############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data muscle ### ############################################################################## ############################################################################## * checking for file ‘muscle/DESCRIPTION’ ... OK * preparing ‘muscle’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package ‘muscle’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ 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 -DR_NO_REMAP -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; ^ aligngivenpath.cpp:654:11: warning: variable 'uColIndexA' set but not used [-Wunused-but-set-variable] unsigned uColIndexA = 0; ^ aligngivenpath.cpp:655:11: warning: variable 'uColIndexB' set but not used [-Wunused-but-set-variable] unsigned uColIndexB = 0; ^ 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) ^ 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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:126:11: warning: variable 'uCharCount' set but not used [-Wunused-but-set-variable] unsigned uCharCount = 0; ^ 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) ^ 26 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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -c diffobjscore.cpp -o diffobjscore.o diffobjscore.cpp:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable] const unsigned uSeqCount = msa.GetSeqCount(); ^ diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable] const unsigned uColCount = msa.GetColCount(); ^ 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 -DR_NO_REMAP -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 -DR_NO_REMAP -c difftrees.cpp -o difftrees.o difftrees.cpp:161:17: warning: unused variable 'uLeafCount2' [-Wunused-variable] const unsigned uLeafCount2 = Tree2.GetLeafCount(); ^ difftrees.cpp:296:11: warning: variable 'uDiffCount' set but not used [-Wunused-but-set-variable] unsigned uDiffCount = 0; ^ 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) ^ 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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -c fasta.cpp -o fasta.o fasta.cpp:15:11: warning: unused variable 'uSeqCount' [-Wunused-variable] unsigned uSeqCount = 0; ^ fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable] unsigned uColCount = uInsane; ^ 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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -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 -DR_NO_REMAP -c glbalignss.cpp -o glbalignss.o glbalignss.cpp:177:16: warning: unused variable 'ptrRowA' [-Wunused-variable] const SCORE *ptrRowA = MxRowA[i]; ^ glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable] const unsigned uPrefixCountA = uLengthA + 1; ^ glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] const unsigned uPrefixCountB = uLengthB + 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 -DR_NO_REMAP -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 -DR_NO_REMAP -c globals.cpp -o globals.o globals.cpp:107:2: error: use of undeclared identifier 'error' error("error in muscle\n"); ^ 1 error generated. make: *** [globals.o] Error 1 ERROR: compilation failed for package ‘muscle’ * removing ‘/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpTj8dHj/Rinst33b68edf659/muscle’ ----------------------------------- ERROR: package installation failed