~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:182:15: note: uninitialized use occurs here
182 | cEdgeType = cPrevEdgeType;
| ^~~~~~~~~~~~~
Muscle/tracebacksw.cpp:130:9: note: remove the 'if' if its condition is always true
130 | else if (EQ(Score, scoreSD))
| ^~~~~~~~~~~~~~~~~~~~~~~
131 | cPrevEdgeType = 'S';
| ~
132 | else
| ~~~~
133 | Quit("TraceBack2: failed to match D");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:92:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
92 | else if (EQ(scoreMatch, Score))
| ^~~~~~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:8:18: note: expanded from macro 'EQ'
8 | #define EQ(a, b) (fabs(a-b) < 0.1)
| ^~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:182:15: note: uninitialized use occurs here
182 | cEdgeType = cPrevEdgeType;
| ^~~~~~~~~~~~~
Muscle/tracebacksw.cpp:92:9: note: remove the 'if' if its condition is always true
92 | else if (EQ(scoreMatch, Score))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
93 | cPrevEdgeType = 'S';
| ~
94 | else
| ~~~~
95 | Quit("TraceBack2: failed to match M score=%g M=%g D=%g I=%g S=%g",
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
96 | Score, scoreMM, scoreDM, scoreIM, scoreSM);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Muscle/tracebacksw.cpp:43:21: note: initialize the variable 'cPrevEdgeType' to silence this warning
43 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
7 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/upgma2.cpp:272:4: warning: variable 'dtNewDist' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
272 | default:
| ^~~~~~~
Muscle/upgma2.cpp:292:17: note: uninitialized use occurs here
292 | g_Dist[vL] = dtNewDist;
| ^~~~~~~~~
Muscle/upgma2.cpp:252:20: note: initialize the variable 'dtNewDist' to silence this warning
252 | dist_t dtNewDist;
| ^
| = 0.0
Muscle/upgma2.cpp:366:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
366 | 0, 2, 14, 14, 20,
| ^~~~~~~~~~~~~~~~~
| { }
Muscle/upgma2.cpp:367:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
367 | 2, 0, 14, 14, 20,
| ^~~~~~~~~~~~~~~~~
| { }
Muscle/upgma2.cpp:368:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
368 | 14, 14, 0, 4, 20,
| ^~~~~~~~~~~~~~~~~~
| { }
Muscle/upgma2.cpp:369:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
369 | 14, 14, 4, 0, 20,
| ^~~~~~~~~~~~~~~~~~
| { }
Muscle/upgma2.cpp:370:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
370 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
Muscle/upgma2.cpp:68:13: warning: unused function 'ListState' [-Wunused-function]
68 | static void ListState()
| ^~~~~~~~~
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from Muscle/muscle.h:37:
Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
Muscle/writescorefile.cpp:37:4: warning: variable 'Score' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
37 | default:
| ^~~~~~~
Muscle/writescorefile.cpp:40:12: note: uninitialized use occurs here
40 | dSum += Score;
| ^~~~~
Muscle/writescorefile.cpp:27:16: note: initialize the variable 'Score' to silence this warning
27 | 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]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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]
292 | int firstSeq, numSeqsInSub;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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:
In file included from ./Muscle/muscle.h:37:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
59 | static double ScoreToDouble(SCORE Score)
| ^~~~~~~~~~~~~
1 warning generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -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-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -lpthread -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.23-bioc/meat/enhancerHomologSearch.buildbin-libdir/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)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR enhancerHomologSearch.buildbin-libdir/enhancerHomologSearch/libs/enhancerHomologSearch.so
>>>>>>>
>>>>>>> Paths before fix:
enhancerHomologSearch.buildbin-libdir/enhancerHomologSearch/libs/enhancerHomologSearch.so:
enhancerHomologSearch.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib (compatibility version 4.6.0, current version 4.6.0)
/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1356.0.0)
/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 2000.67.0)
>>>>>>> Fix with install_name_tool:
ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib not found!
