############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL enhancerHomologSearch ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library’ * installing *source* package ‘enhancerHomologSearch’ ... ** using staged installation ** libs clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/alignment/Alignment.cpp -o ClustalW/alignment/Alignment.o 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:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ ClustalW/alignment/Alignment.cpp:1715:24: warning: unused variable 'posToAddTo' [-Wunused-variable] SeqArray::iterator posToAddTo = sectionToRealign.begin(); ^ In file included from ClustalW/alignment/Alignment.cpp:25: In file included from ClustalW/alignment/Alignment.h:41: In file included from ClustalW/alignment/Sequence.h:20: In file included from ClustalW/alignment/../substitutionMatrix/../general/userparams.h:8: In file included from ClustalW/alignment/../general/UserParameters.h:22: In file included from ClustalW/alignment/../substitutionMatrix/../general/utils.h:8: In file included from ClustalW/alignment/../general/Utility.h:15: In file included from ClustalW/alignment/../substitutionMatrix/../general/clustalw.h:44: ClustalW/alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/alignment/AlignmentOutput.cpp -o ClustalW/alignment/AlignmentOutput.o 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:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 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:20: In file included from ClustalW/alignment/../substitutionMatrix/../general/userparams.h:8: In file included from ClustalW/alignment/../general/UserParameters.h:22: In file included from ClustalW/alignment/../substitutionMatrix/../general/utils.h:8: In file included from ClustalW/alignment/../general/Utility.h:15: In file included from ClustalW/alignment/../substitutionMatrix/../general/clustalw.h:44: ClustalW/alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/alignment/ObjectiveScore.cpp -o ClustalW/alignment/ObjectiveScore.o In file included from ClustalW/alignment/ObjectiveScore.cpp:10: In file included from ClustalW/alignment/ObjectiveScore.h:14: In file included from ClustalW/alignment/../general/clustalw.h:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from ClustalW/alignment/ObjectiveScore.cpp:10: In file included from ClustalW/alignment/ObjectiveScore.h:14: In file included from ClustalW/alignment/../substitutionMatrix/../general/clustalw.h:44: ClustalW/alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ In file included from ClustalW/alignment/ObjectiveScore.cpp:10: ClustalW/alignment/ObjectiveScore.h:40:14: warning: private field 'scale' is not used [-Wunused-private-field] long scale; ^ ClustalW/alignment/ObjectiveScore.h:41:13: warning: private field 'weightScale' is not used [-Wunused-private-field] int weightScale; ^ ClustalW/alignment/ObjectiveScore.h:42:13: warning: private field 'sagaGapEx' is not used [-Wunused-private-field] int sagaGapEx, sagaGapOp; ^ ClustalW/alignment/ObjectiveScore.h:42:24: warning: private field 'sagaGapOp' is not used [-Wunused-private-field] int sagaGapEx, sagaGapOp; ^ 6 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/alignment/Sequence.cpp -o ClustalW/alignment/Sequence.o In file included from ClustalW/alignment/Sequence.cpp:10: In file included from ClustalW/alignment/Sequence.h:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from ClustalW/alignment/Sequence.cpp:10: In file included from ClustalW/alignment/Sequence.h:20: 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:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/Clustal.cpp -o ClustalW/Clustal.o In file included from ClustalW/Clustal.cpp:27: In file included from ./ClustalW/Clustal.h:15: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from ClustalW/Clustal.cpp:27: In file included from ./ClustalW/Clustal.h:16: In file included from ./ClustalW/fileInput/../alignment/../general/clustalw.h:44: ./ClustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/fileInput/ClustalFileParser.cpp -o ClustalW/fileInput/ClustalFileParser.o In file included from ClustalW/fileInput/ClustalFileParser.cpp:19: In file included from ClustalW/fileInput/ClustalFileParser.h:10: In file included from ClustalW/fileInput/FileParser.h:22: In file included from ClustalW/fileInput/../alignment/Sequence.h:20: In file included from ClustalW/fileInput/../alignment/../general/userparams.h:8: In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22: In file included from ClustalW/fileInput/../alignment/../general/utils.h:8: In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15: In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from ClustalW/fileInput/ClustalFileParser.cpp:19: In file included from ClustalW/fileInput/ClustalFileParser.h:10: In file included from ClustalW/fileInput/FileParser.h:22: In file included from ClustalW/fileInput/../alignment/Sequence.h:20: In file included from ClustalW/fileInput/../general/userparams.h:8: In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22: In file included from ClustalW/fileInput/../alignment/../general/utils.h:8: In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15: In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44: ClustalW/fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/fileInput/EMBLFileParser.cpp -o ClustalW/fileInput/EMBLFileParser.o In file included from ClustalW/fileInput/EMBLFileParser.cpp:16: In file included from ClustalW/fileInput/EMBLFileParser.h:10: In file included from ClustalW/fileInput/FileParser.h:22: In file included from ClustalW/fileInput/../alignment/Sequence.h:20: In file included from ClustalW/fileInput/../alignment/../general/userparams.h:8: In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22: In file included from ClustalW/fileInput/../alignment/../general/utils.h:8: In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15: In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from ClustalW/fileInput/EMBLFileParser.cpp:16: In file included from ClustalW/fileInput/EMBLFileParser.h:10: In file included from ClustalW/fileInput/FileParser.h:22: In file included from ClustalW/fileInput/../alignment/Sequence.h:20: In file included from ClustalW/fileInput/../general/userparams.h:8: In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22: In file included from ClustalW/fileInput/../alignment/../general/utils.h:8: In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15: In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44: ClustalW/fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/fileInput/FileParser.cpp -o ClustalW/fileInput/FileParser.o In file included from ClustalW/fileInput/FileParser.cpp:14: In file included from ClustalW/fileInput/FileParser.h:22: In file included from ClustalW/fileInput/../alignment/Sequence.h:20: In file included from ClustalW/fileInput/../alignment/../general/userparams.h:8: In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22: In file included from ClustalW/fileInput/../alignment/../general/utils.h:8: In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15: In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ ClustalW/fileInput/FileParser.cpp:38:7: warning: unused variable 'n' [-Wunused-variable] int n = (*input).inputSeqs.size(); ^ In file included from ClustalW/fileInput/FileParser.cpp:14: In file included from ClustalW/fileInput/FileParser.h:22: In file included from ClustalW/fileInput/../alignment/Sequence.h:20: In file included from ClustalW/fileInput/../general/userparams.h:8: In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22: In file included from ClustalW/fileInput/../alignment/../general/utils.h:8: In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15: In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44: ClustalW/fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/fileInput/FileReader.cpp -o ClustalW/fileInput/FileReader.o In file included from ClustalW/fileInput/FileReader.cpp:29: In file included from ClustalW/fileInput/FileReader.h:12: In file included from ClustalW/fileInput/../alignment/Alignment.h:41: In file included from ClustalW/fileInput/../alignment/Sequence.h:20: In file included from ClustalW/fileInput/../alignment/../general/userparams.h:8: In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22: In file included from ClustalW/fileInput/../alignment/../general/utils.h:8: In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15: In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ ClustalW/fileInput/FileReader.cpp:421:10: warning: variable 'maxAlnLength' set but not used [-Wunused-but-set-variable] int maxAlnLength; // Get values from the Alignment object. ^ In file included from ClustalW/fileInput/FileReader.cpp:29: In file included from ClustalW/fileInput/FileReader.h:12: In file included from ClustalW/fileInput/../alignment/Alignment.h:41: In file included from ClustalW/fileInput/../alignment/Sequence.h:20: In file included from ClustalW/fileInput/../general/userparams.h:8: In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22: In file included from ClustalW/fileInput/../general/utils.h:8: In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15: In file included from ClustalW/fileInput/../alignment/../substitutionMatrix/../general/clustalw.h:44: ClustalW/fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/fileInput/GDEFileParser.cpp -o ClustalW/fileInput/GDEFileParser.o In file included from ClustalW/fileInput/GDEFileParser.cpp:16: In file included from ClustalW/fileInput/GDEFileParser.h:10: In file included from ClustalW/fileInput/FileParser.h:22: In file included from ClustalW/fileInput/../alignment/Sequence.h:20: In file included from ClustalW/fileInput/../alignment/../general/userparams.h:8: In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22: In file included from ClustalW/fileInput/../alignment/../general/utils.h:8: In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15: In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from ClustalW/fileInput/GDEFileParser.cpp:16: In file included from ClustalW/fileInput/GDEFileParser.h:10: In file included from ClustalW/fileInput/FileParser.h:22: In file included from ClustalW/fileInput/../alignment/Sequence.h:20: In file included from ClustalW/fileInput/../general/userparams.h:8: In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22: In file included from ClustalW/fileInput/../alignment/../general/utils.h:8: In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15: In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44: ClustalW/fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/fileInput/InFileStream.cpp -o ClustalW/fileInput/InFileStream.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/fileInput/MSFFileParser.cpp -o ClustalW/fileInput/MSFFileParser.o In file included from ClustalW/fileInput/MSFFileParser.cpp:16: In file included from ClustalW/fileInput/MSFFileParser.h:10: In file included from ClustalW/fileInput/FileParser.h:22: In file included from ClustalW/fileInput/../alignment/Sequence.h:20: In file included from ClustalW/fileInput/../alignment/../general/userparams.h:8: In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22: In file included from ClustalW/fileInput/../alignment/../general/utils.h:8: In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15: In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from ClustalW/fileInput/MSFFileParser.cpp:16: In file included from ClustalW/fileInput/MSFFileParser.h:10: In file included from ClustalW/fileInput/FileParser.h:22: In file included from ClustalW/fileInput/../alignment/Sequence.h:20: In file included from ClustalW/fileInput/../general/userparams.h:8: In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22: In file included from ClustalW/fileInput/../alignment/../general/utils.h:8: In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15: In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44: ClustalW/fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/fileInput/PearsonFileParser.cpp -o ClustalW/fileInput/PearsonFileParser.o In file included from ClustalW/fileInput/PearsonFileParser.cpp:26: In file included from ClustalW/fileInput/PearsonFileParser.h:14: In file included from ClustalW/fileInput/FileParser.h:22: In file included from ClustalW/fileInput/../alignment/Sequence.h:20: In file included from ClustalW/fileInput/../alignment/../general/userparams.h:8: In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22: In file included from ClustalW/fileInput/../alignment/../general/utils.h:8: In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15: In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from ClustalW/fileInput/PearsonFileParser.cpp:26: In file included from ClustalW/fileInput/PearsonFileParser.h:14: In file included from ClustalW/fileInput/FileParser.h:22: In file included from ClustalW/fileInput/../alignment/Sequence.h:20: In file included from ClustalW/fileInput/../general/userparams.h:8: In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22: In file included from ClustalW/fileInput/../alignment/../general/utils.h:8: In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15: In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44: ClustalW/fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/fileInput/PIRFileParser.cpp -o ClustalW/fileInput/PIRFileParser.o In file included from ClustalW/fileInput/PIRFileParser.cpp:16: In file included from ClustalW/fileInput/PIRFileParser.h:10: In file included from ClustalW/fileInput/FileParser.h:22: In file included from ClustalW/fileInput/../alignment/Sequence.h:20: In file included from ClustalW/fileInput/../alignment/../general/userparams.h:8: In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22: In file included from ClustalW/fileInput/../alignment/../general/utils.h:8: In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15: In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from ClustalW/fileInput/PIRFileParser.cpp:16: In file included from ClustalW/fileInput/PIRFileParser.h:10: In file included from ClustalW/fileInput/FileParser.h:22: In file included from ClustalW/fileInput/../alignment/Sequence.h:20: In file included from ClustalW/fileInput/../general/userparams.h:8: In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22: In file included from ClustalW/fileInput/../alignment/../general/utils.h:8: In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15: In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44: ClustalW/fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/fileInput/RSFFileParser.cpp -o ClustalW/fileInput/RSFFileParser.o In file included from ClustalW/fileInput/RSFFileParser.cpp:16: In file included from ClustalW/fileInput/RSFFileParser.h:10: In file included from ClustalW/fileInput/FileParser.h:22: In file included from ClustalW/fileInput/../alignment/Sequence.h:20: In file included from ClustalW/fileInput/../alignment/../general/userparams.h:8: In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22: In file included from ClustalW/fileInput/../alignment/../general/utils.h:8: In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15: In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from ClustalW/fileInput/RSFFileParser.cpp:16: In file included from ClustalW/fileInput/RSFFileParser.h:10: In file included from ClustalW/fileInput/FileParser.h:22: In file included from ClustalW/fileInput/../alignment/Sequence.h:20: In file included from ClustalW/fileInput/../general/userparams.h:8: In file included from ClustalW/fileInput/../alignment/../general/UserParameters.h:22: In file included from ClustalW/fileInput/../alignment/../general/utils.h:8: In file included from ClustalW/fileInput/../alignment/../general/Utility.h:15: In file included from ClustalW/fileInput/../alignment/../general/clustalw.h:44: ClustalW/fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/general/ClustalWResources.cpp -o ClustalW/general/ClustalWResources.o In file included from ClustalW/general/ClustalWResources.cpp:14: In file included from ClustalW/general/clustalw.h:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from ClustalW/general/ClustalWResources.cpp:14: In file included from ClustalW/general/clustalw.h:44: ClustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/general/DebugLog.cpp -o ClustalW/general/DebugLog.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/general/InvalidCombination.cpp -o ClustalW/general/InvalidCombination.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/general/OutputFile.cpp -o ClustalW/general/OutputFile.o In file included from ClustalW/general/OutputFile.cpp:10: In file included from ClustalW/general/utils.h:8: In file included from ClustalW/general/Utility.h:15: In file included from ClustalW/general/clustalw.h:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 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:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/general/Stats.cpp -o ClustalW/general/Stats.o In file included from ClustalW/general/Stats.cpp:15: In file included from ClustalW/general/../alignment/Alignment.h:41: In file included from ClustalW/general/../alignment/Sequence.h:20: In file included from ClustalW/general/../alignment/../general/userparams.h:8: In file included from ClustalW/general/UserParameters.h:22: In file included from ClustalW/general/utils.h:8: In file included from ClustalW/general/Utility.h:15: In file included from ClustalW/general/clustalw.h:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from ClustalW/general/Stats.cpp:15: In file included from ClustalW/general/../alignment/Alignment.h:41: In file included from ClustalW/general/../alignment/Sequence.h:20: In file included from ClustalW/general/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from ClustalW/general/UserParameters.h:22: In file included from ClustalW/general/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from ClustalW/general/Utility.h:15: In file included from ClustalW/general/../alignment/../substitutionMatrix/../general/clustalw.h:44: ClustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/general/SymMatrix.cpp -o ClustalW/general/SymMatrix.o In file included from ClustalW/general/SymMatrix.cpp:10: ClustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/general/UserParameters.cpp -o ClustalW/general/UserParameters.o In file included from ClustalW/general/UserParameters.cpp:24: In file included from ClustalW/general/UserParameters.h:22: In file included from ClustalW/general/utils.h:8: In file included from ClustalW/general/Utility.h:15: In file included from ClustalW/general/clustalw.h:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 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:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/general/Utility.cpp -o ClustalW/general/Utility.o 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ ClustalW/general/Utility.cpp:251:8: warning: variable 'n' set but not used [-Wunused-but-set-variable] int n; ^ In file included from ClustalW/general/Utility.cpp:19: In file included from ClustalW/general/Utility.h:15: In file included from ClustalW/general/clustalw.h:44: ClustalW/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/general/VectorOutOfRange.cpp -o ClustalW/general/VectorOutOfRange.o ClustalW/general/VectorOutOfRange.cpp:28:12: warning: address of stack memory associated with local variable 'outputMessage' returned [-Wreturn-stack-address] return outputMessage.c_str(); ^~~~~~~~~~~~~ ClustalW/general/VectorOutOfRange.cpp:37:12: warning: address of stack memory associated with local variable 'outputMessage' returned [-Wreturn-stack-address] return outputMessage.c_str(); ^~~~~~~~~~~~~ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/Help.cpp -o ClustalW/Help.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/interface/CommandLineParser.cpp -o ClustalW/interface/CommandLineParser.o In file included from ClustalW/interface/CommandLineParser.cpp:13: In file included from ClustalW/interface/CommandLineParser.h:18: In file included from ClustalW/interface/../Clustal.h:15: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 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/general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/multipleAlign/Iteration.cpp -o ClustalW/multipleAlign/Iteration.o 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:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ ClustalW/multipleAlign/Iteration.cpp:171:9: warning: variable 'count' set but not used [-Wunused-but-set-variable] int count; ^ In file included from ClustalW/multipleAlign/Iteration.cpp:13: In file included from ClustalW/multipleAlign/Iteration.h:8: In file included from ClustalW/multipleAlign/../tree/../alignment/Alignment.h:41: In file included from ClustalW/multipleAlign/../alignment/Sequence.h:20: In file included from ClustalW/multipleAlign/../general/userparams.h:8: In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22: In file included from ClustalW/multipleAlign/../general/utils.h:8: In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15: In file included from ClustalW/multipleAlign/../tree/../general/clustalw.h:44: ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/multipleAlign/LowScoreSegProfile.cpp -o ClustalW/multipleAlign/LowScoreSegProfile.o In file included from ClustalW/multipleAlign/LowScoreSegProfile.cpp:9: In file included from ClustalW/multipleAlign/LowScoreSegProfile.h:13: In file included from ClustalW/multipleAlign/../alignment/Alignment.h:41: In file included from ClustalW/multipleAlign/../alignment/Sequence.h:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 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:20: In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22: In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15: In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h:44: ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/multipleAlign/MSA.cpp -o ClustalW/multipleAlign/MSA.o In file included from ClustalW/multipleAlign/MSA.cpp:16: In file included from ClustalW/multipleAlign/MSA.h:10: In file included from ClustalW/multipleAlign/ProfileBase.h:14: In file included from ClustalW/multipleAlign/../alignment/Alignment.h:41: In file included from ClustalW/multipleAlign/../alignment/Sequence.h:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ ClustalW/multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable] int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18 ^ In file included from ClustalW/multipleAlign/MSA.cpp:16: In file included from ClustalW/multipleAlign/MSA.h:10: In file included from ClustalW/multipleAlign/ProfileBase.h:14: In file included from ClustalW/multipleAlign/../alignment/Alignment.h:41: In file included from ClustalW/multipleAlign/../alignment/Sequence.h:20: In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22: In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15: In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h:44: ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/multipleAlign/MyersMillerProfileAlign.cpp -o ClustalW/multipleAlign/MyersMillerProfileAlign.o In file included from ClustalW/multipleAlign/MyersMillerProfileAlign.cpp:10: In file included from ClustalW/multipleAlign/MyersMillerProfileAlign.h:10: 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:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from ClustalW/multipleAlign/MyersMillerProfileAlign.cpp:10: In file included from ClustalW/multipleAlign/MyersMillerProfileAlign.h:10: 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:20: In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22: In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15: In file included from ClustalW/multipleAlign/../general/clustalw.h:44: ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ In file included from ClustalW/multipleAlign/MyersMillerProfileAlign.cpp:10: ClustalW/multipleAlign/MyersMillerProfileAlign.h:60:13: warning: private field 'matrix' is not used [-Wunused-private-field] int matrix[32][32]; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/multipleAlign/ProfileBase.cpp -o ClustalW/multipleAlign/ProfileBase.o In file included from ClustalW/multipleAlign/ProfileBase.cpp:9: In file included from ClustalW/multipleAlign/ProfileBase.h:14: In file included from ClustalW/multipleAlign/../alignment/Alignment.h:41: In file included from ClustalW/multipleAlign/../alignment/Sequence.h:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 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:20: In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22: In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15: In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h:44: ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/multipleAlign/ProfileStandard.cpp -o ClustalW/multipleAlign/ProfileStandard.o In file included from ClustalW/multipleAlign/ProfileStandard.cpp:9: In file included from ClustalW/multipleAlign/ProfileStandard.h:9: In file included from ClustalW/multipleAlign/../alignment/Alignment.h:41: In file included from ClustalW/multipleAlign/../alignment/Sequence.h:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 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:20: In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22: In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15: In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h:44: ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/multipleAlign/ProfileWithSub.cpp -o ClustalW/multipleAlign/ProfileWithSub.o In file included from ClustalW/multipleAlign/ProfileWithSub.cpp:9: In file included from ClustalW/multipleAlign/ProfileWithSub.h:9: In file included from ClustalW/multipleAlign/../alignment/Alignment.h:41: In file included from ClustalW/multipleAlign/../alignment/Sequence.h:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 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:20: In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from ClustalW/multipleAlign/../alignment/../general/UserParameters.h:22: In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from ClustalW/multipleAlign/../alignment/../general/Utility.h:15: In file included from ClustalW/multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h:44: ClustalW/multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/pairwise/FastPairwiseAlign.cpp -o ClustalW/pairwise/FastPairwiseAlign.o In file included from ClustalW/pairwise/FastPairwiseAlign.cpp:10: In file included from ClustalW/pairwise/FastPairwiseAlign.h:9: In file included from ClustalW/pairwise/PairwiseAlignBase.h:10: In file included from ClustalW/pairwise/../alignment/Alignment.h:41: In file included from ClustalW/pairwise/../alignment/Sequence.h:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 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:20: In file included from ClustalW/pairwise/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from ClustalW/pairwise/../alignment/../general/UserParameters.h:22: In file included from ClustalW/pairwise/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from ClustalW/pairwise/../alignment/../general/Utility.h:15: In file included from ClustalW/pairwise/../alignment/../substitutionMatrix/../general/clustalw.h:44: ClustalW/pairwise/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/pairwise/FullPairwiseAlign.cpp -o ClustalW/pairwise/FullPairwiseAlign.o 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:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 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:20: In file included from ClustalW/pairwise/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from ClustalW/pairwise/../alignment/../general/UserParameters.h:22: In file included from ClustalW/pairwise/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from ClustalW/pairwise/../alignment/../general/Utility.h:15: In file included from ClustalW/pairwise/../alignment/../substitutionMatrix/../general/clustalw.h:44: ClustalW/pairwise/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/substitutionMatrix/SubMatrix.cpp -o ClustalW/substitutionMatrix/SubMatrix.o In file included from ClustalW/substitutionMatrix/SubMatrix.cpp:15: In file included from ClustalW/substitutionMatrix/SubMatrix.h:28: In file included from ClustalW/substitutionMatrix/../general/clustalw.h:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ ClustalW/substitutionMatrix/SubMatrix.cpp:697:9: warning: variable 'av1' set but not used [-Wunused-but-set-variable] int av1, av2, av3, min, max; ^ ClustalW/substitutionMatrix/SubMatrix.cpp:1308:20: warning: unused variable 'ulimit' [-Wunused-variable] int n, llimit, ulimit; ^ ClustalW/substitutionMatrix/SubMatrix.cpp:1307:9: warning: unused variable 'nmat' [-Wunused-variable] int nmat; ^ ClustalW/substitutionMatrix/SubMatrix.cpp:1308:12: warning: unused variable 'llimit' [-Wunused-variable] int n, llimit, ulimit; ^ ClustalW/substitutionMatrix/SubMatrix.cpp:1305:10: warning: unused variable 'inline1' [-Wunused-variable] char inline1[1024]; ^ ClustalW/substitutionMatrix/SubMatrix.cpp:1308:9: warning: unused variable 'n' [-Wunused-variable] int n, llimit, ulimit; ^ ClustalW/substitutionMatrix/SubMatrix.cpp:1845:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable] int maxRes; ^ ClustalW/substitutionMatrix/SubMatrix.cpp:1905:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable] int maxRes; ^ In file included from ClustalW/substitutionMatrix/SubMatrix.cpp:15: In file included from ClustalW/substitutionMatrix/SubMatrix.h:28: In file included from ClustalW/substitutionMatrix/../general/clustalw.h:44: ClustalW/substitutionMatrix/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 10 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/tree/AlignmentSteps.cpp -o ClustalW/tree/AlignmentSteps.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/tree/ClusterTree.cpp -o ClustalW/tree/ClusterTree.o 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:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ ClustalW/tree/ClusterTree.cpp:580:9: warning: variable 'rs' set but not used [-Wunused-but-set-variable] int rs = 0, rl = 0; ^ ClustalW/tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable] int rs = 0, rl = 0; ^ ClustalW/tree/ClusterTree.cpp:967:22: warning: variable 'tempSeed' set but not used [-Wunused-but-set-variable] unsigned int tempSeed; ^ In file included from ClustalW/tree/ClusterTree.cpp:9: In file included from ClustalW/tree/ClusterTree.h:20: In file included from ClustalW/tree/../alignment/Alignment.h:41: In file included from ClustalW/tree/../alignment/Sequence.h:20: In file included from ClustalW/tree/../general/userparams.h:8: In file included from ClustalW/tree/../alignment/../general/UserParameters.h:22: In file included from ClustalW/tree/../general/utils.h:8: In file included from ClustalW/tree/../alignment/../general/Utility.h:15: In file included from ClustalW/tree/../general/clustalw.h:44: ClustalW/tree/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/tree/ClusterTreeOutput.cpp -o ClustalW/tree/ClusterTreeOutput.o In file included from ClustalW/tree/ClusterTreeOutput.cpp:9: In file included from ClustalW/tree/ClusterTreeOutput.h:11: In file included from ClustalW/tree/../alignment/Alignment.h:41: In file included from ClustalW/tree/../alignment/Sequence.h:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 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:20: In file included from ClustalW/tree/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from ClustalW/tree/../alignment/../general/UserParameters.h:22: In file included from ClustalW/tree/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from ClustalW/tree/../alignment/../general/Utility.h:15: In file included from ClustalW/tree/../general/clustalw.h:44: ClustalW/tree/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/tree/NJTree.cpp -o ClustalW/tree/NJTree.o In file included from ClustalW/tree/NJTree.cpp:10: In file included from ClustalW/tree/NJTree.h:11: In file included from ClustalW/tree/ClusterTreeAlgorithm.h:12: In file included from ClustalW/tree/../general/clustalw.h:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 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:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/tree/RandomGenerator.cpp -o ClustalW/tree/RandomGenerator.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/tree/Tree.cpp -o ClustalW/tree/Tree.o In file included from ClustalW/tree/Tree.cpp:10: In file included from ClustalW/tree/Tree.h:13: In file included from ClustalW/tree/../alignment/Alignment.h:41: In file included from ClustalW/tree/../alignment/Sequence.h:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 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:20: In file included from ClustalW/tree/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from ClustalW/tree/../alignment/../general/UserParameters.h:22: In file included from ClustalW/tree/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from ClustalW/tree/../alignment/../general/Utility.h:15: In file included from ClustalW/tree/../alignment/../substitutionMatrix/../general/clustalw.h:44: ClustalW/tree/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/tree/TreeInterface.cpp -o ClustalW/tree/TreeInterface.o In file included from ClustalW/tree/TreeInterface.cpp:15: In file included from ClustalW/tree/TreeInterface.h:19: In file included from ClustalW/tree/../alignment/Alignment.h:41: In file included from ClustalW/tree/../alignment/Sequence.h:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from ClustalW/tree/TreeInterface.cpp:15: In file included from ClustalW/tree/TreeInterface.h:19: In file included from ClustalW/tree/UPGMA/../../alignment/Alignment.h:41: In file included from ClustalW/tree/../alignment/Sequence.h:20: In file included from ClustalW/tree/../general/userparams.h:8: In file included from ClustalW/tree/../alignment/../general/UserParameters.h:22: In file included from ClustalW/tree/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from ClustalW/tree/../alignment/../general/Utility.h:15: In file included from ClustalW/tree/../general/clustalw.h:44: ClustalW/tree/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/tree/UnRootedClusterTree.cpp -o ClustalW/tree/UnRootedClusterTree.o In file included from ClustalW/tree/UnRootedClusterTree.cpp:9: In file included from ClustalW/tree/UnRootedClusterTree.h:8: In file included from ClustalW/tree/ClusterTree.h:20: In file included from ClustalW/tree/../alignment/Alignment.h:41: In file included from ClustalW/tree/../alignment/Sequence.h:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 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:20: In file included from ClustalW/tree/../general/userparams.h:8: In file included from ClustalW/tree/../alignment/../general/UserParameters.h:22: In file included from ClustalW/tree/../general/utils.h:8: In file included from ClustalW/tree/../alignment/../general/Utility.h:15: In file included from ClustalW/tree/../general/clustalw.h:44: ClustalW/tree/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/tree/UPGMA/Node.cpp -o ClustalW/tree/UPGMA/Node.o In file included from ClustalW/tree/UPGMA/Node.cpp:7: In file included from ClustalW/tree/UPGMA/../../general/clustalw.h:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 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:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/tree/UPGMA/RootedClusterTree.cpp -o ClustalW/tree/UPGMA/RootedClusterTree.o In file included from ClustalW/tree/UPGMA/RootedClusterTree.cpp:9: In file included from ClustalW/tree/UPGMA/RootedClusterTree.h:8: In file included from ClustalW/tree/UPGMA/../ClusterTree.h:20: In file included from ClustalW/tree/UPGMA/../../alignment/Alignment.h:41: In file included from ClustalW/tree/UPGMA/../../alignment/Sequence.h:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 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:20: In file included from ClustalW/tree/UPGMA/../../general/userparams.h:8: In file included from ClustalW/tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from ClustalW/tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h:8: In file included from ClustalW/tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from ClustalW/tree/UPGMA/../../general/clustalw.h:44: ClustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/tree/UPGMA/RootedGuideTree.cpp -o ClustalW/tree/UPGMA/RootedGuideTree.o In file included from ClustalW/tree/UPGMA/RootedGuideTree.cpp:10: In file included from ClustalW/tree/UPGMA/RootedGuideTree.h:17: In file included from ClustalW/tree/UPGMA/../../alignment/Alignment.h:41: In file included from ClustalW/tree/UPGMA/../../alignment/Sequence.h:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 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:20: In file included from ClustalW/tree/UPGMA/../../general/userparams.h:8: In file included from ClustalW/tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from ClustalW/tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h:8: In file included from ClustalW/tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from ClustalW/tree/UPGMA/../../alignment/../substitutionMatrix/../general/clustalw.h:44: ClustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/tree/UPGMA/RootedTreeOutput.cpp -o ClustalW/tree/UPGMA/RootedTreeOutput.o In file included from ClustalW/tree/UPGMA/RootedTreeOutput.cpp:9: In file included from ClustalW/tree/UPGMA/RootedTreeOutput.h:15: In file included from ClustalW/tree/UPGMA/RootedGuideTree.h:17: In file included from ClustalW/tree/UPGMA/../../alignment/Alignment.h:41: In file included from ClustalW/tree/UPGMA/../../alignment/Sequence.h:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 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:20: In file included from ClustalW/tree/UPGMA/../../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from ClustalW/tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from ClustalW/tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h:8: In file included from ClustalW/tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from ClustalW/tree/UPGMA/../../general/clustalw.h:44: ClustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ClustalW/tree/UPGMA/UPGMAAlgorithm.cpp -o ClustalW/tree/UPGMA/UPGMAAlgorithm.o In file included from ClustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4: In file included from ClustalW/tree/UPGMA/UPGMAAlgorithm.h:6: In file included from ClustalW/tree/UPGMA/../../general/clustalw.h:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from ClustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4: In file included from ClustalW/tree/UPGMA/UPGMAAlgorithm.h:6: In file included from ClustalW/tree/UPGMA/../../alignment/../substitutionMatrix/../general/clustalw.h:44: ClustalW/tree/UPGMA/../../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/aligngivenpath.cpp -o Muscle/aligngivenpath.o In file included from Muscle/aligngivenpath.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/aligngivenpath.cpp:186:17: warning: unused variable 'uLengthA' [-Wunused-variable] const unsigned uLengthA = msaA.GetColCount(); ^ Muscle/aligngivenpath.cpp:187:17: warning: unused variable 'uLengthB' [-Wunused-variable] const unsigned uLengthB = msaB.GetColCount(); ^ Muscle/aligngivenpath.cpp:335:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^ Muscle/aligngivenpath.cpp:336:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^ Muscle/aligngivenpath.cpp:346:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^ Muscle/aligngivenpath.cpp:354:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^ In file included from Muscle/aligngivenpath.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 8 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/aligngivenpathsw.cpp -o Muscle/aligngivenpathsw.o In file included from Muscle/aligngivenpathsw.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/aligngivenpathsw.cpp:58:17: warning: unused variable 'uLengthA' [-Wunused-variable] const unsigned uLengthA = msaA.GetColCount(); ^ Muscle/aligngivenpathsw.cpp:59:17: warning: unused variable 'uLengthB' [-Wunused-variable] const unsigned uLengthB = msaB.GetColCount(); ^ Muscle/aligngivenpathsw.cpp:204:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^ Muscle/aligngivenpathsw.cpp:205:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^ Muscle/aligngivenpathsw.cpp:215:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^ Muscle/aligngivenpathsw.cpp:223:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^ In file included from Muscle/aligngivenpathsw.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 8 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/aligntwomsas.cpp -o Muscle/aligntwomsas.o In file included from Muscle/aligntwomsas.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/aligntwomsas.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/aligntwoprofs.cpp -o Muscle/aligntwoprofs.o In file included from Muscle/aligntwoprofs.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/aligntwoprofs.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/aln.cpp -o Muscle/aln.o In file included from Muscle/aln.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/aln.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/alpha.cpp -o Muscle/alpha.o In file included from Muscle/alpha.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/alpha.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/anchors.cpp -o Muscle/anchors.o In file included from Muscle/anchors.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/anchors.cpp:162:13: warning: unused variable 'uWindowCenter' [-Wunused-variable] unsigned uWindowCenter = uBestColIndex + uWindowLength/2; ^ In file included from Muscle/anchors.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/anchors.cpp:53:13: warning: unused function 'FindBestColsGrade' [-Wunused-function] static void FindBestColsGrade(const SCORE Score[], unsigned uCount, ^ Muscle/anchors.cpp:105:13: warning: unused function 'ListBestCols' [-Wunused-function] static void ListBestCols(const MSA &msa, const SCORE Score[], const SCORE SmoothScore[], ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/bittraceback.cpp -o Muscle/bittraceback.o In file included from Muscle/bittraceback.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/bittraceback.cpp:146:7: warning: unused variable 'Bits' [-Wunused-variable] char Bits = TraceBack[uLengthA][uLengthB]; ^ In file included from Muscle/bittraceback.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/bittraceback.cpp:15:20: warning: unused function 'BitsToStr' [-Wunused-function] static const char *BitsToStr(char Bits) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/blosum62.cpp -o Muscle/blosum62.o In file included from Muscle/blosum62.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/blosum62.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/blosumla.cpp -o Muscle/blosumla.o In file included from Muscle/blosumla.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/blosumla.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/blosumla.cpp:7:14: warning: unused variable 'Blosum62LA' [-Wunused-variable] static float Blosum62LA[20][20] = ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/clust.cpp -o Muscle/clust.o In file included from Muscle/clust.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/clust.cpp:186:17: warning: unused variable 'uClusterCount' [-Wunused-variable] const unsigned uClusterCount = GetClusterCount(); ^ Muscle/clust.cpp:206:17: warning: unused variable 'uClusterCount' [-Wunused-variable] const unsigned uClusterCount = GetClusterCount(); ^ Muscle/clust.cpp:365:14: warning: unused variable 'dDistLR' [-Wunused-variable] const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex); ^ In file included from Muscle/clust.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/cluster.cpp -o Muscle/cluster.o In file included from Muscle/cluster.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/cluster.cpp:284:8: warning: variable 'bFound' set but not used [-Wunused-but-set-variable] bool bFound = false; ^ Muscle/cluster.cpp:267:9: warning: unused variable 'dMaxDist' [-Wunused-variable] double dMaxDist = 0.0; ^ In file included from Muscle/cluster.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/cluster.cpp:10:21: warning: unused function 'Max' [-Wunused-function] static inline float Max(float d1, float d2) ^ Muscle/cluster.cpp:15:21: warning: unused function 'Mean' [-Wunused-function] static inline float Mean(float d1, float d2) ^ 6 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/clwwt.cpp -o Muscle/clwwt.o In file included from Muscle/clwwt.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/clwwt.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/color.cpp -o Muscle/color.o In file included from Muscle/color.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/color.cpp:7:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] +4, -2, +0, -2, -1, -2, +0, -2, -1, -1, -1, -1, -2, -1, -1, -1, +1, +0, +0, -3, -1, -2, -1, // A ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:8:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -2, +6, -3, +6, +2, -3, -1, -1, -3, -1, -4, -3, +1, -1, +0, -2, +0, -1, -3, -4, -1, -3, +2, // B ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:9:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] +0, -3, +9, -3, -4, -2, -3, -3, -1, -3, -1, -1, -3, -3, -3, -3, -1, -1, -1, -2, -1, -2, -4, // C ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:10:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -2, +6, -3, +6, +2, -3, -1, -1, -3, -1, -4, -3, +1, -1, +0, -2, +0, -1, -3, -4, -1, -3, +2, // D ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:11:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, +2, -4, +2, +5, -3, -2, +0, -3, +1, -3, -2, +0, -1, +2, +0, +0, -1, -2, -3, -1, -2, +5, // E ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:13:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -2, -3, -2, -3, -3, +6, -3, -1, +0, -3, +0, +0, -3, -4, -3, -3, -2, -2, -1, +1, -1, +3, -3, // F ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:14:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] +0, -1, -3, -1, -2, -3, +6, -2, -4, -2, -4, -3, +0, -2, -2, -2, +0, -2, -3, -2, -1, -3, -2, // G ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:15:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -2, -1, -3, -1, +0, -1, -2, +8, -3, -1, -3, -2, +1, -2, +0, +0, -1, -2, -3, -2, -1, +2, +0, // H ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:16:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -3, -1, -3, -3, +0, -4, -3, +4, -3, +2, +1, -3, -3, -3, -3, -2, -1, +3, -3, -1, -1, -3, // I ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:17:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -1, -3, -1, +1, -3, -2, -1, -3, +5, -2, -1, +0, -1, +1, +2, +0, -1, -2, -3, -1, -2, +1, // K ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:19:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -4, -1, -4, -3, +0, -4, -3, +2, -2, +4, +2, -3, -3, -2, -2, -2, -1, +1, -2, -1, -1, -3, // L ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:20:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -3, -1, -3, -2, +0, -3, -2, +1, -1, +2, +5, -2, -2, +0, -1, -1, -1, +1, -1, -1, -1, -2, // M ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:21:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -2, +1, -3, +1, +0, -3, +0, +1, -3, +0, -3, -2, +6, -2, +0, +0, +1, +0, -3, -4, -1, -2, +0, // N ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:22:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -1, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, +7, -1, -2, -1, -1, -2, -4, -1, -3, -1, // P ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:23:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, +0, -3, +0, +2, -3, -2, +0, -3, +1, -2, +0, +0, -1, +5, +1, +0, -1, -2, -2, -1, -1, +2, // Q ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:25:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -2, -3, -2, +0, -3, -2, +0, -3, +2, -2, -1, +0, -2, +1, +5, -1, -1, -3, -3, -1, -2, +0, // R ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:26:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] +1, +0, -1, +0, +0, -2, +0, -1, -2, +0, -2, -1, +1, -1, +0, -1, +4, +1, -2, -3, -1, -2, +0, // S ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:27:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] +0, -1, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, +0, -1, -1, -1, +1, +5, +0, -2, -1, -2, -1, // T ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:28:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] +0, -3, -1, -3, -2, -1, -3, -3, +3, -2, +1, +1, -3, -2, -2, -3, -2, +0, +4, -3, -1, -1, -2, // V ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:29:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -3, -4, -2, -4, -3, +1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3, -2, -3,+11, -1, +2, -3, // W ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:31:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, // X ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:32:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -2, -3, -2, -3, -2, +3, -3, +2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2, -1, +2, -1, +7, -2, // Y ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/color.cpp:33:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, +2, -4, +2, +5, -3, -2, +0, -3, +1, -3, -2, +0, -1, +2, +0, +0, -1, -2, -3, -1, -2, +5, // Z ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } In file included from Muscle/color.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/color.cpp:72:12: warning: unused function 'BlosumScore' [-Wunused-function] static int BlosumScore(char c1, char c2) ^ 26 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/cons.cpp -o Muscle/cons.o In file included from Muscle/cons.cpp:7: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/cons.cpp:7: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/diaglist.cpp -o Muscle/diaglist.o In file included from Muscle/diaglist.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/diaglist.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/diffobjscore.cpp -o Muscle/diffobjscore.o In file included from Muscle/diffobjscore.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable] const unsigned uColCount = msa.GetColCount(); ^ Muscle/diffobjscore.cpp:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable] const unsigned uSeqCount = msa.GetSeqCount(); ^ In file included from Muscle/diffobjscore.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/diffpaths.cpp -o Muscle/diffpaths.o In file included from Muscle/diffpaths.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/diffpaths.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/difftrees.cpp -o Muscle/difftrees.o In file included from Muscle/difftrees.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/difftrees.cpp:161:17: warning: unused variable 'uLeafCount2' [-Wunused-variable] const unsigned uLeafCount2 = Tree2.GetLeafCount(); ^ In file included from Muscle/difftrees.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/difftreese.cpp -o Muscle/difftreese.o In file included from Muscle/difftreese.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/difftreese.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/distcalc.cpp -o Muscle/distcalc.o In file included from Muscle/distcalc.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/distcalc.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/distfunc.cpp -o Muscle/distfunc.o In file included from Muscle/distfunc.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/distfunc.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/distpwkimura.cpp -o Muscle/distpwkimura.o In file included from Muscle/distpwkimura.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/distpwkimura.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/domuscle.cpp -o Muscle/domuscle.o In file included from Muscle/domuscle.cpp:1: In file included from ./RMuscle.h:4: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/domuscle.cpp:1: In file included from ./RMuscle.h:7: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ Muscle/domuscle.cpp:74:4: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(NewFileName, "%s/%s", Path, FileName); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ Muscle/domuscle.cpp:180:6: warning: unused variable 'PNlength' [-Wunused-variable] int PNlength = (msaInput->inputSeqs).Length(); ^ In file included from Muscle/domuscle.cpp:1: In file included from ./RMuscle.h:4: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/dosp.cpp -o Muscle/dosp.o In file included from Muscle/dosp.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/dosp.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/dpreglist.cpp -o Muscle/dpreglist.o In file included from Muscle/dpreglist.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/dpreglist.cpp:82:19: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable] const unsigned uDiagLengthMinusCaps = uEndVertexA - uStartVertexA - 1; ^ In file included from Muscle/dpreglist.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/drawtree.cpp -o Muscle/drawtree.o In file included from Muscle/drawtree.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/drawtree.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/edgelist.cpp -o Muscle/edgelist.o In file included from Muscle/edgelist.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/edgelist.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/enumopts.cpp -o Muscle/enumopts.o In file included from Muscle/enumopts.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:12:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ALPHA, Amino) ^~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :345:1: note: expanded from here "Amino" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:13:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ALPHA, DNA) ^~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :348:1: note: expanded from here "DNA" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:14:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ALPHA, RNA) ^~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :351:1: note: expanded from here "RNA" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:15:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(ALPHA) ^~~~~~~~ { Muscle/enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:18:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQTYPE, Protein) ^~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :355:1: note: expanded from here "Protein" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:19:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQTYPE, DNA) ^~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :358:1: note: expanded from here "DNA" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:20:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQTYPE, RNA) ^~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :361:1: note: expanded from here "RNA" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:21:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQTYPE, Auto) ^~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :364:1: note: expanded from here "Auto" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:22:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(SEQTYPE) ^~~~~~~~~~ { Muscle/enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:25:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ROOT, Pseudo) ^~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :368:1: note: expanded from here "Pseudo" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:26:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ROOT, MidLongestSpan) ^~~~~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :371:1: note: expanded from here "MidLongestSpan" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:27:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ROOT, MinAvgLeafDist) ^~~~~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :374:1: note: expanded from here "MinAvgLeafDist" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:28:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(ROOT) ^~~~~~~ { Muscle/enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:31:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(CLUSTER, UPGMA) ^~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :378:1: note: expanded from here "UPGMA" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:32:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(CLUSTER, UPGMAMax) ^~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :381:1: note: expanded from here "UPGMAMax" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:33:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(CLUSTER, UPGMAMin) ^~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :384:1: note: expanded from here "UPGMAMin" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:34:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(CLUSTER, UPGMB) ^~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :387:1: note: expanded from here "UPGMB" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:35:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(CLUSTER, NeighborJoining) ^~~~~~~~~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :390:1: note: expanded from here "NeighborJoining" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:36:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(CLUSTER) ^~~~~~~~~~ { Muscle/enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:39:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(JOIN, NearestNeighbor) ^~~~~~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :394:1: note: expanded from here "NearestNeighbor" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:40:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(JOIN, NeighborJoining) ^~~~~~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :397:1: note: expanded from here "NeighborJoining" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:41:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(JOIN) ^~~~~~~ { Muscle/enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:44:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(LINKAGE, Min) ^~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :401:1: note: expanded from here "Min" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:45:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(LINKAGE, Avg) ^~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :404:1: note: expanded from here "Avg" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:46:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(LINKAGE, Max) ^~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :407:1: note: expanded from here "Max" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:47:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(LINKAGE, NeighborJoining) ^~~~~~~~~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :410:1: note: expanded from here "NeighborJoining" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:48:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(LINKAGE, Biased) ^~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :413:1: note: expanded from here "Biased" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:49:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(LINKAGE) ^~~~~~~~~~ { Muscle/enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:52:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Kmer6_6) ^~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :5:1: note: expanded from here "Kmer6_6" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:53:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Kmer20_3) ^~~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :8:1: note: expanded from here "Kmer20_3" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:54:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Kmer20_4) ^~~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :11:1: note: expanded from here "Kmer20_4" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:55:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Kbit20_3) ^~~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :14:1: note: expanded from here "Kbit20_3" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:56:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Kmer4_6) ^~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :17:1: note: expanded from here "Kmer4_6" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:57:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, PctIdKimura) ^~~~~~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :20:1: note: expanded from here "PctIdKimura" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:58:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, PctIdLog) ^~~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :23:1: note: expanded from here "PctIdLog" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:59:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, PWKimura) ^~~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :26:1: note: expanded from here "PWKimura" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:60:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, PWScoreDist) ^~~~~~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :29:1: note: expanded from here "PWScoreDist" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:61:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, ScoreDist) ^~~~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :32:1: note: expanded from here "ScoreDist" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:62:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Edit) ^~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :35:1: note: expanded from here "Edit" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:63:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(DISTANCE) ^~~~~~~~~~~ { Muscle/enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:66:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(PPSCORE, LE) ^~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :39:1: note: expanded from here "LE" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:67:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(PPSCORE, SP) ^~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :42:1: note: expanded from here "SP" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:68:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(PPSCORE, SV) ^~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :45:1: note: expanded from here "SV" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:69:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(PPSCORE, SPN) ^~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :48:1: note: expanded from here "SPN" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:70:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(PPSCORE) ^~~~~~~~~~ { Muscle/enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:73:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, None) ^~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :52:1: note: expanded from here "None" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:74:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, Henikoff) ^~~~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :55:1: note: expanded from here "Henikoff" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:75:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, HenikoffPB) ^~~~~~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :58:1: note: expanded from here "HenikoffPB" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:76:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, GSC) ^~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :61:1: note: expanded from here "GSC" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:77:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, ClustalW) ^~~~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :64:1: note: expanded from here "ClustalW" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:78:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, ThreeWay) ^~~~~~~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :67:1: note: expanded from here "ThreeWay" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:79:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(SEQWEIGHT) ^~~~~~~~~~~~ { Muscle/enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:82:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, SP) // Sum of Pairs of sequences ^~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :71:1: note: expanded from here "SP" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:83:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, DP) // Dynamic Programming score ^~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :74:1: note: expanded from here "DP" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:84:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, XP) // Cross Pairs = sum of pairs between two MSAs ^~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :77:1: note: expanded from here "XP" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:85:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, PS) // sum of Prof-Seq score for all seqs in MSA ^~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :80:1: note: expanded from here "PS" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:86:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, SPF) // sum of pairs, fast approximation ^~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :83:1: note: expanded from here "SPF" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:87:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, SPM) // sp if <= 100 seqs, spf otherwise ^~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :86:1: note: expanded from here "SPM" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:88:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(OBJSCORE) ^~~~~~~~~~~ { Muscle/enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:91:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(TERMGAPS, Full) ^~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :90:1: note: expanded from here "Full" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:92:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(TERMGAPS, Half) ^~~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :93:1: note: expanded from here "Half" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:93:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(TERMGAPS, Ext) ^~~~~~~~~~~~~~~~ { Muscle/enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :96:1: note: expanded from here "Ext" ^ In file included from Muscle/enumopts.cpp:8: ./Muscle/enums.h:94:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(TERMGAPS) ^~~~~~~~~~~ { Muscle/enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from Muscle/enumopts.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 65 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/enumtostr.cpp -o Muscle/enumtostr.o In file included from Muscle/enumtostr.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/enumtostr.cpp:10: ./Muscle/enums.h:15:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] e(ALPHA) ^ Muscle/enumtostr.cpp:9:16: note: expanded from macro 'e' #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; } ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/enumtostr.cpp:10: ./Muscle/enums.h:22:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] e(SEQTYPE) ^ Muscle/enumtostr.cpp:9:16: note: expanded from macro 'e' #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; } ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/enumtostr.cpp:10: ./Muscle/enums.h:28:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] e(ROOT) ^ Muscle/enumtostr.cpp:9:16: note: expanded from macro 'e' #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; } ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/enumtostr.cpp:10: ./Muscle/enums.h:36:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] e(CLUSTER) ^ Muscle/enumtostr.cpp:9:16: note: expanded from macro 'e' #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; } ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/enumtostr.cpp:10: ./Muscle/enums.h:41:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] e(JOIN) ^ Muscle/enumtostr.cpp:9:16: note: expanded from macro 'e' #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; } ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/enumtostr.cpp:10: ./Muscle/enums.h:49:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] e(LINKAGE) ^ Muscle/enumtostr.cpp:9:16: note: expanded from macro 'e' #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; } ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/enumtostr.cpp:10: ./Muscle/enums.h:63:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] e(DISTANCE) ^ Muscle/enumtostr.cpp:9:16: note: expanded from macro 'e' #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; } ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/enumtostr.cpp:10: ./Muscle/enums.h:70:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] e(PPSCORE) ^ Muscle/enumtostr.cpp:9:16: note: expanded from macro 'e' #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; } ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/enumtostr.cpp:10: ./Muscle/enums.h:79:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] e(SEQWEIGHT) ^ Muscle/enumtostr.cpp:9:16: note: expanded from macro 'e' #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; } ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/enumtostr.cpp:10: ./Muscle/enums.h:88:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] e(OBJSCORE) ^ Muscle/enumtostr.cpp:9:16: note: expanded from macro 'e' #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; } ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/enumtostr.cpp:10: ./Muscle/enums.h:94:1: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] e(TERMGAPS) ^ Muscle/enumtostr.cpp:9:16: note: expanded from macro 'e' #define e(t) } sprintf(szMsg, #t "_%d", x); return szMsg; } ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/enumtostr.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 13 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/estring.cpp -o Muscle/estring.o In file included from Muscle/estring.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/estring.cpp:397:8: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if (nB > 0) ^~~~~~ Muscle/estring.cpp:409:11: note: uninitialized use occurs here switch (cType) ^~~~~ Muscle/estring.cpp:397:4: note: remove the 'if' if its condition is always true if (nB > 0) ^~~~~~~~~~~ Muscle/estring.cpp:395:12: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (nA < 0) ^~~~~~ Muscle/estring.cpp:409:11: note: uninitialized use occurs here switch (cType) ^~~~~ Muscle/estring.cpp:395:8: note: remove the 'if' if its condition is always true else if (nA < 0) ^~~~~~~~~~~ Muscle/estring.cpp:386:13: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (nB < 0) ^~~~~~ Muscle/estring.cpp:409:11: note: uninitialized use occurs here switch (cType) ^~~~~ Muscle/estring.cpp:386:9: note: remove the 'if' if its condition is always true else if (nB < 0) ^~~~~~~~~~~ Muscle/estring.cpp:377:13: note: initialize the variable 'cType' to silence this warning char cType; ^ = '\0' In file included from Muscle/estring.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/estring.cpp:464:13: warning: unused function 'CanMultiplyEstrings' [-Wunused-function] static bool CanMultiplyEstrings(const short es1[], const short es2[]) ^ 6 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/fasta.cpp -o Muscle/fasta.o In file included from Muscle/fasta.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/fasta.cpp:15:11: warning: unused variable 'uSeqCount' [-Wunused-variable] unsigned uSeqCount = 0; ^ Muscle/fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable] unsigned uColCount = uInsane; ^ In file included from Muscle/fasta.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/fasta2.cpp -o Muscle/fasta2.o In file included from Muscle/fasta2.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/fasta2.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/fastclust.cpp -o Muscle/fastclust.o In file included from Muscle/fastclust.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/fastclust.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/fastdist.cpp -o Muscle/fastdist.o In file included from Muscle/fastdist.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/fastdist.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/fastdistjones.cpp -o Muscle/fastdistjones.o In file included from Muscle/fastdistjones.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/fastdistjones.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/fastdistkbit.cpp -o Muscle/fastdistkbit.o In file included from Muscle/fastdistkbit.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/fastdistkbit.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/fastdistkmer.cpp -o Muscle/fastdistkmer.o In file included from Muscle/fastdistkmer.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/fastdistkmer.cpp:235:11: warning: unused variable 'KD' [-Wunused-variable] double KD = KimuraDist(EstimatedPctId); ^ In file included from Muscle/fastdistkmer.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/fastdistmafft.cpp -o Muscle/fastdistmafft.o In file included from Muscle/fastdistmafft.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/fastdistmafft.cpp:239:15: warning: unused variable 'pName1' [-Wunused-variable] const char *pName1 = s1.GetName(); ^ In file included from Muscle/fastdistmafft.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/fastdistmafft.cpp:104:13: warning: unused function 'ListCount' [-Wunused-function] static void ListCount(const unsigned char Count[]) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/fastdistnuc.cpp -o Muscle/fastdistnuc.o In file included from Muscle/fastdistnuc.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/fastdistnuc.cpp:223:15: warning: unused variable 'pName1' [-Wunused-variable] const char *pName1 = s1.GetName(); ^ In file included from Muscle/fastdistnuc.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/fastdistnuc.cpp:33:17: warning: unused variable 'uResidueGroupCount' [-Wunused-variable] static unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]); ^ Muscle/fastdistnuc.cpp:85:13: warning: unused function 'ListCount' [-Wunused-function] static void ListCount(const unsigned char Count[]) ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/fastscorepath2.cpp -o Muscle/fastscorepath2.o In file included from Muscle/fastscorepath2.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/fastscorepath2.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/finddiags.cpp -o Muscle/finddiags.o In file included from Muscle/finddiags.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/finddiags.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/finddiags.cpp:11:14: warning: unused function 'TupleToStr' [-Wunused-function] static char *TupleToStr(int t) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/finddiagsn.cpp -o Muscle/finddiagsn.o In file included from Muscle/finddiagsn.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/finddiagsn.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/finddiagsn.cpp:12:14: warning: unused function 'TupleToStr' [-Wunused-function] static char *TupleToStr(int t) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/glbalign.cpp -o Muscle/glbalign.o In file included from Muscle/glbalign.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/glbalign.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/glbalign352.cpp -o Muscle/glbalign352.o In file included from Muscle/glbalign352.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/glbalign352.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/glbaligndiag.cpp -o Muscle/glbaligndiag.o In file included from Muscle/glbaligndiag.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/glbaligndiag.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/glbalignla.cpp -o Muscle/glbalignla.o In file included from Muscle/glbalignla.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/glbalignla.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/glbalignle.cpp -o Muscle/glbalignle.o In file included from Muscle/glbalignle.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/glbalignle.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/glbalignns.cpp -o Muscle/glbalignns.o In file included from Muscle/glbalignns.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/glbalignns.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/glbalignsimple.cpp -o Muscle/glbalignsimple.o In file included from Muscle/glbalignsimple.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/glbalignsimple.cpp:24:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(str, "%6.1f", s); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/glbalignsimple.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/glbalignsimple.cpp:28:13: warning: unused function 'ListTB' [-Wunused-function] static void ListTB(const char *TBM_, const ProfPos *PA, const ProfPos *PB, ^ Muscle/glbalignsimple.cpp:52:13: warning: unused function 'ListDP' [-Wunused-function] static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB, ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/glbalignsp.cpp -o Muscle/glbalignsp.o In file included from Muscle/glbalignsp.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/glbalignsp.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/glbalignspn.cpp -o Muscle/glbalignspn.o In file included from Muscle/glbalignspn.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/glbalignspn.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/glbalignss.cpp -o Muscle/glbalignss.o In file included from Muscle/glbalignss.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/glbalignss.cpp:177:16: warning: unused variable 'ptrRowA' [-Wunused-variable] const SCORE *ptrRowA = MxRowA[i]; ^ Muscle/glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] const unsigned uPrefixCountB = uLengthB + 1; ^ Muscle/glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable] const unsigned uPrefixCountA = uLengthA + 1; ^ In file included from Muscle/glbalignss.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/glbalignss.cpp:11:14: warning: unused function 'Subst' [-Wunused-function] static SCORE Subst(const Seq &seqA, const Seq &seqB, unsigned i, unsigned j) ^ 6 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/glbalndimer.cpp -o Muscle/glbalndimer.o In file included from Muscle/glbalndimer.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/glbalndimer.cpp:19:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(str, "%6.3g", s); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/glbalndimer.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/glbalndimer.cpp:14:20: warning: unused function 'LocalScoreToStr' [-Wunused-function] static const char *LocalScoreToStr(SCORE s) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/globals.cpp -o Muscle/globals.o In file included from Muscle/globals.cpp:6: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/globals.cpp:64:2: warning: 'vsprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead. [-Wdeprecated-declarations] vsprintf(szStr, szFormat, ArgList); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:207:1: note: 'vsprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ Muscle/globals.cpp:88:2: warning: 'vsprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead. [-Wdeprecated-declarations] vsprintf(szStr, szFormat, ArgList); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:207:1: note: 'vsprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ Muscle/globals.cpp:113:2: warning: 'vsprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead. [-Wdeprecated-declarations] vsprintf(szStr, szFormat, ArgList); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:207:1: note: 'vsprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/globals.cpp:6: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/globalslinux.cpp -o Muscle/globalslinux.o In file included from Muscle/globalslinux.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/globalslinux.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/globalsosx.cpp -o Muscle/globalsosx.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/globalsother.cpp -o Muscle/globalsother.o In file included from Muscle/globalsother.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/globalsother.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/globalswin32.cpp -o Muscle/globalswin32.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/gonnet.cpp -o Muscle/gonnet.o In file included from Muscle/gonnet.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/gonnet.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/gonnet.cpp:137:14: warning: unused variable 'Gonnet160' [-Wunused-variable] static SCORE Gonnet160[20][20] = ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/gotowt.cpp -o Muscle/gotowt.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/henikoffweight.cpp -o Muscle/henikoffweight.o In file included from Muscle/henikoffweight.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/henikoffweight.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/henikoffweightpb.cpp -o Muscle/henikoffweightpb.o In file included from Muscle/henikoffweightpb.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/henikoffweightpb.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/html.cpp -o Muscle/html.o In file included from Muscle/html.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/html.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/hydro.cpp -o Muscle/hydro.o In file included from Muscle/hydro.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/hydro.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/intmath.cpp -o Muscle/intmath.o In file included from Muscle/intmath.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/intmath.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/local.cpp -o Muscle/local.o In file included from Muscle/local.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/local.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/main.cpp -o Muscle/main.o In file included from Muscle/main.cpp:3: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/main.cpp:3: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/makerootmsa.cpp -o Muscle/makerootmsa.o In file included from Muscle/makerootmsa.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/makerootmsa.cpp:18:17: warning: unused variable 'uSeqLength' [-Wunused-variable] const unsigned uSeqLength = s.Length(); ^ Muscle/makerootmsa.cpp:94:17: warning: unused variable 'Path' [-Wunused-variable] const PWPath &Path = Nodes[uNodeIndex].m_Path; ^ Muscle/makerootmsa.cpp:168:17: warning: unused variable 'uTreeNodeCount' [-Wunused-variable] const unsigned uTreeNodeCount = GuideTree.GetNodeCount(); ^ In file included from Muscle/makerootmsa.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/makerootmsa.cpp:12:13: warning: unused function 'PathSeq' [-Wunused-function] static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut) ^ 6 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/makerootmsab.cpp -o Muscle/makerootmsab.o In file included from Muscle/makerootmsab.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/makerootmsab.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/maketree.cpp -o Muscle/maketree.o In file included from Muscle/maketree.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/maketree.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/mhack.cpp -o Muscle/mhack.o In file included from Muscle/mhack.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/mhack.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/mpam200.cpp -o Muscle/mpam200.o In file included from Muscle/mpam200.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/mpam200.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/msa.cpp -o Muscle/msa.o In file included from Muscle/msa.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/msa.cpp:397:3: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(szStr, "%u", u); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ Muscle/msa.cpp:411:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(szStr, "%u", u); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/msa.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/msa.cpp:385:13: warning: unused function 'FmtChar' [-Wunused-function] static void FmtChar(char c, unsigned uWidth) ^ Muscle/msa.cpp:392:13: warning: unused function 'FmtInt' [-Wunused-function] static void FmtInt(unsigned u, unsigned uWidth) ^ Muscle/msa.cpp:407:13: warning: unused function 'FmtInt0' [-Wunused-function] static void FmtInt0(unsigned u, unsigned uWidth) ^ Muscle/msa.cpp:419:13: warning: unused function 'FmtPad' [-Wunused-function] static void FmtPad(unsigned n) ^ 8 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/msa2.cpp -o Muscle/msa2.o In file included from Muscle/msa2.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/msa2.cpp:479:17: warning: unused variable 'uColCountCat' [-Wunused-variable] const unsigned uColCountCat = uColCount1 + uColCount2; ^ In file included from Muscle/msa2.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/msadistkimura.cpp -o Muscle/msadistkimura.o In file included from Muscle/msadistkimura.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/msadistkimura.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/msf.cpp -o Muscle/msf.o In file included from Muscle/msf.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/msf.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/msf.cpp:24:20: warning: unused function 'strfind' [-Wunused-function] static const char *strfind(const char *s, const char *t) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/muscle.cpp -o Muscle/muscle.o In file included from Muscle/muscle.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/muscle.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/muscleout.cpp -o Muscle/muscleout.o In file included from Muscle/muscleout.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/muscleout.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/nucmx.cpp -o Muscle/nucmx.o In file included from Muscle/nucmx.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/nucmx.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/nwdasimple.cpp -o Muscle/nwdasimple.o In file included from Muscle/nwdasimple.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/nwdasimple.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/nwdasimple2.cpp -o Muscle/nwdasimple2.o In file included from Muscle/nwdasimple2.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/nwdasimple2.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/nwdasmall.cpp -o Muscle/nwdasmall.o In file included from Muscle/nwdasmall.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/nwdasmall.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/nwrec.cpp -o Muscle/nwrec.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/nwsmall.cpp -o Muscle/nwsmall.o In file included from Muscle/nwsmall.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/nwsmall.cpp:390:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ Muscle/nwsmall.cpp:394:14: note: uninitialized use occurs here TB[i][j] |= Bit; ^~~ Muscle/nwsmall.cpp:378:10: note: initialize the variable 'Bit' to silence this warning char Bit; ^ = '\0' Muscle/nwsmall.cpp:408:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ Muscle/nwsmall.cpp:412:14: note: uninitialized use occurs here TB[i][j] |= Bit; ^~~ Muscle/nwsmall.cpp:399:10: note: initialize the variable 'Bit' to silence this warning char Bit; ^ = '\0' Muscle/nwsmall.cpp:426:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ Muscle/nwsmall.cpp:430:14: note: uninitialized use occurs here TB[i][j] |= Bit; ^~~ Muscle/nwsmall.cpp:417:10: note: initialize the variable 'Bit' to silence this warning char Bit; ^ = '\0' In file included from Muscle/nwsmall.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/nwsmall.cpp:397:20: warning: unused function 'SetBitTBD' [-Wunused-function] static inline void SetBitTBD(char **TB, unsigned i, unsigned j, char c) ^ Muscle/nwsmall.cpp:415:20: warning: unused function 'SetBitTBI' [-Wunused-function] static inline void SetBitTBI(char **TB, unsigned i, unsigned j, char c) ^ 7 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/objscore.cpp -o Muscle/objscore.o In file included from Muscle/objscore.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/objscore.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/objscore2.cpp -o Muscle/objscore2.o In file included from Muscle/objscore2.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/objscore2.cpp:67:7: warning: unused variable 'bGapping2' [-Wunused-variable] bool bGapping2 = false; ^ Muscle/objscore2.cpp:85:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable] bool bRightTermGap = false; ^ Muscle/objscore2.cpp:70:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable] bool bLeftTermGap = false; ^ Muscle/objscore2.cpp:66:7: warning: unused variable 'bGapping1' [-Wunused-variable] bool bGapping1 = false; ^ Muscle/objscore2.cpp:65:8: warning: unused variable 'scoreGaps' [-Wunused-variable] SCORE scoreGaps = 0; ^ Muscle/objscore2.cpp:143:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable] bool bLeftTermGap = false; ^ Muscle/objscore2.cpp:158:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable] bool bRightTermGap = false; ^ Muscle/objscore2.cpp:317:17: warning: unused variable 'uColCount2' [-Wunused-variable] const unsigned uColCount2 = msa2.GetColCount(); ^ Muscle/objscore2.cpp:496:17: warning: unused variable 'w' [-Wunused-variable] const WEIGHT w = w1*w2; ^ In file included from Muscle/objscore2.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 11 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/objscoreda.cpp -o Muscle/objscoreda.o In file included from Muscle/objscoreda.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/objscoreda.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/onexception.cpp -o Muscle/onexception.o In file included from Muscle/onexception.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/onexception.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/options.cpp -o Muscle/options.o In file included from Muscle/options.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/options.cpp:18:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "in", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:19:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "in1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:20:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "in2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:21:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "out", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:22:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MaxIters", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:23:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MaxHours", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:24:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "GapOpen", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:25:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "GapOpen2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:26:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "GapExtend", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:27:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "GapExtend2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:28:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "GapAmbig", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:29:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Center", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:30:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SmoothScoreCeil", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:31:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MinBestColScore", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:32:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MinSmoothScore", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:33:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ObjScore", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:34:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SmoothWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:35:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "RefineWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:36:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "FromWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:37:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ToWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:38:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SaveWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:39:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "WindowOffset", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:40:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "FirstWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:41:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "AnchorSpacing", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:42:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Log", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:43:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "LogA", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:44:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MaxTrees", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:45:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SUEFF", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:46:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Distance", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:47:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Distance1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:48:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Distance2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:49:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Weight", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:50:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Weight1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:51:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Weight2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:52:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Cluster", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:53:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Cluster1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:54:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Cluster2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:55:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Root1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:56:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Root2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:57:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Tree1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:58:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Tree2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:59:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "UseTree", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:60:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "UseTree_NoWarn", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:61:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "DiagLength", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:62:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "DiagMargin", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:63:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "DiagBreak", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:64:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Hydro", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:65:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "HydroFactor", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:66:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SPScore", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:67:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SeqType", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:68:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MaxMB", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:69:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ComputeWeights", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:70:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MaxSubFam", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:71:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ScoreFile", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:72:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "TermGaps", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:73:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "FASTAOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:74:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "CLWOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:75:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "CLWStrictOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:76:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "HTMLOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:77:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MSFOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:78:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PHYIOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:79:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PHYSOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:80:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Matrix", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:81:3: warning: suggest braces around initialization of subobject [-Wmissing-braces] "DistMx1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:82:3: warning: suggest braces around initialization of subobject [-Wmissing-braces] "DistMx2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:83:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Weight", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:89:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "LE", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:90:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SP", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:91:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SV", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:92:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SPN", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:93:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Core", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:94:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "NoCore", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:95:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Diags1", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:96:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Diags2", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:97:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Diags", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:98:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Quiet", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:99:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MSF", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:100:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Verbose", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:101:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Anchors", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:102:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "NoAnchors", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:103:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Refine", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:104:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "RefineW", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:105:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SW", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:106:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Profile", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:107:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PPScore", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:108:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ClusterOnly", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:109:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Brenner", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:110:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Dimer", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:111:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "clw", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:112:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "clwstrict", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:113:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "HTML", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:114:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Version", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:115:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Stable", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:116:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Group", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:117:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "FASTA", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:118:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ProfDB", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:119:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PAS", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:120:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PHYI", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:121:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PHYS", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:122:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "TomHydro", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/options.cpp:123:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MakeTree", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } In file included from Muscle/options.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 103 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/outweights.cpp -o Muscle/outweights.o In file included from Muscle/outweights.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/outweights.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/pam200mafft.cpp -o Muscle/pam200mafft.o In file included from Muscle/pam200mafft.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/pam200mafft.cpp:9:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 408, 20, 54, 52, -182, 179, -68, 109, -35, -47, 39, 106, 206, -14, -12, 257, 293, 191, -306, -219, 0, 0, 0, // A ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:10:5: warning: suggest braces around initialization of subobject [-Wmissing-braces] 20, 1190, -228, -295, 94, 6, 63, -131, -184, -176, -112, -29, -122, -195, 49, 185, 13, -49, 199, 333, 0, 0, 0, // C ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:11:5: warning: suggest braces around initialization of subobject [-Wmissing-braces] 54, -228, 645, 516, -399, 168, 98, -225, 75, -341, -235, 352, -149, 142, -44, 65, 7, -147, -418, -128, 0, 0, 0, // D ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:12:5: warning: suggest braces around initialization of subobject [-Wmissing-braces] 52, -295, 516, 630, -460, 145, 45, -225, 195, -307, -222, 186, -121, 299, 54, -10, -36, -130, -366, -285, 0, 0, 0, // E ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:13:3: warning: suggest braces around initialization of subobject [-Wmissing-braces] -182, 94, -399, -460, 908, -387, 82, 100, -423, 340, 87, -216, -160, -274, -307, -31, -153, 51, 19, 604, 0, 0, 0, // F ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:14:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 179, 6, 168, 145, -387, 682, -94, -196, -14, -304, -226, 99, -57, -48, 117, 175, 41, -73, -38, -329, 0, 0, 0, // G ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:15:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] -68, 63, 98, 45, 82, -94, 786, -185, 164, -72, -132, 258, 86, 388, 277, 55, -15, -197, -181, 488, 0, 0, 0, // H ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:16:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 109, -131, -225, -225, 100, -196, -185, 574, -204, 308, 411, -94, -95, -202, -188, 1, 182, 489, -254, -133, 0, 0, 0, // I ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:17:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] -35, -184, 75, 195, -423, -14, 164, -204, 652, -229, -98, 206, -66, 335, 486, 22, 39, -207, -196, -244, 0, 0, 0, // K ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:18:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] -47, -176, -341, -307, 340, -304, -72, 308, -229, 611, 389, -203, 73, -66, -150, -49, -21, 259, -46, -9, 0, 0, 0, // L ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:19:5: warning: suggest braces around initialization of subobject [-Wmissing-braces] 39, -112, -235, -222, 87, -226, -132, 411, -98, 389, 776, -111, -78, -104, -109, -29, 149, 351, -209, -162, 0, 0, 0, // M ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:20:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 106, -29, 352, 186, -216, 99, 258, -94, 206, -203, -111, 536, -1, 108, 93, 260, 188, -98, -359, 12, 0, 0, 0, // N ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:21:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 206, -122, -149, -121, -160, -57, 86, -95, -66, 73, -78, -1, 756, 142, 25, 241, 159, -55, -353, -206, 0, 0, 0, // P ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:22:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] -14, -195, 142, 299, -274, -48, 388, -202, 335, -66, -104, 108, 142, 655, 321, 7, -15, -175, -223, -53, 0, 0, 0, // Q ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:23:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] -12, 49, -44, 54, -307, 117, 277, -188, 486, -150, -109, 93, 25, 321, 626, 48, 16, -181, 124, -113, 0, 0, 0, // R ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:24:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 257, 185, 65, -10, -31, 175, 55, 1, 22, -49, -29, 260, 241, 7, 48, 373, 279, 28, -193, -35, 0, 0, 0, // S ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:25:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 293, 13, 7, -36, -153, 41, -15, 182, 39, -21, 149, 188, 159, -15, 16, 279, 442, 163, -323, -170, 0, 0, 0, // T ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:26:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 191, -49, -147, -130, 51, -73, -197, 489, -207, 259, 351, -98, -55, -175, -181, 28, 163, 525, -225, -177, 0, 0, 0, // V ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:27:3: warning: suggest braces around initialization of subobject [-Wmissing-braces] -306, 199, -418, -366, 19, -38, -181, -254, -196, -46, -209, -359, -353, -223, 124, -193, -323, -225, 1495, 83, 0, 0, 0, // W ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:28:3: warning: suggest braces around initialization of subobject [-Wmissing-braces] -219, 333, -128, -285, 604, -329, 488, -133, -244, -9, -162, 12, -206, -53, -113, -35, -170, -177, 83, 999, 0, 0, 0, // Y ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:29:6: warning: suggest braces around initialization of subobject [-Wmissing-braces] 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // B ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:30:6: warning: suggest braces around initialization of subobject [-Wmissing-braces] 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // Z ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } Muscle/pam200mafft.cpp:31:6: warning: suggest braces around initialization of subobject [-Wmissing-braces] 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // X ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } In file included from Muscle/pam200mafft.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/pam200mafft.cpp:6:14: warning: unused variable 'PAM200' [-Wunused-variable] static float PAM200[23][23] = ^ 26 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/params.cpp -o Muscle/params.o In file included from Muscle/params.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/params.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/phy.cpp -o Muscle/phy.o In file included from Muscle/phy.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/phy.cpp:665:9: warning: unused variable 'dEdgeLength' [-Wunused-variable] double dEdgeLength = GetEdgeLength(uNode1, uNode2); ^ In file included from Muscle/phy.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/phy2.cpp -o Muscle/phy2.o In file included from Muscle/phy2.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/phy2.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/phy3.cpp -o Muscle/phy3.o In file included from Muscle/phy3.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/phy3.cpp:125:15: warning: unused variable 'dThisDist' [-Wunused-variable] const double dThisDist = tree.GetEdgeLength(uNode1, uNode2); ^ Muscle/phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable] unsigned uMaxFrom = NULL_NEIGHBOR; ^ Muscle/phy3.cpp:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable] const unsigned uLeafCount = tree.GetLeafCount(); ^ Muscle/phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable] unsigned uMaxTo = NULL_NEIGHBOR; ^ Muscle/phy3.cpp:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable] double dAllMaxDist = -1e20; ^ Muscle/phy3.cpp:263:11: warning: variable 'uMostDistantLeaf' set but not used [-Wunused-but-set-variable] unsigned uMostDistantLeaf = NULL_NEIGHBOR; ^ In file included from Muscle/phy3.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/phy3.cpp:45:13: warning: unused function 'ListEIs' [-Wunused-function] static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount) ^ 9 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/phy4.cpp -o Muscle/phy4.o In file included from Muscle/phy4.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/phy4.cpp:242:3: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(szName, "Subfam_%u", uSubfamIndex + 1); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/phy4.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/phyfromclust.cpp -o Muscle/phyfromclust.o In file included from Muscle/phyfromclust.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/phyfromclust.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/phyfromfile.cpp -o Muscle/phyfromfile.o In file included from Muscle/phyfromfile.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/phyfromfile.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/physeq.cpp -o Muscle/physeq.o In file included from Muscle/physeq.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/physeq.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/phytofile.cpp -o Muscle/phytofile.o In file included from Muscle/phytofile.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/phytofile.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/posgap.cpp -o Muscle/posgap.o In file included from Muscle/posgap.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/posgap.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/ppscore.cpp -o Muscle/ppscore.o In file included from Muscle/ppscore.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/ppscore.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/profdb.cpp -o Muscle/profdb.o In file included from Muscle/profdb.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/profdb.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/profile.cpp -o Muscle/profile.o In file included from Muscle/profile.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/profile.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/profilefrommsa.cpp -o Muscle/profilefrommsa.o In file included from Muscle/profilefrommsa.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/profilefrommsa.cpp:20:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(str, "%5.1f", s); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ Muscle/profilefrommsa.cpp:248:17: warning: unused variable 'uSeqCount' [-Wunused-variable] const unsigned uSeqCount = a.GetSeqCount(); ^ Muscle/profilefrommsa.cpp:256:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable] unsigned uHydrophobicRunLength = 0; ^ In file included from Muscle/profilefrommsa.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/profilefrommsa.cpp:15:20: warning: unused function 'LocalScoreToStr' [-Wunused-function] static const char *LocalScoreToStr(SCORE s) ^ 6 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/progalign.cpp -o Muscle/progalign.o In file included from Muscle/progalign.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/progalign.cpp:41:17: warning: unused variable 'uIterCount' [-Wunused-variable] const unsigned uIterCount = uSeqCount - 1; ^ In file included from Muscle/progalign.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/progress.cpp -o Muscle/progress.o In file included from Muscle/progress.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/progress.cpp:42:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(Str, "%.0f MB(%.0f%%)", MaxMB, Pct); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ Muscle/progress.cpp:112:2: warning: 'vsprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead. [-Wdeprecated-declarations] vsprintf(szStr, szFormat, ArgList); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:207:1: note: 'vsprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/progress.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/progressivealign.cpp -o Muscle/progressivealign.o In file included from Muscle/progressivealign.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/progressivealign.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/pwpath.cpp -o Muscle/pwpath.o In file included from Muscle/pwpath.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/pwpath.cpp:80:16: warning: unused variable 'LastEdge' [-Wunused-variable] const PWEdge &LastEdge = GetEdge(uEdgeCount - 1); ^ Muscle/pwpath.cpp:213:11: warning: unused variable 'uEdgeIndex' [-Wunused-variable] unsigned uEdgeIndex = 0; ^ In file included from Muscle/pwpath.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/readmx.cpp -o Muscle/readmx.o In file included from Muscle/readmx.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/readmx.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/readmx.cpp:30:17: warning: unused function 'MxCharToLetter' [-Wunused-function] static unsigned MxCharToLetter(char c) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/realigndiffs.cpp -o Muscle/realigndiffs.o In file included from Muscle/realigndiffs.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/realigndiffs.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/realigndiffse.cpp -o Muscle/realigndiffse.o In file included from Muscle/realigndiffse.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/realigndiffse.cpp:77:13: warning: unused variable 'uNewRight' [-Wunused-variable] unsigned uNewRight = NewTree.GetRight(uNewNodeIndex); ^ Muscle/realigndiffse.cpp:80:13: warning: unused variable 'uOldRight' [-Wunused-variable] unsigned uOldRight = OldTree.GetRight(uOld); ^ In file included from Muscle/realigndiffse.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/refine.cpp -o Muscle/refine.o In file included from Muscle/refine.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/refine.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/refinehoriz.cpp -o Muscle/refinehoriz.o In file included from Muscle/refinehoriz.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/refinehoriz.cpp:260:4: warning: variable 'bRight' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ Muscle/refinehoriz.cpp:263:56: note: uninitialized use occurs here RefineHeightParts(msaIn, tree, Internals, bReverse, bRight, ^~~~~~ Muscle/refinehoriz.cpp:251:15: note: initialize the variable 'bRight' to silence this warning bool bRight; ^ = false In file included from Muscle/refinehoriz.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/refinesubfams.cpp -o Muscle/refinesubfams.o In file included from Muscle/refinesubfams.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/refinesubfams.cpp:63:17: warning: unused variable 'uNodeCount' [-Wunused-variable] const unsigned uNodeCount = tree.GetNodeCount(); ^ In file included from Muscle/refinesubfams.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/refinetree.cpp -o Muscle/refinetree.o In file included from Muscle/refinetree.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/refinetree.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/refinetreee.cpp -o Muscle/refinetreee.o In file included from Muscle/refinetreee.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/refinetreee.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/refinevert.cpp -o Muscle/refinevert.o In file included from Muscle/refinevert.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/refinevert.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/refinew.cpp -o Muscle/refinew.o In file included from Muscle/refinew.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/refinew.cpp:22:17: warning: unused variable 'uColCountCat' [-Wunused-variable] const unsigned uColCountCat = uColCount1 + uColCount2; ^ Muscle/refinew.cpp:130:4: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(fn, "win%d_inaln.tmp", uWindowIndex); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ Muscle/refinew.cpp:134:4: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(fn, "win%d_inseqs.tmp", uWindowIndex); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ Muscle/refinew.cpp:138:4: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(fn, "win%d_outaln.tmp", uWindowIndex); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ Muscle/refinew.cpp:125:13: warning: unused variable 'uOutCols' [-Wunused-variable] unsigned uOutCols = msaOut.GetColCount(); ^ In file included from Muscle/refinew.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 7 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/savebest.cpp -o Muscle/savebest.o In file included from Muscle/savebest.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/savebest.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/scoredist.cpp -o Muscle/scoredist.o In file included from Muscle/scoredist.cpp:3: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/scoredist.cpp:3: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/scoredist.cpp:17:21: warning: unused variable 'Dayhoff_CalibrationFactor' [-Wunused-const-variable] static const double Dayhoff_CalibrationFactor = 1.3370; ^ Muscle/scoredist.cpp:19:21: warning: unused variable 'MV_CalibrationFactor' [-Wunused-const-variable] static const double MV_CalibrationFactor = 1.1775; ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/scoregaps.cpp -o Muscle/scoregaps.o In file included from Muscle/scoregaps.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/scoregaps.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/scoregaps.cpp:37:13: warning: unused function 'FreeGapInfo' [-Wunused-function] static void FreeGapInfo(GAPINFO *GI) ^ Muscle/scoregaps.cpp:80:14: warning: unused function 'Penalty' [-Wunused-function] static SCORE Penalty(unsigned Length, bool Term) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/scorehistory.cpp -o Muscle/scorehistory.o In file included from Muscle/scorehistory.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/scorehistory.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/scorepp.cpp -o Muscle/scorepp.o In file included from Muscle/scorepp.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/scorepp.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/seq.cpp -o Muscle/seq.o In file included from Muscle/seq.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/seq.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/seqvect.cpp -o Muscle/seqvect.o In file included from Muscle/seqvect.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/seqvect.cpp:201:17: warning: binding dereferenced null pointer to reference has undefined behavior [-Wnull-dereference] return (Seq &) *((Seq *) 0); ^~~~~~~~~~~~ In file included from Muscle/seqvect.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/seqvect.cpp:6:14: warning: unused variable 'MAX_FASTA_LINE' [-Wunused-const-variable] const size_t MAX_FASTA_LINE = 16000; ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/setblosumweights.cpp -o Muscle/setblosumweights.o In file included from Muscle/setblosumweights.cpp:42: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/setblosumweights.cpp:42: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/setgscweights.cpp -o Muscle/setgscweights.o In file included from Muscle/setgscweights.cpp:104: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/setgscweights.cpp:104: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/setnewhandler.cpp -o Muscle/setnewhandler.o In file included from Muscle/setnewhandler.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/setnewhandler.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/spfast.cpp -o Muscle/spfast.o In file included from Muscle/spfast.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/spfast.cpp:252:17: warning: unused variable 'uSeqCount' [-Wunused-variable] const unsigned uSeqCount = msa.GetSeqCount(); ^ In file included from Muscle/spfast.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/spfast.cpp:14:20: warning: unused function 'GapTypeToStr' [-Wunused-function] static const char *GapTypeToStr(int GapType) ^ Muscle/spfast.cpp:59:14: warning: unused function 'SPColBrute' [-Wunused-function] static SCORE SPColBrute(const MSA &msa, unsigned uColIndex) ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/sptest.cpp -o Muscle/sptest.o In file included from Muscle/sptest.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/sptest.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/stabilize.cpp -o Muscle/stabilize.o In file included from Muscle/stabilize.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/stabilize.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/subfam.cpp -o Muscle/subfam.o In file included from Muscle/subfam.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/subfam.cpp:171:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(CmdLine, "probcons %s > %s 2> /dev/null", InTmp, OutTmp); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ Muscle/subfam.cpp:173:6: warning: unused variable 'NotUsed' [-Wunused-variable] int NotUsed = system(CmdLine); ^ Muscle/subfam.cpp:243:4: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(NewFileName, "%s/%s", Path, FileName); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/subfam.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/subfams.cpp -o Muscle/subfams.o In file included from Muscle/subfams.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/subfams.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/subfams.cpp:10:13: warning: unused function 'GetMostDistantPair' [-Wunused-function] static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2) ^ Muscle/subfams.cpp:40:13: warning: unused function 'InitializeSingleSource' [-Wunused-function] static void InitializeSingleSource(DistFunc &DF, unsigned uIndex) ^ Muscle/subfams.cpp:52:13: warning: unused function 'Relax' [-Wunused-function] static void Relax(DistFunc &DF, unsigned u, unsigned v) ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/sw.cpp -o Muscle/sw.o In file included from Muscle/sw.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/sw.cpp:16:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(str, "%6.2f", s); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/sw.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/sw.cpp:20:13: warning: unused function 'ListDP' [-Wunused-function] static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB, ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/termgaps.cpp -o Muscle/termgaps.o In file included from Muscle/termgaps.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/termgaps.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/textfile.cpp -o Muscle/textfile.o In file included from Muscle/textfile.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/textfile.cpp:111:6: warning: unused variable 'i' [-Wunused-variable] int i = fputc(c, m_ptrFile); ^ Muscle/textfile.cpp:124:6: warning: unused variable 'iError' [-Wunused-variable] int iError = fputs(szLine, m_ptrFile); ^ Muscle/textfile.cpp:133:2: warning: 'vsprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead. [-Wdeprecated-declarations] vsprintf(szStr, szFormat, ArgList); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:207:1: note: 'vsprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/textfile.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/threewaywt.cpp -o Muscle/threewaywt.o In file included from Muscle/threewaywt.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/threewaywt.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/tomhydro.cpp -o Muscle/tomhydro.o In file included from Muscle/tomhydro.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/tomhydro.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/traceback.cpp -o Muscle/traceback.o In file included from Muscle/traceback.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/traceback.cpp:21:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] const unsigned uPrefixCountB = uLengthB + 1; ^ Muscle/traceback.cpp:195:3: warning: variable 'cPrevEdgeType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ Muscle/traceback.cpp:202:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ Muscle/traceback.cpp:186:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(Score, scoreSI)) ^~~~~~~~~~~~~~~~~~ Muscle/traceback.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ Muscle/traceback.cpp:202:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ Muscle/traceback.cpp:186:9: note: remove the 'if' if its condition is always true else if (EQ(Score, scoreSI)) ^~~~~~~~~~~~~~~~~~~~~~~ Muscle/traceback.cpp:150:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(Score, scoreSD)) ^~~~~~~~~~~~~~~~~~ Muscle/traceback.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ Muscle/traceback.cpp:202:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ Muscle/traceback.cpp:150:9: note: remove the 'if' if its condition is always true else if (EQ(Score, scoreSD)) ^~~~~~~~~~~~~~~~~~~~~~~ Muscle/traceback.cpp:112:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(scoreSM, Score)) ^~~~~~~~~~~~~~~~~~ Muscle/traceback.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ Muscle/traceback.cpp:202:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ Muscle/traceback.cpp:112:9: note: remove the 'if' if its condition is always true else if (EQ(scoreSM, Score)) ^~~~~~~~~~~~~~~~~~~~~~~ Muscle/traceback.cpp:68:21: note: initialize the variable 'cPrevEdgeType' to silence this warning char cPrevEdgeType; ^ = '\0' In file included from Muscle/traceback.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 7 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/tracebackopt.cpp -o Muscle/tracebackopt.o In file included from Muscle/tracebackopt.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/tracebackopt.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/tracebacksw.cpp -o Muscle/tracebacksw.o In file included from Muscle/tracebacksw.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/tracebacksw.cpp:22:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] const unsigned uPrefixCountB = uLengthB + 1; ^ Muscle/tracebacksw.cpp:29:8: warning: unused variable 'scoreMax' [-Wunused-variable] SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB); ^ Muscle/tracebacksw.cpp:175:3: warning: variable 'cPrevEdgeType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ Muscle/tracebacksw.cpp:182:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ Muscle/tracebacksw.cpp:166:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(Score, scoreSI)) ^~~~~~~~~~~~~~~~~~ Muscle/tracebacksw.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ Muscle/tracebacksw.cpp:182:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ Muscle/tracebacksw.cpp:166:9: note: remove the 'if' if its condition is always true else if (EQ(Score, scoreSI)) ^~~~~~~~~~~~~~~~~~~~~~~ Muscle/tracebacksw.cpp:130:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(Score, scoreSD)) ^~~~~~~~~~~~~~~~~~ Muscle/tracebacksw.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ Muscle/tracebacksw.cpp:182:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ Muscle/tracebacksw.cpp:130:9: note: remove the 'if' if its condition is always true else if (EQ(Score, scoreSD)) ^~~~~~~~~~~~~~~~~~~~~~~ Muscle/tracebacksw.cpp:92:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(scoreMatch, Score)) ^~~~~~~~~~~~~~~~~~~~~ Muscle/tracebacksw.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ Muscle/tracebacksw.cpp:182:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ Muscle/tracebacksw.cpp:92:9: note: remove the 'if' if its condition is always true else if (EQ(scoreMatch, Score)) ^~~~~~~~~~~~~~~~~~~~~~~~~~ Muscle/tracebacksw.cpp:43:21: note: initialize the variable 'cPrevEdgeType' to silence this warning char cPrevEdgeType; ^ = '\0' In file included from Muscle/tracebacksw.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 8 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/treefrommsa.cpp -o Muscle/treefrommsa.o In file included from Muscle/treefrommsa.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/treefrommsa.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/typetostr.cpp -o Muscle/typetostr.o In file included from Muscle/typetostr.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/typetostr.cpp:35:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(pStr, "%8g", Score); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ Muscle/typetostr.cpp:52:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(pStr, "%.3g", Score); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from Muscle/typetostr.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/upgma2.cpp -o Muscle/upgma2.o In file included from Muscle/upgma2.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/upgma2.cpp:272:4: warning: variable 'dtNewDist' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ Muscle/upgma2.cpp:292:17: note: uninitialized use occurs here g_Dist[vL] = dtNewDist; ^~~~~~~~~ Muscle/upgma2.cpp:252:20: note: initialize the variable 'dtNewDist' to silence this warning dist_t dtNewDist; ^ = 0.0 Muscle/upgma2.cpp:366:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 0, 2, 14, 14, 20, ^~~~~~~~~~~~~~~~~ { } Muscle/upgma2.cpp:367:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 2, 0, 14, 14, 20, ^~~~~~~~~~~~~~~~~ { } Muscle/upgma2.cpp:368:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 14, 14, 0, 4, 20, ^~~~~~~~~~~~~~~~~~ { } Muscle/upgma2.cpp:369:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 14, 14, 4, 0, 20, ^~~~~~~~~~~~~~~~~~ { } Muscle/upgma2.cpp:370:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 20, 20, 20, 20, 0, ^~~~~~~~~~~~~~~~~~ { } In file included from Muscle/upgma2.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ Muscle/upgma2.cpp:68:13: warning: unused function 'ListState' [-Wunused-function] static void ListState() ^ 9 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/usage.cpp -o Muscle/usage.o In file included from Muscle/usage.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/usage.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/validateids.cpp -o Muscle/validateids.o In file included from Muscle/validateids.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/validateids.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/vtml2.cpp -o Muscle/vtml2.o In file included from Muscle/vtml2.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from Muscle/vtml2.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Muscle/writescorefile.cpp -o Muscle/writescorefile.o In file included from Muscle/writescorefile.cpp:1: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ Muscle/writescorefile.cpp:37:4: warning: variable 'Score' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ Muscle/writescorefile.cpp:40:12: note: uninitialized use occurs here dSum += Score; ^~~~~ Muscle/writescorefile.cpp:27:16: note: initialize the variable 'Score' to silence this warning double Score; ^ = 0.0 In file included from Muscle/writescorefile.cpp:1: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c RClustalW.cpp -o RClustalW.o In file included from RClustalW.cpp:1: In file included from ./RClustalW.h:4: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 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:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c RClustalWMain.cpp -o RClustalWMain.o In file included from RClustalWMain.cpp:5: In file included from ./ClustalW/alignment/Alignment.h:41: In file included from ./ClustalW/alignment/Sequence.h:20: 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:48: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from RClustalWMain.cpp:5: In file included from ./ClustalW/fileInput/../alignment/Alignment.h:41: In file included from ./ClustalW/fileInput/../alignment/Sequence.h:20: In file included from ./ClustalW/interface/../general/userparams.h:8: In file included from ./ClustalW/general/UserParameters.h:22: In file included from ./ClustalW/interface/../general/utils.h:8: In file included from ./ClustalW/general/Utility.h:15: In file included from ./ClustalW/interface/../general/clustalw.h:44: ./ClustalW/alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c RMuscle.cpp -o RMuscle.o In file included from RMuscle.cpp:1: In file included from ./RMuscle.h:4: ./Muscle/muscle.h:53:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from RMuscle.cpp:1: In file included from ./RMuscle.h:7: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from RMuscle.cpp:1: In file included from ./RMuscle.h:4: In file included from ./Muscle/muscle.h:37: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ushuffle.c -o ushuffle.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I. -I"./ClustalW" -I"./Muscle" -I"./ushuffle" -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c ushuffler.cpp -o ushuffler.o In file included from ushuffler.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: -undefined dynamic_lookup may not work with chained fixups ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame installing to /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-enhancerHomologSearch/00new/enhancerHomologSearch/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (enhancerHomologSearch)