############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL muscle ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘muscle’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c aligngivenpath.cpp -o aligngivenpath.o aligngivenpath.cpp: In function 'void AppendTplInserts(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)': aligngivenpath.cpp:186:24: warning: unused variable 'uLengthA' [-Wunused-variable] 186 | const unsigned uLengthA = msaA.GetColCount(); | ^~~~~~~~ aligngivenpath.cpp:187:24: warning: unused variable 'uLengthB' [-Wunused-variable] 187 | const unsigned uLengthB = msaB.GetColCount(); | ^~~~~~~~ aligngivenpath.cpp: In function 'void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)': aligngivenpath.cpp:335:40: warning: unused variable 'uColA' [-Wunused-variable] 335 | const unsigned uColA = uPrefixLengthA - 1; | ^~~~~ aligngivenpath.cpp:336:40: warning: unused variable 'uColB' [-Wunused-variable] 336 | const unsigned uColB = uPrefixLengthB - 1; | ^~~~~ aligngivenpath.cpp:346:40: warning: unused variable 'uColA' [-Wunused-variable] 346 | const unsigned uColA = uPrefixLengthA - 1; | ^~~~~ aligngivenpath.cpp:354:40: warning: unused variable 'uColB' [-Wunused-variable] 354 | const unsigned uColB = uPrefixLengthB - 1; | ^~~~~ In file included from muscle.h:34, from aligngivenpath.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c aligngivenpathsw.cpp -o aligngivenpathsw.o aligngivenpathsw.cpp: In function 'void AppendUnalignedTerminals(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)': aligngivenpathsw.cpp:58:24: warning: unused variable 'uLengthA' [-Wunused-variable] 58 | const unsigned uLengthA = msaA.GetColCount(); | ^~~~~~~~ aligngivenpathsw.cpp:59:24: warning: unused variable 'uLengthB' [-Wunused-variable] 59 | const unsigned uLengthB = msaB.GetColCount(); | ^~~~~~~~ aligngivenpathsw.cpp: In function 'void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)': aligngivenpathsw.cpp:204:40: warning: unused variable 'uColA' [-Wunused-variable] 204 | const unsigned uColA = uPrefixLengthA - 1; | ^~~~~ aligngivenpathsw.cpp:205:40: warning: unused variable 'uColB' [-Wunused-variable] 205 | const unsigned uColB = uPrefixLengthB - 1; | ^~~~~ aligngivenpathsw.cpp:215:40: warning: unused variable 'uColA' [-Wunused-variable] 215 | const unsigned uColA = uPrefixLengthA - 1; | ^~~~~ aligngivenpathsw.cpp:223:40: warning: unused variable 'uColB' [-Wunused-variable] 223 | const unsigned uColB = uPrefixLengthB - 1; | ^~~~~ In file included from muscle.h:34, from aligngivenpathsw.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c aligntwomsas.cpp -o aligntwomsas.o In file included from muscle.h:34, from aligntwomsas.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c aligntwoprofs.cpp -o aligntwoprofs.o In file included from muscle.h:34, from aligntwoprofs.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c aln.cpp -o aln.o In file included from muscle.h:34, from aln.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c alpha.cpp -o alpha.o alpha.cpp: In function 'unsigned int GetAlphaSize(ALPHA)': alpha.cpp:84:16: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] 84 | switch (Alpha) | ^ In file included from muscle.h:34, from alpha.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c anchors.cpp -o anchors.o anchors.cpp: In function 'void MergeBestCols(const SCORE*, const unsigned int*, unsigned int, unsigned int, unsigned int*, unsigned int*)': anchors.cpp:162:34: warning: unused variable 'uWindowCenter' [-Wunused-variable] 162 | unsigned uWindowCenter = uBestColIndex + uWindowLength/2; | ^~~~~~~~~~~~~ anchors.cpp: At global scope: anchors.cpp:105:13: warning: 'void ListBestCols(const MSA&, const SCORE*, const SCORE*, unsigned int*, unsigned int)' defined but not used [-Wunused-function] 105 | static void ListBestCols(const MSA &msa, const SCORE Score[], const SCORE SmoothScore[], | ^~~~~~~~~~~~ anchors.cpp:53:13: warning: 'void FindBestColsGrade(const SCORE*, unsigned int, double, unsigned int*, unsigned int*)' defined but not used [-Wunused-function] 53 | static void FindBestColsGrade(const SCORE Score[], unsigned uCount, | ^~~~~~~~~~~~~~~~~ In file included from muscle.h:34, from anchors.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c bittraceback.cpp -o bittraceback.o bittraceback.cpp: In function 'void BitTraceBack(char**, unsigned int, unsigned int, char, PWPath&)': bittraceback.cpp:146:14: warning: unused variable 'Bits' [-Wunused-variable] 146 | char Bits = TraceBack[uLengthA][uLengthB]; | ^~~~ bittraceback.cpp: At global scope: bittraceback.cpp:15:20: warning: 'const char* BitsToStr(char)' defined but not used [-Wunused-function] 15 | static const char *BitsToStr(char Bits) | ^~~~~~~~~ In file included from muscle.h:34, from bittraceback.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c blosum62.cpp -o blosum62.o In file included from muscle.h:34, from blosum62.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c blosumla.cpp -o blosumla.o blosumla.cpp:7:14: warning: 'Blosum62LA' defined but not used [-Wunused-variable] 7 | static float Blosum62LA[20][20] = | ^~~~~~~~~~ In file included from muscle.h:34, from blosumla.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c clust.cpp -o clust.o clust.cpp: In member function 'void Clust::ChooseJoin(unsigned int*, unsigned int*, float*, float*)': clust.cpp:167:16: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] 167 | switch (m_JoinStyle) | ^ clust.cpp: In member function 'void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)': clust.cpp:184:24: warning: unused variable 'uClusterCount' [-Wunused-variable] 184 | const unsigned uClusterCount = GetClusterCount(); | ^~~~~~~~~~~~~ clust.cpp: In member function 'void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)': clust.cpp:204:24: warning: unused variable 'uClusterCount' [-Wunused-variable] 204 | const unsigned uClusterCount = GetClusterCount(); | ^~~~~~~~~~~~~ clust.cpp: In member function 'float Clust::ComputeDist(unsigned int, unsigned int)': clust.cpp:295:16: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch] 295 | switch (m_CentroidStyle) | ^ clust.cpp: In member function 'float Clust::ComputeDistMAFFT(unsigned int, unsigned int)': clust.cpp:360:21: warning: unused variable 'dDistLR' [-Wunused-variable] 360 | const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex); | ^~~~~~~ clust.cpp: In member function 'float Clust::ComputeMetric(unsigned int, unsigned int) const': clust.cpp:611:16: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] 611 | switch (m_JoinStyle) | ^ In file included from muscle.h:34, from clust.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c cluster.cpp -o cluster.o cluster.cpp: In member function 'void ClusterTree::Create(const DistFunc&)': cluster.cpp:284:22: warning: variable 'bFound' set but not used [-Wunused-but-set-variable] 284 | bool bFound = false; | ^~~~~~ cluster.cpp:267:16: warning: unused variable 'dMaxDist' [-Wunused-variable] 267 | double dMaxDist = 0.0; | ^~~~~~~~ In file included from muscle.h:34, from cluster.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ cluster.cpp: In member function 'void ClusterTree::Create(const DistFunc&)': cluster.cpp:307:47: warning: 'uIndexClosest1' may be used uninitialized [-Wmaybe-uninitialized] 307 | ClusterNode &Child1 = m_Nodes[uIndexClosest1]; | ^~~~~~~~~~~~~~ cluster.cpp:282:26: note: 'uIndexClosest1' was declared here 282 | unsigned uIndexClosest1; | ^~~~~~~~~~~~~~ cluster.cpp:308:47: warning: 'uIndexClosest2' may be used uninitialized [-Wmaybe-uninitialized] 308 | ClusterNode &Child2 = m_Nodes[uIndexClosest2]; | ^~~~~~~~~~~~~~ cluster.cpp:283:26: note: 'uIndexClosest2' was declared here 283 | unsigned uIndexClosest2; | ^~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c clwwt.cpp -o clwwt.o In file included from muscle.h:34, from clwwt.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c color.cpp -o color.o color.cpp:72:12: warning: 'int BlosumScore(char, char)' defined but not used [-Wunused-function] 72 | static int BlosumScore(char c1, char c2) | ^~~~~~~~~~~ In file included from muscle.h:34, from color.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c cons.cpp -o cons.o In file included from muscle.h:34, from cons.cpp:7: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c diaglist.cpp -o diaglist.o In file included from muscle.h:34, from diaglist.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ diaglist.cpp: In member function 'void DiagList::FromPath(const PWPath&)': diaglist.cpp:70:36: warning: 'uStartPosA' may be used uninitialized [-Wmaybe-uninitialized] 70 | Add(uStartPosA, uStartPosB, uLength); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diaglist.cpp:51:18: note: 'uStartPosA' was declared here 51 | unsigned uStartPosA; | ^~~~~~~~~~ diaglist.cpp:70:36: warning: 'uStartPosB' may be used uninitialized [-Wmaybe-uninitialized] 70 | Add(uStartPosA, uStartPosB, uLength); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diaglist.cpp:52:18: note: 'uStartPosB' was declared here 52 | unsigned uStartPosB; | ^~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c diffobjscore.cpp -o diffobjscore.o diffobjscore.cpp: In function 'SCORE ScoreLetters(const MSA&, const unsigned int*, unsigned int)': diffobjscore.cpp:76:24: warning: unused variable 'uSeqCount' [-Wunused-variable] 76 | const unsigned uSeqCount = msa.GetSeqCount(); | ^~~~~~~~~ diffobjscore.cpp:77:24: warning: unused variable 'uColCount' [-Wunused-variable] 77 | const unsigned uColCount = msa.GetColCount(); | ^~~~~~~~~ In file included from muscle.h:34, from diffobjscore.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c diffpaths.cpp -o diffpaths.o In file included from muscle.h:34, from diffpaths.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c difftrees.cpp -o difftrees.o difftrees.cpp: In function 'void DiffTrees(const Tree&, const Tree&, Tree&, unsigned int*)': difftrees.cpp:161:24: warning: unused variable 'uLeafCount2' [-Wunused-variable] 161 | const unsigned uLeafCount2 = Tree2.GetLeafCount(); | ^~~~~~~~~~~ In file included from muscle.h:34, from difftrees.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c difftreese.cpp -o difftreese.o In file included from muscle.h:34, from difftreese.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c distcalc.cpp -o distcalc.o In file included from muscle.h:34, from distcalc.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c distfunc.cpp -o distfunc.o In file included from muscle.h:34, from distfunc.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c distpwkimura.cpp -o distpwkimura.o In file included from muscle.h:34, from distpwkimura.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c domuscle.cpp -o domuscle.o In file included from muscle.h:34, from domuscle.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c dosp.cpp -o dosp.o In file included from muscle.h:34, from dosp.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c dpreglist.cpp -o dpreglist.o dpreglist.cpp: In function 'void DiagListToDPRegionList(const DiagList&, DPRegionList&, unsigned int, unsigned int)': dpreglist.cpp:82:40: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable] 82 | const unsigned uDiagLengthMinusCaps = uEndVertexA - uStartVertexA - 1; | ^~~~~~~~~~~~~~~~~~~~ In file included from muscle.h:34, from dpreglist.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c drawtree.cpp -o drawtree.o In file included from muscle.h:34, from drawtree.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c edgelist.cpp -o edgelist.o In file included from muscle.h:34, from edgelist.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c enumopts.cpp -o enumopts.o In file included from muscle.h:34, from enumopts.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c enumtostr.cpp -o enumtostr.o In file included from muscle.h:34, from enumtostr.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c estring.cpp -o estring.o estring.cpp:464:13: warning: 'bool CanMultiplyEstrings(const short int*, const short int*)' defined but not used [-Wunused-function] 464 | static bool CanMultiplyEstrings(const short es1[], const short es2[]) | ^~~~~~~~~~~~~~~~~~~ In file included from muscle.h:34, from estring.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ estring.cpp: In function 'void EstringsToPath(const short int*, const short int*, PWPath&)': estring.cpp:409:17: warning: 'cType' may be used uninitialized [-Wmaybe-uninitialized] 409 | switch (cType) | ^~~~~~ estring.cpp:377:22: note: 'cType' was declared here 377 | char cType; | ^~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c fasta.cpp -o fasta.o fasta.cpp: In member function 'void MSA::FromFASTAFile(TextFile&)': fasta.cpp:15:18: warning: unused variable 'uSeqCount' [-Wunused-variable] 15 | unsigned uSeqCount = 0; | ^~~~~~~~~ fasta.cpp:16:18: warning: unused variable 'uColCount' [-Wunused-variable] 16 | unsigned uColCount = uInsane; | ^~~~~~~~~ In file included from muscle.h:34, from fasta.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c fasta2.cpp -o fasta2.o In file included from muscle.h:34, from fasta2.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c fastclust.cpp -o fastclust.o In file included from muscle.h:34, from fastclust.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c fastdist.cpp -o fastdist.o In file included from muscle.h:34, from fastdist.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c fastdistjones.cpp -o fastdistjones.o In file included from muscle.h:34, from fastdistjones.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ fastdistjones.cpp: In function 'void DistKmer20_3(const SeqVect&, DistFunc&)': fastdistjones.cpp:158:18: warning: 'void operator delete [](void*)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 158 | delete[] SeqList; | ^~~~~~~ fastdistjones.cpp:121:60: note: returned from 'void* malloc(size_t)' 121 | unsigned short *SeqList = (unsigned short *) malloc(uSeqListBytes); | ~~~~~~^~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c fastdistkbit.cpp -o fastdistkbit.o In file included from muscle.h:34, from fastdistkbit.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c fastdistkmer.cpp -o fastdistkmer.o fastdistkmer.cpp: In function 'void FastDistKmer(const SeqVect&, DistFunc&)': fastdistkmer.cpp:235:32: warning: unused variable 'KD' [-Wunused-variable] 235 | double KD = KimuraDist(EstimatedPctId); | ^~ In file included from muscle.h:34, from fastdistkmer.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c fastdistmafft.cpp -o fastdistmafft.o fastdistmafft.cpp: In function 'void DistKmer6_6(const SeqVect&, DistFunc&)': fastdistmafft.cpp:238:29: warning: unused variable 'pName1' [-Wunused-variable] 238 | const char *pName1 = s1.GetName(); | ^~~~~~ fastdistmafft.cpp: At global scope: fastdistmafft.cpp:104:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function] 104 | static void ListCount(const unsigned char Count[]) | ^~~~~~~~~ In file included from muscle.h:34, from fastdistmafft.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c fastdistnuc.cpp -o fastdistnuc.o fastdistnuc.cpp: In function 'void DistKmer4_6(const SeqVect&, DistFunc&)': fastdistnuc.cpp:223:29: warning: unused variable 'pName1' [-Wunused-variable] 223 | const char *pName1 = s1.GetName(); | ^~~~~~ fastdistnuc.cpp: At global scope: fastdistnuc.cpp:85:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function] 85 | static void ListCount(const unsigned char Count[]) | ^~~~~~~~~ fastdistnuc.cpp:33:17: warning: 'uResidueGroupCount' defined but not used [-Wunused-variable] 33 | static unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]); | ^~~~~~~~~~~~~~~~~~ In file included from muscle.h:34, from fastdistnuc.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c fastscorepath2.cpp -o fastscorepath2.o In file included from muscle.h:34, from fastscorepath2.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c finddiags.cpp -o finddiags.o finddiags.cpp:11:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function] 11 | static char *TupleToStr(int t) | ^~~~~~~~~~ In file included from muscle.h:34, from finddiags.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c finddiagsn.cpp -o finddiagsn.o finddiagsn.cpp: In function 'char* TupleToStr(int)': finddiagsn.cpp:16:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 16 | for (int i = 0; i < K; ++i) | ~~^~~ finddiagsn.cpp: At global scope: finddiagsn.cpp:12:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function] 12 | static char *TupleToStr(int t) | ^~~~~~~~~~ In file included from muscle.h:34, from finddiagsn.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c glbalign.cpp -o glbalign.o In file included from muscle.h:34, from glbalign.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c glbalign352.cpp -o glbalign352.o In file included from muscle.h:34, from glbalign352.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c glbaligndiag.cpp -o glbaligndiag.o In file included from muscle.h:34, from glbaligndiag.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c glbalignla.cpp -o glbalignla.o In file included from muscle.h:34, from glbalignla.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ glbalignla.cpp: In function 'SCORE GlobalAlignLA(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': glbalignla.cpp:363:52: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized] 363 | *ptrTraceBack_ij = (int) uInsertPos - (int) j; | ^~~~~~~~~~~~~~~~ glbalignla.cpp:330:26: note: 'uInsertPos' was declared here 330 | unsigned uInsertPos; | ^~~~~~~~~~ glbalignla.cpp:424:30: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized] 424 | iTraceBack = (int) uInsertPos - (int) uLengthB; | ^~~~~~~~~~~~~~~~ glbalignla.cpp:397:18: note: 'uInsertPos' was declared here 397 | unsigned uInsertPos; | ^~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c glbalignle.cpp -o glbalignle.o In file included from muscle.h:34, from glbalignle.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ glbalignle.cpp: In function 'SCORE GlobalAlignLE(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': glbalignle.cpp:427:30: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized] 427 | iTraceBack = (int) uInsertPos - (int) uLengthB; | ^~~~~~~~~~~~~~~~ glbalignle.cpp:400:18: note: 'uInsertPos' was declared here 400 | unsigned uInsertPos; | ^~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c glbalignns.cpp -o glbalignns.o In file included from muscle.h:34, from glbalignns.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ glbalignns.cpp: In function 'SCORE GlobalAlignNS(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': glbalignns.cpp:305:52: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized] 305 | *ptrTraceBack_ij = (int) uInsertPos - (int) j; | ^~~~~~~~~~~~~~~~ glbalignns.cpp:272:26: note: 'uInsertPos' was declared here 272 | unsigned uInsertPos; | ^~~~~~~~~~ glbalignns.cpp:366:30: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized] 366 | iTraceBack = (int) uInsertPos - (int) uLengthB; | ^~~~~~~~~~~~~~~~ glbalignns.cpp:339:18: note: 'uInsertPos' was declared here 339 | unsigned uInsertPos; | ^~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c glbalignsimple.cpp -o glbalignsimple.o glbalignsimple.cpp:52:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function] 52 | static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB, | ^~~~~~ glbalignsimple.cpp:28:13: warning: 'void ListTB(const char*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function] 28 | static void ListTB(const char *TBM_, const ProfPos *PA, const ProfPos *PB, | ^~~~~~ In file included from muscle.h:34, from glbalignsimple.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c glbalignsp.cpp -o glbalignsp.o In file included from muscle.h:34, from glbalignsp.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ glbalignsp.cpp: In function 'SCORE GlobalAlignSP(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': glbalignsp.cpp:305:52: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized] 305 | *ptrTraceBack_ij = (int) uInsertPos - (int) j; | ^~~~~~~~~~~~~~~~ glbalignsp.cpp:272:26: note: 'uInsertPos' was declared here 272 | unsigned uInsertPos; | ^~~~~~~~~~ glbalignsp.cpp:366:30: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized] 366 | iTraceBack = (int) uInsertPos - (int) uLengthB; | ^~~~~~~~~~~~~~~~ glbalignsp.cpp:339:18: note: 'uInsertPos' was declared here 339 | unsigned uInsertPos; | ^~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c glbalignspn.cpp -o glbalignspn.o In file included from muscle.h:34, from glbalignspn.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ glbalignspn.cpp: In function 'SCORE GlobalAlignSPN(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': glbalignspn.cpp:340:52: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized] 340 | *ptrTraceBack_ij = (int) uInsertPos - (int) j; | ^~~~~~~~~~~~~~~~ glbalignspn.cpp:307:26: note: 'uInsertPos' was declared here 307 | unsigned uInsertPos; | ^~~~~~~~~~ glbalignspn.cpp:401:30: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized] 401 | iTraceBack = (int) uInsertPos - (int) uLengthB; | ^~~~~~~~~~~~~~~~ glbalignspn.cpp:374:18: note: 'uInsertPos' was declared here 374 | unsigned uInsertPos; | ^~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c glbalignss.cpp -o glbalignss.o glbalignss.cpp: In function 'SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)': glbalignss.cpp:177:30: warning: unused variable 'ptrRowA' [-Wunused-variable] 177 | const SCORE *ptrRowA = MxRowA[i]; | ^~~~~~~ glbalignss.cpp:119:24: warning: unused variable 'uPrefixCountA' [-Wunused-variable] 119 | const unsigned uPrefixCountA = uLengthA + 1; | ^~~~~~~~~~~~~ glbalignss.cpp:120:24: warning: unused variable 'uPrefixCountB' [-Wunused-variable] 120 | const unsigned uPrefixCountB = uLengthB + 1; | ^~~~~~~~~~~~~ glbalignss.cpp: At global scope: glbalignss.cpp:11:14: warning: 'SCORE Subst(const Seq&, const Seq&, unsigned int, unsigned int)' defined but not used [-Wunused-function] 11 | static SCORE Subst(const Seq &seqA, const Seq &seqB, unsigned i, unsigned j) | ^~~~~ In file included from muscle.h:34, from glbalignss.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ glbalignss.cpp: In function 'SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)': glbalignss.cpp:252:52: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized] 252 | *ptrTraceBack_ij = (int) uInsertPos - (int) j; | ^~~~~~~~~~~~~~~~ glbalignss.cpp:221:26: note: 'uInsertPos' was declared here 221 | unsigned uInsertPos; | ^~~~~~~~~~ glbalignss.cpp:310:30: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized] 310 | iTraceBack = (int) uInsertPos - (int) uLengthB; | ^~~~~~~~~~~~~~~~ glbalignss.cpp:283:18: note: 'uInsertPos' was declared here 283 | unsigned uInsertPos; | ^~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c glbalndimer.cpp -o glbalndimer.o glbalndimer.cpp: In function 'SCORE ScoreProfPosDimer(const ProfPos&, const ProfPos&)': glbalndimer.cpp:123:16: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch] 123 | switch (g_PPScore) | ^ glbalndimer.cpp:123:16: warning: enumeration value 'PPSCORE_SPN' not handled in switch [-Wswitch] glbalndimer.cpp: At global scope: glbalndimer.cpp:14:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function] 14 | static const char *LocalScoreToStr(SCORE s) | ^~~~~~~~~~~~~~~ In file included from muscle.h:34, from glbalndimer.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c globals.cpp -o globals.o In file included from muscle.h:34, from globals.cpp:6: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c globalslinux.cpp -o globalslinux.o globalslinux.cpp: In function 'double GetNAN()': globalslinux.cpp:21:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 21 | double dNAN = *( double* )nan; | ^~~~~~~~~~~~~~ In file included from muscle.h:34, from globalslinux.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c globalsosx.cpp -o globalsosx.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c globalsother.cpp -o globalsother.o In file included from muscle.h:34, from globalsother.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c globalswin32.cpp -o globalswin32.o In file included from muscle.h:34, from globalswin32.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c gonnet.cpp -o gonnet.o gonnet.cpp:137:14: warning: 'Gonnet160' defined but not used [-Wunused-variable] 137 | static SCORE Gonnet160[20][20] = | ^~~~~~~~~ In file included from muscle.h:34, from gonnet.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c gotowt.cpp -o gotowt.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c henikoffweight.cpp -o henikoffweight.o In file included from muscle.h:34, from henikoffweight.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c henikoffweightpb.cpp -o henikoffweightpb.o In file included from muscle.h:34, from henikoffweightpb.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c html.cpp -o html.o In file included from muscle.h:34, from html.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c hydro.cpp -o hydro.o In file included from muscle.h:34, from hydro.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c intmath.cpp -o intmath.o In file included from muscle.h:34, from intmath.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c local.cpp -o local.o In file included from muscle.h:34, from local.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c main.cpp -o main.o In file included from muscle.h:34, from main.cpp:7: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c makerootmsa.cpp -o makerootmsa.o makerootmsa.cpp: In function 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)': makerootmsa.cpp:18:24: warning: unused variable 'uSeqLength' [-Wunused-variable] 18 | const unsigned uSeqLength = s.Length(); | ^~~~~~~~~~ makerootmsa.cpp: In function 'short int* MakeRootSeqE(const Seq&, const Tree&, unsigned int, const ProgNode*, Seq&, short int*, short int*)': makerootmsa.cpp:94:31: warning: unused variable 'Path' [-Wunused-variable] 94 | const PWPath &Path = Nodes[uNodeIndex].m_Path; | ^~~~ makerootmsa.cpp: In function 'void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)': makerootmsa.cpp:168:24: warning: unused variable 'uTreeNodeCount' [-Wunused-variable] 168 | const unsigned uTreeNodeCount = GuideTree.GetNodeCount(); | ^~~~~~~~~~~~~~ makerootmsa.cpp: At global scope: makerootmsa.cpp:12:13: warning: 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)' defined but not used [-Wunused-function] 12 | static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut) | ^~~~~~~ In file included from muscle.h:34, from makerootmsa.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c makerootmsab.cpp -o makerootmsab.o In file included from muscle.h:34, from makerootmsab.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c maketree.cpp -o maketree.o In file included from muscle.h:34, from maketree.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c mhack.cpp -o mhack.o In file included from muscle.h:34, from mhack.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c mpam200.cpp -o mpam200.o In file included from muscle.h:34, from mpam200.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c msa.cpp -o msa.o msa.cpp:419:13: warning: 'void FmtPad(unsigned int)' defined but not used [-Wunused-function] 419 | static void FmtPad(unsigned n) | ^~~~~~ msa.cpp:407:13: warning: 'void FmtInt0(unsigned int, unsigned int)' defined but not used [-Wunused-function] 407 | static void FmtInt0(unsigned u, unsigned uWidth) | ^~~~~~~ msa.cpp:392:13: warning: 'void FmtInt(unsigned int, unsigned int)' defined but not used [-Wunused-function] 392 | static void FmtInt(unsigned u, unsigned uWidth) | ^~~~~~ msa.cpp:385:13: warning: 'void FmtChar(char, unsigned int)' defined but not used [-Wunused-function] 385 | static void FmtChar(char c, unsigned uWidth) | ^~~~~~~ In file included from muscle.h:34, from msa.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c msa2.cpp -o msa2.o msa2.cpp: In function 'void SetMSAWeightsMuscle(MSA&)': msa2.cpp:357:16: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch] 357 | switch (Method) | ^ msa2.cpp: In function 'void MSAAppend(MSA&, const MSA&)': msa2.cpp:476:24: warning: unused variable 'uColCountCat' [-Wunused-variable] 476 | const unsigned uColCountCat = uColCount1 + uColCount2; | ^~~~~~~~~~~~ In file included from muscle.h:34, from msa2.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c msadistkimura.cpp -o msadistkimura.o In file included from muscle.h:34, from msadistkimura.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c msf.cpp -o msf.o msf.cpp:24:20: warning: 'const char* strfind(const char*, const char*)' defined but not used [-Wunused-function] 24 | static const char *strfind(const char *s, const char *t) | ^~~~~~~ In file included from muscle.h:34, from msf.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c muscle.cpp -o muscle.o In file included from muscle.h:34, from muscle.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c muscleout.cpp -o muscleout.o In file included from muscle.h:34, from muscleout.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c nucmx.cpp -o nucmx.o In file included from muscle.h:34, from nucmx.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c nwdasimple.cpp -o nwdasimple.o In file included from muscle.h:34, from nwdasimple.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c nwdasimple2.cpp -o nwdasimple2.o In file included from muscle.h:34, from nwdasimple2.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c nwdasmall.cpp -o nwdasmall.o In file included from muscle.h:34, from nwdasmall.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c nwrec.cpp -o nwrec.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c nwsmall.cpp -o nwsmall.o In file included from muscle.h:34, from nwsmall.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c objscore.cpp -o objscore.o objscore.cpp: In function 'SCORE ObjScore(const MSA&, const unsigned int*, unsigned int, const unsigned int*, unsigned int)': objscore.cpp:31:16: warning: enumeration value 'OBJSCORE_Undefined' not handled in switch [-Wswitch] 31 | switch (OS) | ^ objscore.cpp:31:16: warning: enumeration value 'OBJSCORE_SPM' not handled in switch [-Wswitch] In file included from muscle.h:34, from objscore.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c objscore2.cpp -o objscore2.o objscore2.cpp: In function 'SCORE TermGapScore(bool)': objscore2.cpp:22:16: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch] 22 | switch (g_TermGaps) | ^ objscore2.cpp: In function 'SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)': objscore2.cpp:62:15: warning: unused variable 'scoreGaps' [-Wunused-variable] 62 | SCORE scoreGaps = 0; | ^~~~~~~~~ objscore2.cpp:63:14: warning: unused variable 'bGapping1' [-Wunused-variable] 63 | bool bGapping1 = false; | ^~~~~~~~~ objscore2.cpp:64:14: warning: unused variable 'bGapping2' [-Wunused-variable] 64 | bool bGapping2 = false; | ^~~~~~~~~ objscore2.cpp:67:14: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable] 67 | bool bLeftTermGap = false; | ^~~~~~~~~~~~ objscore2.cpp:82:14: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable] 82 | bool bRightTermGap = false; | ^~~~~~~~~~~~~ objscore2.cpp: In function 'SCORE ScoreSeqPairGaps(const MSA&, unsigned int, const MSA&, unsigned int)': objscore2.cpp:140:14: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable] 140 | bool bLeftTermGap = false; | ^~~~~~~~~~~~ objscore2.cpp:155:14: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable] 155 | bool bRightTermGap = false; | ^~~~~~~~~~~~~ objscore2.cpp: In function 'SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)': objscore2.cpp:314:24: warning: unused variable 'uColCount2' [-Wunused-variable] 314 | const unsigned uColCount2 = msa2.GetColCount(); | ^~~~~~~~~~ objscore2.cpp: In function 'SCORE ObjScoreXP(const MSA&, const MSA&)': objscore2.cpp:493:38: warning: unused variable 'w' [-Wunused-variable] 493 | const WEIGHT w = w1*w2; | ^ In file included from muscle.h:34, from objscore2.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c objscoreda.cpp -o objscoreda.o In file included from muscle.h:34, from objscoreda.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c onexception.cpp -o onexception.o In file included from muscle.h:34, from onexception.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c optionsR.cpp -o optionsR.o In file included from muscle.h:34, from optionsR.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c outweights.cpp -o outweights.o In file included from muscle.h:34, from outweights.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c pam200mafft.cpp -o pam200mafft.o pam200mafft.cpp:6:14: warning: 'PAM200' defined but not used [-Wunused-variable] 6 | static float PAM200[23][23] = | ^~~~~~ In file included from muscle.h:34, from pam200mafft.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c params.cpp -o params.o params.cpp: In function 'void SetPPScore(bool)': params.cpp:445:16: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch] 445 | switch (g_PPScore) | ^ params.cpp: In function 'void default_params()': params.cpp:659:9: warning: statement has no effect [-Wunused-value] 659 | g_ptrScoreMatrix; | ^~~~~~~~~~~~~~~~ params.cpp:652:21: warning: unused variable 'VTML_LA' [-Wunused-variable] 652 | SCOREMATRIX VTML_LA; | ^~~~~~~ params.cpp:653:21: warning: unused variable 'PAM200' [-Wunused-variable] 653 | SCOREMATRIX PAM200; | ^~~~~~ params.cpp:654:21: warning: unused variable 'PAM200NoCenter' [-Wunused-variable] 654 | SCOREMATRIX PAM200NoCenter; | ^~~~~~~~~~~~~~ params.cpp:655:21: warning: unused variable 'VTML_SP' [-Wunused-variable] 655 | SCOREMATRIX VTML_SP; | ^~~~~~~ params.cpp:656:21: warning: unused variable 'VTML_SPNoCenter' [-Wunused-variable] 656 | SCOREMATRIX VTML_SPNoCenter; | ^~~~~~~~~~~~~~~ params.cpp:657:21: warning: unused variable 'NUC_SP' [-Wunused-variable] 657 | SCOREMATRIX NUC_SP; | ^~~~~~ In file included from muscle.h:34, from params.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c phy.cpp -o phy.o phy.cpp: In member function 'void Tree::RootUnrootedTree(ROOT)': phy.cpp:665:16: warning: unused variable 'dEdgeLength' [-Wunused-variable] 665 | double dEdgeLength = GetEdgeLength(uNode1, uNode2); | ^~~~~~~~~~~ In file included from muscle.h:34, from phy.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c phy2.cpp -o phy2.o In file included from muscle.h:34, from phy2.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c phy3.cpp -o phy3.o phy3.cpp: In function 'void CalcInfo(const Tree&, unsigned int, unsigned int, EdgeInfo**)': phy3.cpp:125:22: warning: unused variable 'dThisDist' [-Wunused-variable] 125 | const double dThisDist = tree.GetEdgeLength(uNode1, uNode2); | ^~~~~~~~~ phy3.cpp: In function 'void FindRoot(const Tree&, unsigned int*, unsigned int*, double*, double*, ROOT)': phy3.cpp:167:24: warning: unused variable 'uLeafCount' [-Wunused-variable] 167 | const unsigned uLeafCount = tree.GetLeafCount(); | ^~~~~~~~~~ phy3.cpp:190:16: warning: unused variable 'dAllMaxDist' [-Wunused-variable] 190 | double dAllMaxDist = -1e20; | ^~~~~~~~~~~ phy3.cpp:191:18: warning: unused variable 'uMaxFrom' [-Wunused-variable] 191 | unsigned uMaxFrom = NULL_NEIGHBOR; | ^~~~~~~~ phy3.cpp:192:18: warning: unused variable 'uMaxTo' [-Wunused-variable] 192 | unsigned uMaxTo = NULL_NEIGHBOR; | ^~~~~~ phy3.cpp: In function 'void RootByMidLongestSpan(const Tree&, EdgeInfo**, unsigned int*, unsigned int*, double*, double*)': phy3.cpp:263:18: warning: variable 'uMostDistantLeaf' set but not used [-Wunused-but-set-variable] 263 | unsigned uMostDistantLeaf = NULL_NEIGHBOR; | ^~~~~~~~~~~~~~~~ phy3.cpp: At global scope: phy3.cpp:45:13: warning: 'void ListEIs(EdgeInfo**, unsigned int)' defined but not used [-Wunused-function] 45 | static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount) | ^~~~~~~ In file included from muscle.h:34, from phy3.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c phy4.cpp -o phy4.o In file included from muscle.h:34, from phy4.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c phyfromclust.cpp -o phyfromclust.o In file included from muscle.h:34, from phyfromclust.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c phyfromfile.cpp -o phyfromfile.o In file included from muscle.h:34, from phyfromfile.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c physeq.cpp -o physeq.o physeq.cpp: In member function 'void MSA::ToPhySequentialFile(TextFile&) const': physeq.cpp:60:41: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 60 | if (Col == ColCount) | ~~~~^~~~~~~~~~~ physeq.cpp:71:33: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 71 | if (Col == ColCount) | ~~~~^~~~~~~~~~~ physeq.cpp: In member function 'void MSA::ToPhyInterleavedFile(TextFile&) const': physeq.cpp:112:41: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 112 | if (Col == ColCount) | ~~~~^~~~~~~~~~~ physeq.cpp:124:25: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 124 | if (Col == ColCount) | ~~~~^~~~~~~~~~~ In file included from muscle.h:34, from physeq.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c phytofile.cpp -o phytofile.o In file included from muscle.h:34, from phytofile.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c posgap.cpp -o posgap.o In file included from muscle.h:34, from posgap.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c ppscore.cpp -o ppscore.o In file included from muscle.h:34, from ppscore.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c profdb.cpp -o profdb.o In file included from clustsetmsa.h:8, from profdb.cpp:9: msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': msadist.h:22:23: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch] 22 | switch(m_Distance) | ^ msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch] In file included from muscle.h:34, from profdb.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c profile.cpp -o profile.o In file included from muscle.h:34, from profile.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c profilefrommsa.cpp -o profilefrommsa.o profilefrommsa.cpp: In function 'void ListProfile(const ProfPos*, unsigned int, const MSA*)': profilefrommsa.cpp:131:24: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 131 | if (-1 == PP.m_uResidueGroup) | ~~~^~~~~~~~~~~~~~~~~~~~~ profilefrommsa.cpp: In function 'unsigned int ResidueGroupFromFCounts(const FCOUNT*)': profilefrommsa.cpp:230:16: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] 230 | switch (g_Alpha) | ^ profilefrommsa.cpp: In function 'ProfPos* ProfileFromMSA(const MSA&)': profilefrommsa.cpp:245:24: warning: unused variable 'uSeqCount' [-Wunused-variable] 245 | const unsigned uSeqCount = a.GetSeqCount(); | ^~~~~~~~~ profilefrommsa.cpp:253:18: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable] 253 | unsigned uHydrophobicRunLength = 0; | ^~~~~~~~~~~~~~~~~~~~~ profilefrommsa.cpp: At global scope: profilefrommsa.cpp:15:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function] 15 | static const char *LocalScoreToStr(SCORE s) | ^~~~~~~~~~~~~~~ In file included from muscle.h:34, from profilefrommsa.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c progalign.cpp -o progalign.o progalign.cpp: In function 'ProgNode* ProgressiveAlignE(const SeqVect&, const Tree&, MSA&)': progalign.cpp:41:24: warning: unused variable 'uIterCount' [-Wunused-variable] 41 | const unsigned uIterCount = uSeqCount - 1; | ^~~~~~~~~~ In file included from muscle.h:34, from progalign.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c progress.cpp -o progress.o In file included from muscle.h:34, from progress.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c progressivealign.cpp -o progressivealign.o In file included from muscle.h:34, from progressivealign.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c pwpath.cpp -o pwpath.o pwpath.cpp: In member function 'void PWPath::Validate() const': pwpath.cpp:79:23: warning: unused variable 'LastEdge' [-Wunused-variable] 79 | const PWEdge &LastEdge = GetEdge(uEdgeCount - 1); | ^~~~~~~~ pwpath.cpp: In member function 'void PWPath::FromFile(TextFile&)': pwpath.cpp:212:18: warning: unused variable 'uEdgeIndex' [-Wunused-variable] 212 | unsigned uEdgeIndex = 0; | ^~~~~~~~~~ In file included from muscle.h:34, from pwpath.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c readmx.cpp -o readmx.o readmx.cpp: In function 'float (* ReadMx(TextFile&))[32][32]': readmx.cpp:83:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 83 | for (int i = 0; i < MAX_ALPHA; ++i) | ~~^~~~~~~~~~~ readmx.cpp:84:35: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 84 | for (int j = 0; j < MAX_ALPHA; ++j) | ~~^~~~~~~~~~~ readmx.cpp: At global scope: readmx.cpp:30:17: warning: 'unsigned int MxCharToLetter(char)' defined but not used [-Wunused-function] 30 | static unsigned MxCharToLetter(char c) | ^~~~~~~~~~~~~~ In file included from muscle.h:34, from readmx.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c realigndiffs.cpp -o realigndiffs.o In file included from muscle.h:34, from realigndiffs.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c realigndiffse.cpp -o realigndiffse.o realigndiffse.cpp: In function 'void RealignDiffsE(const MSA&, const SeqVect&, const Tree&, const Tree&, const unsigned int*, MSA&, ProgNode*)': realigndiffse.cpp:72:34: warning: unused variable 'uNewRight' [-Wunused-variable] 72 | unsigned uNewRight = NewTree.GetRight(uNewNodeIndex); | ^~~~~~~~~ realigndiffse.cpp:75:34: warning: unused variable 'uOldRight' [-Wunused-variable] 75 | unsigned uOldRight = OldTree.GetRight(uOld); | ^~~~~~~~~ In file included from muscle.h:34, from realigndiffse.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c redblack.cpp -o redblack.o In file included from muscle.h:34, from redblack.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c refine.cpp -o refine.o In file included from clustsetmsa.h:8, from refine.cpp:9: msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': msadist.h:22:23: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch] 22 | switch(m_Distance) | ^ msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch] In file included from muscle.h:34, from refine.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c refinehoriz.cpp -o refinehoriz.o In file included from muscle.h:34, from refinehoriz.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ refinehoriz.cpp: In function 'bool RefineHoriz(MSA&, const Tree&, unsigned int, bool, bool)': refinehoriz.cpp:169:23: warning: 'scoreBefore' may be used uninitialized [-Wmaybe-uninitialized] 169 | SCORE scoreBefore; | ^~~~~~~~~~~ refinehoriz.cpp:170:23: warning: 'scoreAfter' may be used uninitialized [-Wmaybe-uninitialized] 170 | SCORE scoreAfter; | ^~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c refinesubfams.cpp -o refinesubfams.o refinesubfams.cpp: In function 'bool RefineSubfams(MSA&, const Tree&, unsigned int)': refinesubfams.cpp:63:24: warning: unused variable 'uNodeCount' [-Wunused-variable] 63 | const unsigned uNodeCount = tree.GetNodeCount(); | ^~~~~~~~~~ In file included from muscle.h:34, from refinesubfams.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c refinetree.cpp -o refinetree.o In file included from muscle.h:34, from refinetree.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c refinetreee.cpp -o refinetreee.o In file included from muscle.h:34, from refinetreee.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c refinevert.cpp -o refinevert.o In file included from muscle.h:34, from refinevert.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c refinew.cpp -o refinew.o refinew.cpp: In function 'void AppendMSA(MSA&, const MSA&)': refinew.cpp:26:24: warning: unused variable 'uColCountCat' [-Wunused-variable] 26 | const unsigned uColCountCat = uColCount1 + uColCount2; | ^~~~~~~~~~~~ refinew.cpp: In function 'void RefineW(const MSA&, MSA&)': refinew.cpp:129:34: warning: unused variable 'uOutCols' [-Wunused-variable] 129 | unsigned uOutCols = msaOut.GetColCount(); | ^~~~~~~~ In file included from muscle.h:34, from refinew.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c savebest.cpp -o savebest.o In file included from muscle.h:34, from savebest.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c scoredist.cpp -o scoredist.o In file included from muscle.h:34, from scoredist.cpp:3: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c scoregaps.cpp -o scoregaps.o scoregaps.cpp:80:14: warning: 'SCORE Penalty(unsigned int, bool)' defined but not used [-Wunused-function] 80 | static SCORE Penalty(unsigned Length, bool Term) | ^~~~~~~ scoregaps.cpp:37:13: warning: 'void FreeGapInfo(GAPINFO*)' defined but not used [-Wunused-function] 37 | static void FreeGapInfo(GAPINFO *GI) | ^~~~~~~~~~~ In file included from muscle.h:34, from scoregaps.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c scorehistory.cpp -o scorehistory.o In file included from muscle.h:34, from scorehistory.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c scorepp.cpp -o scorepp.o In file included from muscle.h:34, from scorepp.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c seq.cpp -o seq.o In file included from muscle.h:34, from seq.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c seqvect.cpp -o seqvect.o In file included from muscle.h:34, from seqvect.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c setblosumweights.cpp -o setblosumweights.o In file included from muscle.h:34, from setblosumweights.cpp:42: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c setgscweights.cpp -o setgscweights.o In file included from muscle.h:34, from setgscweights.cpp:104: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c setnewhandler.cpp -o setnewhandler.o In file included from muscle.h:34, from setnewhandler.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c spfast.cpp -o spfast.o spfast.cpp: In function 'SCORE ObjScoreSPDimer(const MSA&)': spfast.cpp:252:24: warning: unused variable 'uSeqCount' [-Wunused-variable] 252 | const unsigned uSeqCount = msa.GetSeqCount(); | ^~~~~~~~~ spfast.cpp: At global scope: spfast.cpp:59:14: warning: 'SCORE SPColBrute(const MSA&, unsigned int)' defined but not used [-Wunused-function] 59 | static SCORE SPColBrute(const MSA &msa, unsigned uColIndex) | ^~~~~~~~~~ spfast.cpp:14:20: warning: 'const char* GapTypeToStr(int)' defined but not used [-Wunused-function] 14 | static const char *GapTypeToStr(int GapType) | ^~~~~~~~~~~~ In file included from muscle.h:34, from spfast.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c sptest.cpp -o sptest.o In file included from muscle.h:34, from sptest.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c stabilize.cpp -o stabilize.o In file included from muscle.h:34, from stabilize.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c subfam.cpp -o subfam.o subfam.cpp: In function 'void AlignSubFam(SeqVect&, const Tree&, unsigned int, MSA&)': subfam.cpp:173:13: warning: unused variable 'NotUsed' [-Wunused-variable] 173 | int NotUsed = system(CmdLine); | ^~~~~~~ In file included from muscle.h:34, from subfam.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c subfams.cpp -o subfams.o subfams.cpp:52:13: warning: 'void Relax(DistFunc&, unsigned int, unsigned int)' defined but not used [-Wunused-function] 52 | static void Relax(DistFunc &DF, unsigned u, unsigned v) | ^~~~~ subfams.cpp:40:13: warning: 'void InitializeSingleSource(DistFunc&, unsigned int)' defined but not used [-Wunused-function] 40 | static void InitializeSingleSource(DistFunc &DF, unsigned uIndex) | ^~~~~~~~~~~~~~~~~~~~~~ subfams.cpp:10:13: warning: 'void GetMostDistantPair(DistFunc&, unsigned int*, unsigned int*)' defined but not used [-Wunused-function] 10 | static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2) | ^~~~~~~~~~~~~~~~~~ In file included from muscle.h:34, from subfams.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c sw.cpp -o sw.o sw.cpp:20:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function] 20 | static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB, | ^~~~~~ In file included from muscle.h:34, from sw.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c termgaps.cpp -o termgaps.o In file included from muscle.h:34, from termgaps.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c textfile.cpp -o textfile.o textfile.cpp: In member function 'void TextFile::PutChar(char)': textfile.cpp:104:13: warning: unused variable 'i' [-Wunused-variable] 104 | int i = fputc(c, m_ptrFile); | ^ textfile.cpp: In member function 'void TextFile::PutString(const char*)': textfile.cpp:117:13: warning: unused variable 'iError' [-Wunused-variable] 117 | int iError = fputs(szLine, m_ptrFile); | ^~~~~~ In file included from muscle.h:34, from textfile.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c threewaywt.cpp -o threewaywt.o In file included from muscle.h:34, from threewaywt.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c tomhydro.cpp -o tomhydro.o In file included from muscle.h:34, from tomhydro.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c traceback.cpp -o traceback.o traceback.cpp: In function 'SCORE TraceBack(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, PWPath&)': traceback.cpp:21:24: warning: unused variable 'uPrefixCountB' [-Wunused-variable] 21 | const unsigned uPrefixCountB = uLengthB + 1; | ^~~~~~~~~~~~~ In file included from muscle.h:34, from traceback.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c tracebackopt.cpp -o tracebackopt.o In file included from muscle.h:34, from tracebackopt.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c tracebacksw.cpp -o tracebacksw.o tracebacksw.cpp: In function 'void TraceBackSW(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, unsigned int, unsigned int, PWPath&)': tracebacksw.cpp:22:24: warning: unused variable 'uPrefixCountB' [-Wunused-variable] 22 | const unsigned uPrefixCountB = uLengthB + 1; | ^~~~~~~~~~~~~ tracebacksw.cpp:29:15: warning: unused variable 'scoreMax' [-Wunused-variable] 29 | SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB); | ^~~~~~~~ In file included from muscle.h:34, from tracebacksw.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c treefrommsa.cpp -o treefrommsa.o In file included from clustsetmsa.h:8, from treefrommsa.cpp:5: msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': msadist.h:22:23: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch] 22 | switch(m_Distance) | ^ msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch] msadist.h:22:23: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch] In file included from muscle.h:34, from treefrommsa.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c typetostr.cpp -o typetostr.o In file included from muscle.h:34, from typetostr.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ typetostr.cpp: In function 'const char* SecsToStr(long unsigned int)': typetostr.cpp:13:28: warning: ':' directive writing 1 byte into a region of size between 0 and 14 [-Wformat-overflow=] 13 | sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss); | ^ typetostr.cpp:13:22: note: directive argument in the range [0, 59] 13 | sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss); | ^~~~~~~~~~~~~~~~~~~ typetostr.cpp:13:22: note: directive argument in the range [0, 59] typetostr.cpp:13:16: note: 'sprintf' output between 9 and 23 bytes into a destination of size 16 13 | sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c upgma2.cpp -o upgma2.o upgma2.cpp:68:13: warning: 'void ListState()' defined but not used [-Wunused-function] 68 | static void ListState() | ^~~~~~~~~ In file included from muscle.h:34, from upgma2.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ upgma2.cpp: In function 'void UPGMA2(const DistCalc&, Tree&, LINKAGE)': upgma2.cpp:292:36: warning: 'dtNewDist' may be used uninitialized [-Wmaybe-uninitialized] 292 | g_Dist[vL] = dtNewDist; | ~~~~~~~~~~~^~~~~~~~~~~ upgma2.cpp:252:32: note: 'dtNewDist' was declared here 252 | dist_t dtNewDist; | ^~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c usage.cpp -o usage.o In file included from muscle.h:34, from usage.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c validateids.cpp -o validateids.o In file included from muscle.h:34, from validateids.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c vtml2.cpp -o vtml2.o In file included from muscle.h:34, from vtml2.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c writescorefile.cpp -o writescorefile.o In file included from muscle.h:34, from writescorefile.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] 59 | static double ScoreToDouble(SCORE Score) | ^~~~~~~~~~~~~ In function 'double GetColScore(const MSA&, unsigned int)', inlined from 'void WriteScoreFile(const MSA&)' at writescorefile.cpp:59:29: writescorefile.cpp:40:30: warning: 'Score' may be used uninitialized [-Wmaybe-uninitialized] 40 | dSum += Score; | ~~~~~^~~~~~~~ writescorefile.cpp: In function 'void WriteScoreFile(const MSA&)': writescorefile.cpp:27:32: note: 'Score' was declared here 27 | double Score; | ^~~~~ g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/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 -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/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)