BioC 3.2: CHECK report for muscle on perceval

Package: muscle

Version: 3.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings muscle_3.12.0.tar.gz

StartedAt: 2015-11-10 07:28:36 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 07:30:39 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 122.3 seconds

RetCode: 0

Status:  OK

CheckDir: muscle.Rcheck

Warnings: 0

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings muscle_3.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/muscle.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘muscle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘muscle’ version ‘3.12.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘muscle’ can be installed ... [29s/30s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

* installing *source* package ‘muscle’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -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: warning: unused variable ‘uLengthA’
aligngivenpath.cpp:187: warning: unused variable ‘uLengthB’
aligngivenpath.cpp: In function ‘void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)’:
aligngivenpath.cpp:335: warning: unused variable ‘uColA’
aligngivenpath.cpp:336: warning: unused variable ‘uColB’
aligngivenpath.cpp:346: warning: unused variable ‘uColA’
aligngivenpath.cpp:354: warning: unused variable ‘uColB’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -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: warning: unused variable ‘uLengthA’
aligngivenpathsw.cpp:59: warning: unused variable ‘uLengthB’
aligngivenpathsw.cpp: In function ‘void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)’:
aligngivenpathsw.cpp:204: warning: unused variable ‘uColA’
aligngivenpathsw.cpp:205: warning: unused variable ‘uColB’
aligngivenpathsw.cpp:215: warning: unused variable ‘uColA’
aligngivenpathsw.cpp:223: warning: unused variable ‘uColB’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c aligntwomsas.cpp -o aligntwomsas.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c aligntwoprofs.cpp -o aligntwoprofs.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c aln.cpp -o aln.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c alpha.cpp -o alpha.o
alpha.cpp: In function ‘unsigned int GetAlphaSize(ALPHA)’:
alpha.cpp:84: warning: enumeration value ‘ALPHA_Undefined’ not handled in switch
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -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: warning: unused variable ‘uWindowCenter’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
anchors.cpp:54: warning: ‘void FindBestColsGrade(const SCORE*, unsigned int, double, unsigned int*, unsigned int*)’ defined but not used
anchors.cpp:106: warning: ‘void ListBestCols(const MSA&, const SCORE*, const SCORE*, unsigned int*, unsigned int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -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: warning: unused variable ‘Bits’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
bittraceback.cpp:15: warning: ‘const char* BitsToStr(char)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c blosum62.cpp -o blosum62.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c blosumla.cpp -o blosumla.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
blosumla.cpp:7: warning: ‘Blosum62LA’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -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: warning: enumeration value ‘JOIN_Undefined’ not handled in switch
clust.cpp: In member function ‘void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)’:
clust.cpp:184: warning: unused variable ‘uClusterCount’
clust.cpp: In member function ‘void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)’:
clust.cpp:204: warning: unused variable ‘uClusterCount’
clust.cpp: In member function ‘float Clust::ComputeDist(unsigned int, unsigned int)’:
clust.cpp:295: warning: enumeration value ‘LINKAGE_Undefined’ not handled in switch
clust.cpp: In member function ‘float Clust::ComputeDistMAFFT(unsigned int, unsigned int)’:
clust.cpp:360: warning: unused variable ‘dDistLR’
clust.cpp: In member function ‘float Clust::ComputeMetric(unsigned int, unsigned int) const’:
clust.cpp:611: warning: enumeration value ‘JOIN_Undefined’ not handled in switch
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c cluster.cpp -o cluster.o
cluster.cpp: In member function ‘void ClusterTree::Create(const DistFunc&)’:
cluster.cpp:267: warning: unused variable ‘dMaxDist’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c clwwt.cpp -o clwwt.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c color.cpp -o color.o
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
color.cpp:72: warning: ‘int BlosumScore(char, char)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c cons.cpp -o cons.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c diaglist.cpp -o diaglist.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -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: warning: unused variable ‘uSeqCount’
diffobjscore.cpp:77: warning: unused variable ‘uColCount’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c diffpaths.cpp -o diffpaths.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -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: warning: unused variable ‘uLeafCount2’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c difftreese.cpp -o difftreese.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c distcalc.cpp -o distcalc.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c distfunc.cpp -o distfunc.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c distpwkimura.cpp -o distpwkimura.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c domuscle.cpp -o domuscle.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c dosp.cpp -o dosp.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -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: warning: unused variable ‘uDiagLengthMinusCaps’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c drawtree.cpp -o drawtree.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c edgelist.cpp -o edgelist.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c enumopts.cpp -o enumopts.o
In file included from enumopts.cpp:8:
enums.h:15: warning: missing braces around initializer for ‘EnumOpt’
enums.h:15: warning: missing braces around initializer for ‘EnumOpt’
enums.h:15: warning: missing braces around initializer for ‘EnumOpt’
enums.h:15: warning: missing braces around initializer for ‘EnumOpt’
enums.h:22: warning: missing braces around initializer for ‘EnumOpt’
enums.h:22: warning: missing braces around initializer for ‘EnumOpt’
enums.h:22: warning: missing braces around initializer for ‘EnumOpt’
enums.h:22: warning: missing braces around initializer for ‘EnumOpt’
enums.h:22: warning: missing braces around initializer for ‘EnumOpt’
enums.h:28: warning: missing braces around initializer for ‘EnumOpt’
enums.h:28: warning: missing braces around initializer for ‘EnumOpt’
enums.h:28: warning: missing braces around initializer for ‘EnumOpt’
enums.h:28: warning: missing braces around initializer for ‘EnumOpt’
enums.h:36: warning: missing braces around initializer for ‘EnumOpt’
enums.h:36: warning: missing braces around initializer for ‘EnumOpt’
enums.h:36: warning: missing braces around initializer for ‘EnumOpt’
enums.h:36: warning: missing braces around initializer for ‘EnumOpt’
enums.h:36: warning: missing braces around initializer for ‘EnumOpt’
enums.h:36: warning: missing braces around initializer for ‘EnumOpt’
enums.h:41: warning: missing braces around initializer for ‘EnumOpt’
enums.h:41: warning: missing braces around initializer for ‘EnumOpt’
enums.h:41: warning: missing braces around initializer for ‘EnumOpt’
enums.h:49: warning: missing braces around initializer for ‘EnumOpt’
enums.h:49: warning: missing braces around initializer for ‘EnumOpt’
enums.h:49: warning: missing braces around initializer for ‘EnumOpt’
enums.h:49: warning: missing braces around initializer for ‘EnumOpt’
enums.h:49: warning: missing braces around initializer for ‘EnumOpt’
enums.h:49: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:70: warning: missing braces around initializer for ‘EnumOpt’
enums.h:70: warning: missing braces around initializer for ‘EnumOpt’
enums.h:70: warning: missing braces around initializer for ‘EnumOpt’
enums.h:70: warning: missing braces around initializer for ‘EnumOpt’
enums.h:70: warning: missing braces around initializer for ‘EnumOpt’
enums.h:79: warning: missing braces around initializer for ‘EnumOpt’
enums.h:79: warning: missing braces around initializer for ‘EnumOpt’
enums.h:79: warning: missing braces around initializer for ‘EnumOpt’
enums.h:79: warning: missing braces around initializer for ‘EnumOpt’
enums.h:79: warning: missing braces around initializer for ‘EnumOpt’
enums.h:79: warning: missing braces around initializer for ‘EnumOpt’
enums.h:79: warning: missing braces around initializer for ‘EnumOpt’
enums.h:88: warning: missing braces around initializer for ‘EnumOpt’
enums.h:88: warning: missing braces around initializer for ‘EnumOpt’
enums.h:88: warning: missing braces around initializer for ‘EnumOpt’
enums.h:88: warning: missing braces around initializer for ‘EnumOpt’
enums.h:88: warning: missing braces around initializer for ‘EnumOpt’
enums.h:88: warning: missing braces around initializer for ‘EnumOpt’
enums.h:88: warning: missing braces around initializer for ‘EnumOpt’
enums.h:94: warning: missing braces around initializer for ‘EnumOpt’
enums.h:94: warning: missing braces around initializer for ‘EnumOpt’
enums.h:94: warning: missing braces around initializer for ‘EnumOpt’
enums.h:94: warning: missing braces around initializer for ‘EnumOpt’
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c enumtostr.cpp -o enumtostr.o
In file included from enumtostr.cpp:16:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c estring.cpp -o estring.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
estring.cpp:464: warning: ‘bool CanMultiplyEstrings(const short int*, const short int*)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c fasta.cpp -o fasta.o
fasta.cpp: In member function ‘void MSA::FromFASTAFile(TextFile&)’:
fasta.cpp:15: warning: unused variable ‘uSeqCount’
fasta.cpp:16: warning: unused variable ‘uColCount’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c fasta2.cpp -o fasta2.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c fastclust.cpp -o fastclust.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c fastdist.cpp -o fastdist.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c fastdistjones.cpp -o fastdistjones.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c fastdistkbit.cpp -o fastdistkbit.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c fastdistkmer.cpp -o fastdistkmer.o
fastdistkmer.cpp: In function ‘void FastDistKmer(const SeqVect&, DistFunc&)’:
fastdistkmer.cpp:235: warning: unused variable ‘KD’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c fastdistmafft.cpp -o fastdistmafft.o
fastdistmafft.cpp: In function ‘void DistKmer6_6(const SeqVect&, DistFunc&)’:
fastdistmafft.cpp:238: warning: unused variable ‘pName1’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
fastdistmafft.cpp:104: warning: ‘void ListCount(const unsigned char*)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c fastdistnuc.cpp -o fastdistnuc.o
fastdistnuc.cpp: In function ‘void DistKmer4_6(const SeqVect&, DistFunc&)’:
fastdistnuc.cpp:223: warning: unused variable ‘pName1’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
fastdistnuc.cpp:33: warning: ‘uResidueGroupCount’ defined but not used
fastdistnuc.cpp:85: warning: ‘void ListCount(const unsigned char*)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c fastscorepath2.cpp -o fastscorepath2.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c finddiags.cpp -o finddiags.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
finddiags.cpp:11: warning: ‘char* TupleToStr(int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c finddiagsn.cpp -o finddiagsn.o
finddiagsn.cpp: In function ‘char* TupleToStr(int)’:
finddiagsn.cpp:16: warning: comparison between signed and unsigned integer expressions
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
finddiagsn.cpp:12: warning: ‘char* TupleToStr(int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c glbalign.cpp -o glbalign.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c glbalign352.cpp -o glbalign352.o
In file included from glbalign352.cpp:6:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c glbaligndiag.cpp -o glbaligndiag.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c glbalignla.cpp -o glbalignla.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c glbalignle.cpp -o glbalignle.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c glbalignns.cpp -o glbalignns.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c glbalignsimple.cpp -o glbalignsimple.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
glbalignsimple.cpp:29: warning: ‘void ListTB(const char*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)’ defined but not used
glbalignsimple.cpp:53: warning: ‘void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c glbalignsp.cpp -o glbalignsp.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c glbalignspn.cpp -o glbalignspn.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c glbalignss.cpp -o glbalignss.o
glbalignss.cpp: In function ‘SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)’:
glbalignss.cpp:177: warning: unused variable ‘ptrRowA’
glbalignss.cpp:119: warning: unused variable ‘uPrefixCountA’
glbalignss.cpp:120: warning: unused variable ‘uPrefixCountB’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
glbalignss.cpp:11: warning: ‘SCORE Subst(const Seq&, const Seq&, unsigned int, unsigned int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c glbalndimer.cpp -o glbalndimer.o
glbalndimer.cpp: In function ‘SCORE ScoreProfPosDimer(const ProfPos&, const ProfPos&)’:
glbalndimer.cpp:123: warning: enumeration value ‘PPSCORE_Undefined’ not handled in switch
glbalndimer.cpp:123: warning: enumeration value ‘PPSCORE_SPN’ not handled in switch
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
glbalndimer.cpp:14: warning: ‘const char* LocalScoreToStr(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c globals.cpp -o globals.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c globalslinux.cpp -o globalslinux.o
In file included from globalslinux.cpp:1:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c globalsosx.cpp -o globalsosx.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c globalsother.cpp -o globalsother.o
In file included from globalsother.cpp:1:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c globalswin32.cpp -o globalswin32.o
In file included from globalswin32.cpp:1:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c gonnet.cpp -o gonnet.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
gonnet.cpp:137: warning: ‘Gonnet160’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c gotowt.cpp -o gotowt.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c henikoffweight.cpp -o henikoffweight.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c henikoffweightpb.cpp -o henikoffweightpb.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c html.cpp -o html.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c hydro.cpp -o hydro.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c intmath.cpp -o intmath.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c local.cpp -o local.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c main.cpp -o main.o
main.cpp:112: warning: missing braces around initializer for ‘R_CMethodDef’
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c makerootmsa.cpp -o makerootmsa.o
makerootmsa.cpp: In function ‘void PathSeq(const Seq&, const PWPath&, bool, Seq&)’:
makerootmsa.cpp:18: warning: unused variable ‘uSeqLength’
makerootmsa.cpp: In function ‘short int* MakeRootSeqE(const Seq&, const Tree&, unsigned int, const ProgNode*, Seq&, short int*, short int*)’:
makerootmsa.cpp:94: warning: unused variable ‘Path’
makerootmsa.cpp: In function ‘void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)’:
makerootmsa.cpp:168: warning: unused variable ‘uTreeNodeCount’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
makerootmsa.cpp:12: warning: ‘void PathSeq(const Seq&, const PWPath&, bool, Seq&)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c makerootmsab.cpp -o makerootmsab.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c maketree.cpp -o maketree.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c mhack.cpp -o mhack.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c mpam200.cpp -o mpam200.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c msa.cpp -o msa.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
msa.cpp:385: warning: ‘void FmtChar(char, unsigned int)’ defined but not used
msa.cpp:392: warning: ‘void FmtInt(unsigned int, unsigned int)’ defined but not used
msa.cpp:407: warning: ‘void FmtInt0(unsigned int, unsigned int)’ defined but not used
msa.cpp:419: warning: ‘void FmtPad(unsigned int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c msa2.cpp -o msa2.o
msa2.cpp: In function ‘void SetMSAWeightsMuscle(MSA&)’:
msa2.cpp:357: warning: enumeration value ‘SEQWEIGHT_Undefined’ not handled in switch
msa2.cpp: In function ‘void MSAAppend(MSA&, const MSA&)’:
msa2.cpp:476: warning: unused variable ‘uColCountCat’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c msadistkimura.cpp -o msadistkimura.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c msf.cpp -o msf.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
msf.cpp:24: warning: ‘const char* strfind(const char*, const char*)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c muscle.cpp -o muscle.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c muscleout.cpp -o muscleout.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c nucmx.cpp -o nucmx.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c nwdasimple.cpp -o nwdasimple.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c nwdasimple2.cpp -o nwdasimple2.o
In file included from nwdasimple2.cpp:3:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c nwdasmall.cpp -o nwdasmall.o
In file included from nwdasmall.cpp:4:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c nwrec.cpp -o nwrec.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c nwsmall.cpp -o nwsmall.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -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: warning: enumeration value ‘OBJSCORE_Undefined’ not handled in switch
objscore.cpp:31: warning: enumeration value ‘OBJSCORE_SPM’ not handled in switch
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c objscore2.cpp -o objscore2.o
objscore2.cpp: In function ‘SCORE TermGapScore(bool)’:
objscore2.cpp:22: warning: enumeration value ‘TERMGAPS_Undefined’ not handled in switch
objscore2.cpp: In function ‘SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)’:
objscore2.cpp:62: warning: unused variable ‘scoreGaps’
objscore2.cpp:63: warning: unused variable ‘bGapping1’
objscore2.cpp:64: warning: unused variable ‘bGapping2’
objscore2.cpp: In function ‘SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)’:
objscore2.cpp:314: warning: unused variable ‘uColCount2’
objscore2.cpp: In function ‘SCORE ObjScoreXP(const MSA&, const MSA&)’:
objscore2.cpp:493: warning: unused variable ‘w’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c objscoreda.cpp -o objscoreda.o
In file included from objscoreda.cpp:4:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c onexception.cpp -o onexception.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c optionsR.cpp -o optionsR.o
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:87: warning: missing braces around initializer for ‘VALUE_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
optionsR.cpp:127: warning: missing braces around initializer for ‘FLAG_OPT’
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c outweights.cpp -o outweights.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c pam200mafft.cpp -o pam200mafft.o
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
pam200mafft.cpp:6: warning: ‘PAM200’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c params.cpp -o params.o
params.cpp: In function ‘void SetPPScore(bool)’:
params.cpp:445: warning: enumeration value ‘PPSCORE_Undefined’ not handled in switch
params.cpp: In function ‘void default_params()’:
params.cpp:659: warning: statement has no effect
params.cpp:652: warning: unused variable ‘VTML_LA’
params.cpp:653: warning: unused variable ‘PAM200’
params.cpp:654: warning: unused variable ‘PAM200NoCenter’
params.cpp:655: warning: unused variable ‘VTML_SP’
params.cpp:656: warning: unused variable ‘VTML_SPNoCenter’
params.cpp:657: warning: unused variable ‘NUC_SP’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c phy.cpp -o phy.o
phy.cpp: In member function ‘void Tree::RootUnrootedTree(ROOT)’:
phy.cpp:665: warning: unused variable ‘dEdgeLength’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c phy2.cpp -o phy2.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -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: warning: unused variable ‘dThisDist’
phy3.cpp: In function ‘void FindRoot(const Tree&, unsigned int*, unsigned int*, double*, double*, ROOT)’:
phy3.cpp:167: warning: unused variable ‘uLeafCount’
phy3.cpp:190: warning: unused variable ‘dAllMaxDist’
phy3.cpp:191: warning: unused variable ‘uMaxFrom’
phy3.cpp:192: warning: unused variable ‘uMaxTo’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
phy3.cpp:45: warning: ‘void ListEIs(EdgeInfo**, unsigned int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c phy4.cpp -o phy4.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c phyfromclust.cpp -o phyfromclust.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c phyfromfile.cpp -o phyfromfile.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c physeq.cpp -o physeq.o
physeq.cpp: In member function ‘void MSA::ToPhySequentialFile(TextFile&) const’:
physeq.cpp:60: warning: comparison between signed and unsigned integer expressions
physeq.cpp:71: warning: comparison between signed and unsigned integer expressions
physeq.cpp: In member function ‘void MSA::ToPhyInterleavedFile(TextFile&) const’:
physeq.cpp:112: warning: comparison between signed and unsigned integer expressions
physeq.cpp:124: warning: comparison between signed and unsigned integer expressions
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c phytofile.cpp -o phytofile.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c posgap.cpp -o posgap.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ppscore.cpp -o ppscore.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -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: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c profile.cpp -o profile.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c profilefrommsa.cpp -o profilefrommsa.o
profilefrommsa.cpp: In function ‘void ListProfile(const ProfPos*, unsigned int, const MSA*)’:
profilefrommsa.cpp:131: warning: comparison between signed and unsigned integer expressions
profilefrommsa.cpp: In function ‘unsigned int ResidueGroupFromFCounts(const FCOUNT*)’:
profilefrommsa.cpp:230: warning: enumeration value ‘ALPHA_Undefined’ not handled in switch
profilefrommsa.cpp: In function ‘ProfPos* ProfileFromMSA(const MSA&)’:
profilefrommsa.cpp:245: warning: unused variable ‘uSeqCount’
profilefrommsa.cpp:253: warning: unused variable ‘uHydrophobicRunLength’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
profilefrommsa.cpp:15: warning: ‘const char* LocalScoreToStr(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c progalign.cpp -o progalign.o
progalign.cpp: In function ‘ProgNode* ProgressiveAlignE(const SeqVect&, const Tree&, MSA&)’:
progalign.cpp:41: warning: unused variable ‘uIterCount’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c progress.cpp -o progress.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c progressivealign.cpp -o progressivealign.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c pwpath.cpp -o pwpath.o
pwpath.cpp: In member function ‘void PWPath::Validate() const’:
pwpath.cpp:79: warning: unused variable ‘LastEdge’
pwpath.cpp: In member function ‘void PWPath::FromFile(TextFile&)’:
pwpath.cpp:212: warning: unused variable ‘uEdgeIndex’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c readmx.cpp -o readmx.o
readmx.cpp: In function ‘float (* ReadMx(TextFile&))[32][32]’:
readmx.cpp:83: warning: comparison between signed and unsigned integer expressions
readmx.cpp:84: warning: comparison between signed and unsigned integer expressions
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
readmx.cpp:30: warning: ‘unsigned int MxCharToLetter(char)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c realigndiffs.cpp -o realigndiffs.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -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: warning: unused variable ‘uNewRight’
realigndiffse.cpp:75: warning: unused variable ‘uOldRight’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c redblack.cpp -o redblack.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -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: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c refinehoriz.cpp -o refinehoriz.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c refinesubfams.cpp -o refinesubfams.o
refinesubfams.cpp: In function ‘bool RefineSubfams(MSA&, const Tree&, unsigned int)’:
refinesubfams.cpp:63: warning: unused variable ‘uNodeCount’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c refinetree.cpp -o refinetree.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c refinetreee.cpp -o refinetreee.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c refinevert.cpp -o refinevert.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c refinew.cpp -o refinew.o
refinew.cpp: In function ‘void AppendMSA(MSA&, const MSA&)’:
refinew.cpp:26: warning: unused variable ‘uColCountCat’
refinew.cpp: In function ‘void RefineW(const MSA&, MSA&)’:
refinew.cpp:129: warning: unused variable ‘uOutCols’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c savebest.cpp -o savebest.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c scoredist.cpp -o scoredist.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c scoregaps.cpp -o scoregaps.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
scoregaps.cpp:37: warning: ‘void FreeGapInfo(GAPINFO*)’ defined but not used
scoregaps.cpp:80: warning: ‘SCORE Penalty(unsigned int, bool)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c scorehistory.cpp -o scorehistory.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c scorepp.cpp -o scorepp.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c seq.cpp -o seq.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c seqvect.cpp -o seqvect.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c setblosumweights.cpp -o setblosumweights.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c setgscweights.cpp -o setgscweights.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c setnewhandler.cpp -o setnewhandler.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c spfast.cpp -o spfast.o
spfast.cpp: In function ‘SCORE ObjScoreSPDimer(const MSA&)’:
spfast.cpp:252: warning: unused variable ‘uSeqCount’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
spfast.cpp:14: warning: ‘const char* GapTypeToStr(int)’ defined but not used
spfast.cpp:59: warning: ‘SCORE SPColBrute(const MSA&, unsigned int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c sptest.cpp -o sptest.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c stabilize.cpp -o stabilize.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c subfam.cpp -o subfam.o
subfam.cpp: In function ‘void AlignSubFam(SeqVect&, const Tree&, unsigned int, MSA&)’:
subfam.cpp:173: warning: unused variable ‘NotUsed’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c subfams.cpp -o subfams.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
subfams.cpp:10: warning: ‘void GetMostDistantPair(DistFunc&, unsigned int*, unsigned int*)’ defined but not used
subfams.cpp:40: warning: ‘void InitializeSingleSource(DistFunc&, unsigned int)’ defined but not used
subfams.cpp:52: warning: ‘void Relax(DistFunc&, unsigned int, unsigned int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c sw.cpp -o sw.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
sw.cpp:21: warning: ‘void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c termgaps.cpp -o termgaps.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c textfile.cpp -o textfile.o
textfile.cpp: In member function ‘void TextFile::PutChar(char)’:
textfile.cpp:104: warning: unused variable ‘i’
textfile.cpp: In member function ‘void TextFile::PutString(const char*)’:
textfile.cpp:117: warning: unused variable ‘iError’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c threewaywt.cpp -o threewaywt.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c tomhydro.cpp -o tomhydro.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -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: warning: unused variable ‘uPrefixCountB’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c tracebackopt.cpp -o tracebackopt.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -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: warning: unused variable ‘uPrefixCountB’
tracebacksw.cpp:29: warning: unused variable ‘scoreMax’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -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: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c typetostr.cpp -o typetostr.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c upgma2.cpp -o upgma2.o
upgma2.cpp: In member function ‘virtual void DistCalcTest::CalcDistRange(unsigned int, dist_t*) const’:
upgma2.cpp:371: warning: missing braces around initializer for ‘dist_t [5]’
upgma2.cpp:371: warning: missing braces around initializer for ‘dist_t [5]’
upgma2.cpp:371: warning: missing braces around initializer for ‘dist_t [5]’
upgma2.cpp:371: warning: missing braces around initializer for ‘dist_t [5]’
upgma2.cpp:371: warning: missing braces around initializer for ‘dist_t [5]’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
upgma2.cpp:68: warning: ‘void ListState()’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c usage.cpp -o usage.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c validateids.cpp -o validateids.o
In file included from validateids.cpp:4:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c vtml2.cpp -o vtml2.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c writescorefile.cpp -o writescorefile.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
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installing to /Users/biocbuild/bbs-3.2-bioc/meat/muscle.Rcheck/muscle/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (muscle)

name	user	system	elapsed
muscle-package	0.000	0.000	0.001
muscle	2.916	0.053	2.970