############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf muscle.buildbin-libdir && mkdir muscle.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh muscle_3.42.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R muscle.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=muscle.buildbin-libdir muscle_3.42.0.tar.gz' >>>>>>> * installing *source* package ‘muscle’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c aligngivenpath.cpp -o aligngivenpath.o aligngivenpath.cpp:186:17: warning: unused variable 'uLengthA' [-Wunused-variable] const unsigned uLengthA = msaA.GetColCount(); ^ aligngivenpath.cpp:187:17: warning: unused variable 'uLengthB' [-Wunused-variable] const unsigned uLengthB = msaB.GetColCount(); ^ aligngivenpath.cpp:335:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^ aligngivenpath.cpp:336:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^ aligngivenpath.cpp:346:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^ aligngivenpath.cpp:354:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^ In file included from aligngivenpath.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 7 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c aligngivenpathsw.cpp -o aligngivenpathsw.o aligngivenpathsw.cpp:58:17: warning: unused variable 'uLengthA' [-Wunused-variable] const unsigned uLengthA = msaA.GetColCount(); ^ aligngivenpathsw.cpp:59:17: warning: unused variable 'uLengthB' [-Wunused-variable] const unsigned uLengthB = msaB.GetColCount(); ^ aligngivenpathsw.cpp:204:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^ aligngivenpathsw.cpp:205:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^ aligngivenpathsw.cpp:215:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^ aligngivenpathsw.cpp:223:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^ In file included from aligngivenpathsw.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 7 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c aligntwomsas.cpp -o aligntwomsas.o In file included from aligntwomsas.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c aligntwoprofs.cpp -o aligntwoprofs.o In file included from aligntwoprofs.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c aln.cpp -o aln.o In file included from aln.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c alpha.cpp -o alpha.o alpha.cpp:84:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] switch (Alpha) ^~~~~ alpha.cpp:84:10: note: add missing switch cases switch (Alpha) ^ In file included from alpha.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c anchors.cpp -o anchors.o anchors.cpp:162:13: warning: unused variable 'uWindowCenter' [-Wunused-variable] unsigned uWindowCenter = uBestColIndex + uWindowLength/2; ^ In file included from anchors.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ anchors.cpp:53:13: warning: unused function 'FindBestColsGrade' [-Wunused-function] static void FindBestColsGrade(const SCORE Score[], unsigned uCount, ^ anchors.cpp:105:13: warning: unused function 'ListBestCols' [-Wunused-function] static void ListBestCols(const MSA &msa, const SCORE Score[], const SCORE SmoothScore[], ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bittraceback.cpp -o bittraceback.o bittraceback.cpp:146:7: warning: unused variable 'Bits' [-Wunused-variable] char Bits = TraceBack[uLengthA][uLengthB]; ^ In file included from bittraceback.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ bittraceback.cpp:15:20: warning: unused function 'BitsToStr' [-Wunused-function] static const char *BitsToStr(char Bits) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c blosum62.cpp -o blosum62.o In file included from blosum62.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c blosumla.cpp -o blosumla.o In file included from blosumla.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ blosumla.cpp:7:14: warning: unused variable 'Blosum62LA' [-Wunused-variable] static float Blosum62LA[20][20] = ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c clust.cpp -o clust.o clust.cpp:167:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] switch (m_JoinStyle) ^~~~~~~~~~~ clust.cpp:167:10: note: add missing switch cases switch (m_JoinStyle) ^ clust.cpp:184:17: warning: unused variable 'uClusterCount' [-Wunused-variable] const unsigned uClusterCount = GetClusterCount(); ^ clust.cpp:204:17: warning: unused variable 'uClusterCount' [-Wunused-variable] const unsigned uClusterCount = GetClusterCount(); ^ clust.cpp:295:10: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch] switch (m_CentroidStyle) ^~~~~~~~~~~~~~~ clust.cpp:295:10: note: add missing switch cases switch (m_CentroidStyle) ^ clust.cpp:360:14: warning: unused variable 'dDistLR' [-Wunused-variable] const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex); ^ clust.cpp:611:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] switch (m_JoinStyle) ^~~~~~~~~~~ clust.cpp:611:10: note: add missing switch cases switch (m_JoinStyle) ^ In file included from clust.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 7 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cluster.cpp -o cluster.o cluster.cpp:284:8: warning: variable 'bFound' set but not used [-Wunused-but-set-variable] bool bFound = false; ^ cluster.cpp:267:9: warning: unused variable 'dMaxDist' [-Wunused-variable] double dMaxDist = 0.0; ^ In file included from cluster.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ cluster.cpp:10:21: warning: unused function 'Max' [-Wunused-function] static inline float Max(float d1, float d2) ^ cluster.cpp:15:21: warning: unused function 'Mean' [-Wunused-function] static inline float Mean(float d1, float d2) ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c clwwt.cpp -o clwwt.o In file included from clwwt.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c color.cpp -o color.o 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 color.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ color.cpp:72:12: warning: unused function 'BlosumScore' [-Wunused-function] static int BlosumScore(char c1, char c2) ^ 25 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cons.cpp -o cons.o In file included from cons.cpp:7: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c diaglist.cpp -o diaglist.o In file included from diaglist.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c diffobjscore.cpp -o diffobjscore.o diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable] const unsigned uColCount = msa.GetColCount(); ^ diffobjscore.cpp:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable] const unsigned uSeqCount = msa.GetSeqCount(); ^ In file included from diffobjscore.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c diffpaths.cpp -o diffpaths.o In file included from diffpaths.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c difftrees.cpp -o difftrees.o difftrees.cpp:161:17: warning: unused variable 'uLeafCount2' [-Wunused-variable] const unsigned uLeafCount2 = Tree2.GetLeafCount(); ^ In file included from difftrees.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c difftreese.cpp -o difftreese.o In file included from difftreese.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c distcalc.cpp -o distcalc.o In file included from distcalc.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c distfunc.cpp -o distfunc.o In file included from distfunc.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c distpwkimura.cpp -o distpwkimura.o In file included from distpwkimura.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c domuscle.cpp -o domuscle.o In file included from domuscle.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dosp.cpp -o dosp.o In file included from dosp.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dpreglist.cpp -o dpreglist.o dpreglist.cpp:82:19: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable] const unsigned uDiagLengthMinusCaps = uEndVertexA - uStartVertexA - 1; ^ In file included from dpreglist.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c drawtree.cpp -o drawtree.o In file included from drawtree.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c edgelist.cpp -o edgelist.o In file included from edgelist.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c enumopts.cpp -o enumopts.o In file included from enumopts.cpp:8: ./enums.h:12:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ALPHA, Amino) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :112:1: note: expanded from here "Amino" ^ In file included from enumopts.cpp:8: ./enums.h:13:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ALPHA, DNA) ^~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :115:1: note: expanded from here "DNA" ^ In file included from enumopts.cpp:8: ./enums.h:14:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ALPHA, RNA) ^~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :118:1: note: expanded from here "RNA" ^ In file included from enumopts.cpp:8: ./enums.h:15:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(ALPHA) ^~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:18:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQTYPE, Protein) ^~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :122:1: note: expanded from here "Protein" ^ In file included from enumopts.cpp:8: ./enums.h:19:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQTYPE, DNA) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :125:1: note: expanded from here "DNA" ^ In file included from enumopts.cpp:8: ./enums.h:20:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQTYPE, RNA) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :128:1: note: expanded from here "RNA" ^ In file included from enumopts.cpp:8: ./enums.h:21:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQTYPE, Auto) ^~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :131:1: note: expanded from here "Auto" ^ In file included from enumopts.cpp:8: ./enums.h:22:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(SEQTYPE) ^~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:25:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ROOT, Pseudo) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :135:1: note: expanded from here "Pseudo" ^ In file included from enumopts.cpp:8: ./enums.h:26:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ROOT, MidLongestSpan) ^~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :138:1: note: expanded from here "MidLongestSpan" ^ In file included from enumopts.cpp:8: ./enums.h:27:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ROOT, MinAvgLeafDist) ^~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :141:1: note: expanded from here "MinAvgLeafDist" ^ In file included from enumopts.cpp:8: ./enums.h:28:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(ROOT) ^~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:31:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(CLUSTER, UPGMA) ^~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :145:1: note: expanded from here "UPGMA" ^ In file included from enumopts.cpp:8: ./enums.h:32:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(CLUSTER, UPGMAMax) ^~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :148:1: note: expanded from here "UPGMAMax" ^ In file included from enumopts.cpp:8: ./enums.h:33:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(CLUSTER, UPGMAMin) ^~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :151:1: note: expanded from here "UPGMAMin" ^ In file included from enumopts.cpp:8: ./enums.h:34:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(CLUSTER, UPGMB) ^~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :154:1: note: expanded from here "UPGMB" ^ In file included from enumopts.cpp:8: ./enums.h:35:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(CLUSTER, NeighborJoining) ^~~~~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :157:1: note: expanded from here "NeighborJoining" ^ In file included from enumopts.cpp:8: ./enums.h:36:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(CLUSTER) ^~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:39:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(JOIN, NearestNeighbor) ^~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :161:1: note: expanded from here "NearestNeighbor" ^ In file included from enumopts.cpp:8: ./enums.h:40:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(JOIN, NeighborJoining) ^~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :164:1: note: expanded from here "NeighborJoining" ^ In file included from enumopts.cpp:8: ./enums.h:41:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(JOIN) ^~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:44:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(LINKAGE, Min) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :168:1: note: expanded from here "Min" ^ In file included from enumopts.cpp:8: ./enums.h:45:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(LINKAGE, Avg) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :171:1: note: expanded from here "Avg" ^ In file included from enumopts.cpp:8: ./enums.h:46:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(LINKAGE, Max) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :174:1: note: expanded from here "Max" ^ In file included from enumopts.cpp:8: ./enums.h:47:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(LINKAGE, NeighborJoining) ^~~~~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :177:1: note: expanded from here "NeighborJoining" ^ In file included from enumopts.cpp:8: ./enums.h:48:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(LINKAGE, Biased) ^~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :180:1: note: expanded from here "Biased" ^ In file included from enumopts.cpp:8: ./enums.h:49:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(LINKAGE) ^~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:52:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Kmer6_6) ^~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :184:1: note: expanded from here "Kmer6_6" ^ In file included from enumopts.cpp:8: ./enums.h:53:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Kmer20_3) ^~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :187:1: note: expanded from here "Kmer20_3" ^ In file included from enumopts.cpp:8: ./enums.h:54:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Kmer20_4) ^~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :190:1: note: expanded from here "Kmer20_4" ^ In file included from enumopts.cpp:8: ./enums.h:55:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Kbit20_3) ^~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :193:1: note: expanded from here "Kbit20_3" ^ In file included from enumopts.cpp:8: ./enums.h:56:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Kmer4_6) ^~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :196:1: note: expanded from here "Kmer4_6" ^ In file included from enumopts.cpp:8: ./enums.h:57:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, PctIdKimura) ^~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :199:1: note: expanded from here "PctIdKimura" ^ In file included from enumopts.cpp:8: ./enums.h:58:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, PctIdLog) ^~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :202:1: note: expanded from here "PctIdLog" ^ In file included from enumopts.cpp:8: ./enums.h:59:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, PWKimura) ^~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :205:1: note: expanded from here "PWKimura" ^ In file included from enumopts.cpp:8: ./enums.h:60:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, PWScoreDist) ^~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :208:1: note: expanded from here "PWScoreDist" ^ In file included from enumopts.cpp:8: ./enums.h:61:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, ScoreDist) ^~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :211:1: note: expanded from here "ScoreDist" ^ In file included from enumopts.cpp:8: ./enums.h:62:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Edit) ^~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :214:1: note: expanded from here "Edit" ^ In file included from enumopts.cpp:8: ./enums.h:63:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(DISTANCE) ^~~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:66:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(PPSCORE, LE) ^~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :218:1: note: expanded from here "LE" ^ In file included from enumopts.cpp:8: ./enums.h:67:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(PPSCORE, SP) ^~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :221:1: note: expanded from here "SP" ^ In file included from enumopts.cpp:8: ./enums.h:68:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(PPSCORE, SV) ^~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :224:1: note: expanded from here "SV" ^ In file included from enumopts.cpp:8: ./enums.h:69:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(PPSCORE, SPN) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :227:1: note: expanded from here "SPN" ^ In file included from enumopts.cpp:8: ./enums.h:70:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(PPSCORE) ^~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:73:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, None) ^~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :231:1: note: expanded from here "None" ^ In file included from enumopts.cpp:8: ./enums.h:74:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, Henikoff) ^~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :234:1: note: expanded from here "Henikoff" ^ In file included from enumopts.cpp:8: ./enums.h:75:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, HenikoffPB) ^~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :237:1: note: expanded from here "HenikoffPB" ^ In file included from enumopts.cpp:8: ./enums.h:76:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, GSC) ^~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :240:1: note: expanded from here "GSC" ^ In file included from enumopts.cpp:8: ./enums.h:77:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, ClustalW) ^~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :243:1: note: expanded from here "ClustalW" ^ In file included from enumopts.cpp:8: ./enums.h:78:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, ThreeWay) ^~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :246:1: note: expanded from here "ThreeWay" ^ In file included from enumopts.cpp:8: ./enums.h:79:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(SEQWEIGHT) ^~~~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:82:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, SP) // Sum of Pairs of sequences ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :250:1: note: expanded from here "SP" ^ In file included from enumopts.cpp:8: ./enums.h:83:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, DP) // Dynamic Programming score ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :253:1: note: expanded from here "DP" ^ In file included from enumopts.cpp:8: ./enums.h:84:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, XP) // Cross Pairs = sum of pairs between two MSAs ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :256:1: note: expanded from here "XP" ^ In file included from enumopts.cpp:8: ./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 ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :259:1: note: expanded from here "PS" ^ In file included from enumopts.cpp:8: ./enums.h:86:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, SPF) // sum of pairs, fast approximation ^~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :262:1: note: expanded from here "SPF" ^ In file included from enumopts.cpp:8: ./enums.h:87:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, SPM) // sp if <= 100 seqs, spf otherwise ^~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :265:1: note: expanded from here "SPM" ^ In file included from enumopts.cpp:8: ./enums.h:88:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(OBJSCORE) ^~~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:91:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(TERMGAPS, Full) ^~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :269:1: note: expanded from here "Full" ^ In file included from enumopts.cpp:8: ./enums.h:92:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(TERMGAPS, Half) ^~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :272:1: note: expanded from here "Half" ^ In file included from enumopts.cpp:8: ./enums.h:93:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(TERMGAPS, Ext) ^~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :275:1: note: expanded from here "Ext" ^ In file included from enumopts.cpp:8: ./enums.h:94:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(TERMGAPS) ^~~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 64 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c enumtostr.cpp -o enumtostr.o In file included from enumtostr.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c estring.cpp -o estring.o estring.cpp:397:8: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if (nB > 0) ^~~~~~ estring.cpp:409:11: note: uninitialized use occurs here switch (cType) ^~~~~ estring.cpp:397:4: note: remove the 'if' if its condition is always true if (nB > 0) ^~~~~~~~~~~ estring.cpp:395:12: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (nA < 0) ^~~~~~ estring.cpp:409:11: note: uninitialized use occurs here switch (cType) ^~~~~ estring.cpp:395:8: note: remove the 'if' if its condition is always true else if (nA < 0) ^~~~~~~~~~~ estring.cpp:386:13: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (nB < 0) ^~~~~~ estring.cpp:409:11: note: uninitialized use occurs here switch (cType) ^~~~~ estring.cpp:386:9: note: remove the 'if' if its condition is always true else if (nB < 0) ^~~~~~~~~~~ estring.cpp:377:13: note: initialize the variable 'cType' to silence this warning char cType; ^ = '\0' In file included from estring.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ estring.cpp:464:13: warning: unused function 'CanMultiplyEstrings' [-Wunused-function] static bool CanMultiplyEstrings(const short es1[], const short es2[]) ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fasta.cpp -o fasta.o fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable] unsigned uColCount = uInsane; ^ fasta.cpp:15:11: warning: unused variable 'uSeqCount' [-Wunused-variable] unsigned uSeqCount = 0; ^ In file included from fasta.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fasta2.cpp -o fasta2.o In file included from fasta2.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastclust.cpp -o fastclust.o In file included from fastclust.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastdist.cpp -o fastdist.o In file included from fastdist.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastdistjones.cpp -o fastdistjones.o In file included from fastdistjones.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastdistkbit.cpp -o fastdistkbit.o In file included from fastdistkbit.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastdistkmer.cpp -o fastdistkmer.o fastdistkmer.cpp:235:11: warning: unused variable 'KD' [-Wunused-variable] double KD = KimuraDist(EstimatedPctId); ^ In file included from fastdistkmer.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastdistmafft.cpp -o fastdistmafft.o fastdistmafft.cpp:238:15: warning: unused variable 'pName1' [-Wunused-variable] const char *pName1 = s1.GetName(); ^ In file included from fastdistmafft.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ fastdistmafft.cpp:104:13: warning: unused function 'ListCount' [-Wunused-function] static void ListCount(const unsigned char Count[]) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastdistnuc.cpp -o fastdistnuc.o fastdistnuc.cpp:223:15: warning: unused variable 'pName1' [-Wunused-variable] const char *pName1 = s1.GetName(); ^ In file included from fastdistnuc.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ fastdistnuc.cpp:33:17: warning: unused variable 'uResidueGroupCount' [-Wunused-variable] static unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]); ^ fastdistnuc.cpp:85:13: warning: unused function 'ListCount' [-Wunused-function] static void ListCount(const unsigned char Count[]) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastscorepath2.cpp -o fastscorepath2.o In file included from fastscorepath2.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c finddiags.cpp -o finddiags.o In file included from finddiags.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ finddiags.cpp:11:14: warning: unused function 'TupleToStr' [-Wunused-function] static char *TupleToStr(int t) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c finddiagsn.cpp -o finddiagsn.o In file included from finddiagsn.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ finddiagsn.cpp:12:14: warning: unused function 'TupleToStr' [-Wunused-function] static char *TupleToStr(int t) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalign.cpp -o glbalign.o In file included from glbalign.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalign352.cpp -o glbalign352.o In file included from glbalign352.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbaligndiag.cpp -o glbaligndiag.o In file included from glbaligndiag.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalignla.cpp -o glbalignla.o In file included from glbalignla.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalignle.cpp -o glbalignle.o In file included from glbalignle.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalignns.cpp -o glbalignns.o In file included from glbalignns.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalignsimple.cpp -o glbalignsimple.o In file included from glbalignsimple.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ glbalignsimple.cpp:28:13: warning: unused function 'ListTB' [-Wunused-function] static void ListTB(const char *TBM_, const ProfPos *PA, const ProfPos *PB, ^ glbalignsimple.cpp:52:13: warning: unused function 'ListDP' [-Wunused-function] static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB, ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalignsp.cpp -o glbalignsp.o In file included from glbalignsp.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalignspn.cpp -o glbalignspn.o In file included from glbalignspn.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalignss.cpp -o glbalignss.o glbalignss.cpp:177:16: warning: unused variable 'ptrRowA' [-Wunused-variable] const SCORE *ptrRowA = MxRowA[i]; ^ glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] const unsigned uPrefixCountB = uLengthB + 1; ^ glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable] const unsigned uPrefixCountA = uLengthA + 1; ^ In file included from glbalignss.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ glbalignss.cpp:11:14: warning: unused function 'Subst' [-Wunused-function] static SCORE Subst(const Seq &seqA, const Seq &seqB, unsigned i, unsigned j) ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalndimer.cpp -o glbalndimer.o glbalndimer.cpp:123:10: warning: enumeration values 'PPSCORE_Undefined' and 'PPSCORE_SPN' not handled in switch [-Wswitch] switch (g_PPScore) ^~~~~~~~~ glbalndimer.cpp:123:10: note: add missing switch cases switch (g_PPScore) ^ In file included from glbalndimer.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ glbalndimer.cpp:14:20: warning: unused function 'LocalScoreToStr' [-Wunused-function] static const char *LocalScoreToStr(SCORE s) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c globals.cpp -o globals.o In file included from globals.cpp:6: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c globalslinux.cpp -o globalslinux.o In file included from globalslinux.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c globalsosx.cpp -o globalsosx.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c globalsother.cpp -o globalsother.o In file included from globalsother.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c globalswin32.cpp -o globalswin32.o In file included from globalswin32.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gonnet.cpp -o gonnet.o In file included from gonnet.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ gonnet.cpp:137:14: warning: unused variable 'Gonnet160' [-Wunused-variable] static SCORE Gonnet160[20][20] = ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gotowt.cpp -o gotowt.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c henikoffweight.cpp -o henikoffweight.o In file included from henikoffweight.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c henikoffweightpb.cpp -o henikoffweightpb.o In file included from henikoffweightpb.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c html.cpp -o html.o In file included from html.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hydro.cpp -o hydro.o In file included from hydro.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c intmath.cpp -o intmath.o In file included from intmath.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c local.cpp -o local.o In file included from local.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c main.cpp -o main.o main.cpp:111:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] NULL ^~~~ { } /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/stddef.h:84:18: note: expanded from macro 'NULL' # define NULL __null ^~~~~~ In file included from main.cpp:7: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c makerootmsa.cpp -o makerootmsa.o makerootmsa.cpp:18:17: warning: unused variable 'uSeqLength' [-Wunused-variable] const unsigned uSeqLength = s.Length(); ^ makerootmsa.cpp:94:17: warning: unused variable 'Path' [-Wunused-variable] const PWPath &Path = Nodes[uNodeIndex].m_Path; ^ makerootmsa.cpp:168:17: warning: unused variable 'uTreeNodeCount' [-Wunused-variable] const unsigned uTreeNodeCount = GuideTree.GetNodeCount(); ^ In file included from makerootmsa.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ makerootmsa.cpp:12:13: warning: unused function 'PathSeq' [-Wunused-function] static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut) ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c makerootmsab.cpp -o makerootmsab.o In file included from makerootmsab.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c maketree.cpp -o maketree.o In file included from maketree.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mhack.cpp -o mhack.o In file included from mhack.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mpam200.cpp -o mpam200.o In file included from mpam200.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c msa.cpp -o msa.o In file included from msa.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ msa.cpp:385:13: warning: unused function 'FmtChar' [-Wunused-function] static void FmtChar(char c, unsigned uWidth) ^ msa.cpp:392:13: warning: unused function 'FmtInt' [-Wunused-function] static void FmtInt(unsigned u, unsigned uWidth) ^ msa.cpp:407:13: warning: unused function 'FmtInt0' [-Wunused-function] static void FmtInt0(unsigned u, unsigned uWidth) ^ msa.cpp:419:13: warning: unused function 'FmtPad' [-Wunused-function] static void FmtPad(unsigned n) ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c msa2.cpp -o msa2.o msa2.cpp:357:10: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch] switch (Method) ^~~~~~ msa2.cpp:357:10: note: add missing switch cases switch (Method) ^ msa2.cpp:476:17: warning: unused variable 'uColCountCat' [-Wunused-variable] const unsigned uColCountCat = uColCount1 + uColCount2; ^ In file included from msa2.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c msadistkimura.cpp -o msadistkimura.o In file included from msadistkimura.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c msf.cpp -o msf.o In file included from msf.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ msf.cpp:24:20: warning: unused function 'strfind' [-Wunused-function] static const char *strfind(const char *s, const char *t) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c muscle.cpp -o muscle.o In file included from muscle.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c muscleout.cpp -o muscleout.o In file included from muscleout.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nucmx.cpp -o nucmx.o In file included from nucmx.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nwdasimple.cpp -o nwdasimple.o In file included from nwdasimple.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nwdasimple2.cpp -o nwdasimple2.o In file included from nwdasimple2.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nwdasmall.cpp -o nwdasmall.o In file included from nwdasmall.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nwrec.cpp -o nwrec.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nwsmall.cpp -o nwsmall.o nwsmall.cpp:390:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ nwsmall.cpp:394:14: note: uninitialized use occurs here TB[i][j] |= Bit; ^~~ nwsmall.cpp:378:10: note: initialize the variable 'Bit' to silence this warning char Bit; ^ = '\0' nwsmall.cpp:408:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ nwsmall.cpp:412:14: note: uninitialized use occurs here TB[i][j] |= Bit; ^~~ nwsmall.cpp:399:10: note: initialize the variable 'Bit' to silence this warning char Bit; ^ = '\0' nwsmall.cpp:426:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ nwsmall.cpp:430:14: note: uninitialized use occurs here TB[i][j] |= Bit; ^~~ nwsmall.cpp:417:10: note: initialize the variable 'Bit' to silence this warning char Bit; ^ = '\0' In file included from nwsmall.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ nwsmall.cpp:397:20: warning: unused function 'SetBitTBD' [-Wunused-function] static inline void SetBitTBD(char **TB, unsigned i, unsigned j, char c) ^ nwsmall.cpp:415:20: warning: unused function 'SetBitTBI' [-Wunused-function] static inline void SetBitTBI(char **TB, unsigned i, unsigned j, char c) ^ 6 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c objscore.cpp -o objscore.o objscore.cpp:31:10: warning: enumeration values 'OBJSCORE_Undefined' and 'OBJSCORE_SPM' not handled in switch [-Wswitch] switch (OS) ^~ objscore.cpp:31:10: note: add missing switch cases switch (OS) ^ In file included from objscore.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c objscore2.cpp -o objscore2.o objscore2.cpp:22:10: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch] switch (g_TermGaps) ^~~~~~~~~~ objscore2.cpp:22:10: note: add missing switch cases switch (g_TermGaps) ^ objscore2.cpp:62:8: warning: unused variable 'scoreGaps' [-Wunused-variable] SCORE scoreGaps = 0; ^ objscore2.cpp:82:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable] bool bRightTermGap = false; ^ objscore2.cpp:64:7: warning: unused variable 'bGapping2' [-Wunused-variable] bool bGapping2 = false; ^ objscore2.cpp:63:7: warning: unused variable 'bGapping1' [-Wunused-variable] bool bGapping1 = false; ^ objscore2.cpp:67:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable] bool bLeftTermGap = false; ^ objscore2.cpp:140:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable] bool bLeftTermGap = false; ^ objscore2.cpp:155:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable] bool bRightTermGap = false; ^ objscore2.cpp:314:17: warning: unused variable 'uColCount2' [-Wunused-variable] const unsigned uColCount2 = msa2.GetColCount(); ^ objscore2.cpp:493:17: warning: unused variable 'w' [-Wunused-variable] const WEIGHT w = w1*w2; ^ In file included from objscore2.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 11 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c objscoreda.cpp -o objscoreda.o In file included from objscoreda.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c onexception.cpp -o onexception.o In file included from onexception.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c optionsR.cpp -o optionsR.o optionsR.cpp:21:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "in", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:22:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "in1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:23:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "in2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:24:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "out", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:25:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MaxIters", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:26:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MaxHours", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:27:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "GapOpen", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:28:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "GapOpen2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:29:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "GapExtend", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:30:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "GapExtend2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:31:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "GapAmbig", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:32:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Center", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:33:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SmoothScoreCeil", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:34:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MinBestColScore", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:35:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MinSmoothScore", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:36:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ObjScore", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:37:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SmoothWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:38:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "RefineWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:39:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "FromWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:40:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ToWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:41:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SaveWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:42:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "WindowOffset", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:43:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "FirstWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:44:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "AnchorSpacing", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:45:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Log", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:46:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "LogA", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:47:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MaxTrees", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:48:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SUEFF", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:49:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Distance", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:50:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Distance1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:51:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Distance2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:52:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Weight", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:53:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Weight1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:54:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Weight2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:55:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Cluster", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:56:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Cluster1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:57:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Cluster2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:58:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Root1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:59:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Root2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:60:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Tree1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:61:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Tree2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:62:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "UseTree", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:63:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "UseTree_NoWarn", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:64:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "DiagLength", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:65:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "DiagMargin", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:66:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "DiagBreak", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:67:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Hydro", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:68:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "HydroFactor", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:69:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SPScore", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:70:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SeqType", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:71:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MaxMB", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:72:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ComputeWeights", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:73:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MaxSubFam", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:74:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ScoreFile", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:75:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "TermGaps", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:76:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "FASTAOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:77:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "CLWOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:78:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "CLWStrictOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:79:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "HTMLOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:80:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MSFOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:81:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PHYIOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:82:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PHYSOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:83:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Matrix", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:84:3: warning: suggest braces around initialization of subobject [-Wmissing-braces] "DistMx1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:85:3: warning: suggest braces around initialization of subobject [-Wmissing-braces] "DistMx2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:86:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Weight", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:92:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "LE", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:93:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SP", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:94:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SV", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:95:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SPN", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:96:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Core", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:97:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "NoCore", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:98:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Diags1", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:99:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Diags2", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:100:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Diags", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:101:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Quiet", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:102:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MSF", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:103:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Verbose", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:104:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Anchors", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:105:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "NoAnchors", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:106:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Refine", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:107:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "RefineW", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:108:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SW", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:109:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Profile", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:110:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PPScore", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:111:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ClusterOnly", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:112:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Brenner", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:113:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Dimer", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:114:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "clw", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:115:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "clwstrict", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:116:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "HTML", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:117:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Version", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:118:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Stable", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:119:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Group", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:120:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "FASTA", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:121:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ProfDB", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:122:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PAS", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:123:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PHYI", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:124:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PHYS", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:125:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "TomHydro", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } optionsR.cpp:126:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MakeTree", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } In file included from optionsR.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 102 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c outweights.cpp -o outweights.o In file included from outweights.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pam200mafft.cpp -o pam200mafft.o 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } 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 pam200mafft.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ pam200mafft.cpp:6:14: warning: unused variable 'PAM200' [-Wunused-variable] static float PAM200[23][23] = ^ 25 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c params.cpp -o params.o params.cpp:445:10: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch] switch (g_PPScore) ^~~~~~~~~ params.cpp:445:10: note: add missing switch cases switch (g_PPScore) ^ params.cpp:655:14: warning: unused variable 'VTML_SP' [-Wunused-variable] SCOREMATRIX VTML_SP; ^ params.cpp:657:14: warning: unused variable 'NUC_SP' [-Wunused-variable] SCOREMATRIX NUC_SP; ^ params.cpp:654:14: warning: unused variable 'PAM200NoCenter' [-Wunused-variable] SCOREMATRIX PAM200NoCenter; ^ params.cpp:656:14: warning: unused variable 'VTML_SPNoCenter' [-Wunused-variable] SCOREMATRIX VTML_SPNoCenter; ^ params.cpp:653:14: warning: unused variable 'PAM200' [-Wunused-variable] SCOREMATRIX PAM200; ^ params.cpp:652:14: warning: unused variable 'VTML_LA' [-Wunused-variable] SCOREMATRIX VTML_LA; ^ params.cpp:659:2: warning: expression result unused [-Wunused-value] g_ptrScoreMatrix; ^~~~~~~~~~~~~~~~ In file included from params.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 9 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phy.cpp -o phy.o phy.cpp:665:9: warning: unused variable 'dEdgeLength' [-Wunused-variable] double dEdgeLength = GetEdgeLength(uNode1, uNode2); ^ In file included from phy.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phy2.cpp -o phy2.o In file included from phy2.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phy3.cpp -o phy3.o phy3.cpp:125:15: warning: unused variable 'dThisDist' [-Wunused-variable] const double dThisDist = tree.GetEdgeLength(uNode1, uNode2); ^ phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable] unsigned uMaxFrom = NULL_NEIGHBOR; ^ phy3.cpp:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable] const unsigned uLeafCount = tree.GetLeafCount(); ^ phy3.cpp:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable] double dAllMaxDist = -1e20; ^ phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable] unsigned uMaxTo = NULL_NEIGHBOR; ^ phy3.cpp:263:11: warning: variable 'uMostDistantLeaf' set but not used [-Wunused-but-set-variable] unsigned uMostDistantLeaf = NULL_NEIGHBOR; ^ In file included from phy3.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ phy3.cpp:45:13: warning: unused function 'ListEIs' [-Wunused-function] static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount) ^ 8 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phy4.cpp -o phy4.o In file included from phy4.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phyfromclust.cpp -o phyfromclust.o In file included from phyfromclust.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phyfromfile.cpp -o phyfromfile.o In file included from phyfromfile.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c physeq.cpp -o physeq.o In file included from physeq.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phytofile.cpp -o phytofile.o In file included from phytofile.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c posgap.cpp -o posgap.o In file included from posgap.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ppscore.cpp -o ppscore.o In file included from ppscore.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c profdb.cpp -o profdb.o In file included from profdb.cpp:9: In file included from ./clustsetmsa.h:8: ./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch] switch(m_Distance) ^~~~~~~~~~ ./msadist.h:22:10: note: add missing switch cases switch(m_Distance) ^ In file included from profdb.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c profile.cpp -o profile.o In file included from profile.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c profilefrommsa.cpp -o profilefrommsa.o profilefrommsa.cpp:230:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] switch (g_Alpha) ^~~~~~~ profilefrommsa.cpp:230:10: note: add missing switch cases switch (g_Alpha) ^ profilefrommsa.cpp:245:17: warning: unused variable 'uSeqCount' [-Wunused-variable] const unsigned uSeqCount = a.GetSeqCount(); ^ profilefrommsa.cpp:253:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable] unsigned uHydrophobicRunLength = 0; ^ In file included from profilefrommsa.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ profilefrommsa.cpp:15:20: warning: unused function 'LocalScoreToStr' [-Wunused-function] static const char *LocalScoreToStr(SCORE s) ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c progalign.cpp -o progalign.o progalign.cpp:41:17: warning: unused variable 'uIterCount' [-Wunused-variable] const unsigned uIterCount = uSeqCount - 1; ^ In file included from progalign.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c progress.cpp -o progress.o In file included from progress.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c progressivealign.cpp -o progressivealign.o In file included from progressivealign.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwpath.cpp -o pwpath.o pwpath.cpp:79:16: warning: unused variable 'LastEdge' [-Wunused-variable] const PWEdge &LastEdge = GetEdge(uEdgeCount - 1); ^ pwpath.cpp:212:11: warning: unused variable 'uEdgeIndex' [-Wunused-variable] unsigned uEdgeIndex = 0; ^ In file included from pwpath.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c readmx.cpp -o readmx.o In file included from readmx.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ readmx.cpp:30:17: warning: unused function 'MxCharToLetter' [-Wunused-function] static unsigned MxCharToLetter(char c) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c realigndiffs.cpp -o realigndiffs.o In file included from realigndiffs.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c realigndiffse.cpp -o realigndiffse.o realigndiffse.cpp:72:13: warning: unused variable 'uNewRight' [-Wunused-variable] unsigned uNewRight = NewTree.GetRight(uNewNodeIndex); ^ realigndiffse.cpp:75:13: warning: unused variable 'uOldRight' [-Wunused-variable] unsigned uOldRight = OldTree.GetRight(uOld); ^ In file included from realigndiffse.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c redblack.cpp -o redblack.o In file included from redblack.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c refine.cpp -o refine.o In file included from refine.cpp:9: In file included from ./clustsetmsa.h:8: ./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch] switch(m_Distance) ^~~~~~~~~~ ./msadist.h:22:10: note: add missing switch cases switch(m_Distance) ^ In file included from refine.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c refinehoriz.cpp -o refinehoriz.o refinehoriz.cpp:256:4: warning: variable 'bRight' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ refinehoriz.cpp:259:56: note: uninitialized use occurs here RefineHeightParts(msaIn, tree, Internals, bReverse, bRight, ^~~~~~ refinehoriz.cpp:247:15: note: initialize the variable 'bRight' to silence this warning bool bRight; ^ = false In file included from refinehoriz.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c refinesubfams.cpp -o refinesubfams.o refinesubfams.cpp:63:17: warning: unused variable 'uNodeCount' [-Wunused-variable] const unsigned uNodeCount = tree.GetNodeCount(); ^ In file included from refinesubfams.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c refinetree.cpp -o refinetree.o In file included from refinetree.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c refinetreee.cpp -o refinetreee.o In file included from refinetreee.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c refinevert.cpp -o refinevert.o In file included from refinevert.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c refinew.cpp -o refinew.o refinew.cpp:26:17: warning: unused variable 'uColCountCat' [-Wunused-variable] const unsigned uColCountCat = uColCount1 + uColCount2; ^ refinew.cpp:129:13: warning: unused variable 'uOutCols' [-Wunused-variable] unsigned uOutCols = msaOut.GetColCount(); ^ In file included from refinew.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c savebest.cpp -o savebest.o In file included from savebest.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c scoredist.cpp -o scoredist.o In file included from scoredist.cpp:3: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ scoredist.cpp:17:21: warning: unused variable 'Dayhoff_CalibrationFactor' [-Wunused-const-variable] static const double Dayhoff_CalibrationFactor = 1.3370; ^ scoredist.cpp:19:21: warning: unused variable 'MV_CalibrationFactor' [-Wunused-const-variable] static const double MV_CalibrationFactor = 1.1775; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c scoregaps.cpp -o scoregaps.o In file included from scoregaps.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ scoregaps.cpp:37:13: warning: unused function 'FreeGapInfo' [-Wunused-function] static void FreeGapInfo(GAPINFO *GI) ^ scoregaps.cpp:80:14: warning: unused function 'Penalty' [-Wunused-function] static SCORE Penalty(unsigned Length, bool Term) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c scorehistory.cpp -o scorehistory.o In file included from scorehistory.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c scorepp.cpp -o scorepp.o In file included from scorepp.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c seq.cpp -o seq.o In file included from seq.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c seqvect.cpp -o seqvect.o seqvect.cpp:201:17: warning: binding dereferenced null pointer to reference has undefined behavior [-Wnull-dereference] return (Seq &) *((Seq *) 0); ^~~~~~~~~~~~ In file included from seqvect.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ seqvect.cpp:6:14: warning: unused variable 'MAX_FASTA_LINE' [-Wunused-const-variable] const size_t MAX_FASTA_LINE = 16000; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c setblosumweights.cpp -o setblosumweights.o In file included from setblosumweights.cpp:42: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c setgscweights.cpp -o setgscweights.o In file included from setgscweights.cpp:104: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c setnewhandler.cpp -o setnewhandler.o In file included from setnewhandler.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c spfast.cpp -o spfast.o spfast.cpp:252:17: warning: unused variable 'uSeqCount' [-Wunused-variable] const unsigned uSeqCount = msa.GetSeqCount(); ^ In file included from spfast.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ spfast.cpp:14:20: warning: unused function 'GapTypeToStr' [-Wunused-function] static const char *GapTypeToStr(int GapType) ^ spfast.cpp:59:14: warning: unused function 'SPColBrute' [-Wunused-function] static SCORE SPColBrute(const MSA &msa, unsigned uColIndex) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sptest.cpp -o sptest.o In file included from sptest.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stabilize.cpp -o stabilize.o In file included from stabilize.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c subfam.cpp -o subfam.o subfam.cpp:173:6: warning: unused variable 'NotUsed' [-Wunused-variable] int NotUsed = system(CmdLine); ^ In file included from subfam.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c subfams.cpp -o subfams.o In file included from subfams.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ subfams.cpp:10:13: warning: unused function 'GetMostDistantPair' [-Wunused-function] static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2) ^ subfams.cpp:40:13: warning: unused function 'InitializeSingleSource' [-Wunused-function] static void InitializeSingleSource(DistFunc &DF, unsigned uIndex) ^ subfams.cpp:52:13: warning: unused function 'Relax' [-Wunused-function] static void Relax(DistFunc &DF, unsigned u, unsigned v) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sw.cpp -o sw.o In file included from sw.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ sw.cpp:20:13: warning: unused function 'ListDP' [-Wunused-function] static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB, ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c termgaps.cpp -o termgaps.o In file included from termgaps.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c textfile.cpp -o textfile.o textfile.cpp:104:6: warning: unused variable 'i' [-Wunused-variable] int i = fputc(c, m_ptrFile); ^ textfile.cpp:117:6: warning: unused variable 'iError' [-Wunused-variable] int iError = fputs(szLine, m_ptrFile); ^ In file included from textfile.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c threewaywt.cpp -o threewaywt.o In file included from threewaywt.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tomhydro.cpp -o tomhydro.o In file included from tomhydro.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c traceback.cpp -o traceback.o traceback.cpp:21:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] const unsigned uPrefixCountB = uLengthB + 1; ^ traceback.cpp:195:3: warning: variable 'cPrevEdgeType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ traceback.cpp:202:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ traceback.cpp:186:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(Score, scoreSI)) ^~~~~~~~~~~~~~~~~~ traceback.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ traceback.cpp:202:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ traceback.cpp:186:9: note: remove the 'if' if its condition is always true else if (EQ(Score, scoreSI)) ^~~~~~~~~~~~~~~~~~~~~~~ traceback.cpp:150:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(Score, scoreSD)) ^~~~~~~~~~~~~~~~~~ traceback.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ traceback.cpp:202:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ traceback.cpp:150:9: note: remove the 'if' if its condition is always true else if (EQ(Score, scoreSD)) ^~~~~~~~~~~~~~~~~~~~~~~ traceback.cpp:112:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(scoreSM, Score)) ^~~~~~~~~~~~~~~~~~ traceback.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ traceback.cpp:202:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ traceback.cpp:112:9: note: remove the 'if' if its condition is always true else if (EQ(scoreSM, Score)) ^~~~~~~~~~~~~~~~~~~~~~~ traceback.cpp:68:21: note: initialize the variable 'cPrevEdgeType' to silence this warning char cPrevEdgeType; ^ = '\0' In file included from traceback.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 6 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tracebackopt.cpp -o tracebackopt.o In file included from tracebackopt.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tracebacksw.cpp -o tracebacksw.o tracebacksw.cpp:22:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] const unsigned uPrefixCountB = uLengthB + 1; ^ tracebacksw.cpp:29:8: warning: unused variable 'scoreMax' [-Wunused-variable] SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB); ^ tracebacksw.cpp:175:3: warning: variable 'cPrevEdgeType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ tracebacksw.cpp:182:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ tracebacksw.cpp:166:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(Score, scoreSI)) ^~~~~~~~~~~~~~~~~~ tracebacksw.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ tracebacksw.cpp:182:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ tracebacksw.cpp:166:9: note: remove the 'if' if its condition is always true else if (EQ(Score, scoreSI)) ^~~~~~~~~~~~~~~~~~~~~~~ tracebacksw.cpp:130:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(Score, scoreSD)) ^~~~~~~~~~~~~~~~~~ tracebacksw.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ tracebacksw.cpp:182:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ tracebacksw.cpp:130:9: note: remove the 'if' if its condition is always true else if (EQ(Score, scoreSD)) ^~~~~~~~~~~~~~~~~~~~~~~ tracebacksw.cpp:92:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(scoreMatch, Score)) ^~~~~~~~~~~~~~~~~~~~~ tracebacksw.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ tracebacksw.cpp:182:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ tracebacksw.cpp:92:9: note: remove the 'if' if its condition is always true else if (EQ(scoreMatch, Score)) ^~~~~~~~~~~~~~~~~~~~~~~~~~ tracebacksw.cpp:43:21: note: initialize the variable 'cPrevEdgeType' to silence this warning char cPrevEdgeType; ^ = '\0' In file included from tracebacksw.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 7 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c treefrommsa.cpp -o treefrommsa.o In file included from treefrommsa.cpp:5: In file included from ./clustsetmsa.h:8: ./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch] switch(m_Distance) ^~~~~~~~~~ ./msadist.h:22:10: note: add missing switch cases switch(m_Distance) ^ In file included from treefrommsa.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c typetostr.cpp -o typetostr.o In file included from typetostr.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c upgma2.cpp -o upgma2.o upgma2.cpp:272:4: warning: variable 'dtNewDist' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ upgma2.cpp:292:17: note: uninitialized use occurs here g_Dist[vL] = dtNewDist; ^~~~~~~~~ upgma2.cpp:252:20: note: initialize the variable 'dtNewDist' to silence this warning dist_t dtNewDist; ^ = 0.0 upgma2.cpp:366:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 0, 2, 14, 14, 20, ^~~~~~~~~~~~~~~~~ { } upgma2.cpp:367:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 2, 0, 14, 14, 20, ^~~~~~~~~~~~~~~~~ { } upgma2.cpp:368:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 14, 14, 0, 4, 20, ^~~~~~~~~~~~~~~~~~ { } upgma2.cpp:369:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 14, 14, 4, 0, 20, ^~~~~~~~~~~~~~~~~~ { } upgma2.cpp:370:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 20, 20, 20, 20, 0, ^~~~~~~~~~~~~~~~~~ { } In file included from upgma2.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ upgma2.cpp:68:13: warning: unused function 'ListState' [-Wunused-function] static void ListState() ^ 8 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c usage.cpp -o usage.o In file included from usage.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c validateids.cpp -o validateids.o In file included from validateids.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vtml2.cpp -o vtml2.o In file included from vtml2.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c writescorefile.cpp -o writescorefile.o writescorefile.cpp:37:4: warning: variable 'Score' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ writescorefile.cpp:40:12: note: uninitialized use occurs here dSum += Score; ^~~~~ writescorefile.cpp:27:16: note: initialize the variable 'Score' to silence this warning double Score; ^ = 0.0 In file included from writescorefile.cpp:1: In file included from ./muscle.h:34: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -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 muscle.so aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignla.o glbalignle.o glbalignns.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o gotowt.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o optionsR.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o redblack.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/muscle.buildbin-libdir/00LOCK-muscle/00new/muscle/libs ** R ** data *** moving datasets to lazyload DB ** 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 (muscle) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR muscle.buildbin-libdir/muscle/libs/muscle.so >>>>>>> >>>>>>> Paths before fix: muscle.buildbin-libdir/muscle/libs/muscle.so: muscle.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "muscle.buildbin-libdir/muscle/libs/muscle.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "muscle.buildbin-libdir/muscle/libs/muscle.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "muscle.buildbin-libdir/muscle/libs/muscle.so" >>>>>>> Paths after fix: muscle.buildbin-libdir/muscle/libs/muscle.so: muscle.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)