BioC 3.2: CHECK report for muscle on moscato1

Package: muscle

Version: 3.12.0

Command: rm -rf muscle.buildbin-libdir muscle.Rcheck && mkdir muscle.buildbin-libdir muscle.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=muscle.buildbin-libdir muscle_3.12.0.tar.gz >muscle.Rcheck\00install.out 2>&1 && cp muscle.Rcheck\00install.out muscle-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=muscle.buildbin-libdir --install="check:muscle-install.out" --force-multiarch --no-vignettes --timings muscle_3.12.0.tar.gz

StartedAt: 2016-04-23 05:11:32 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 05:16:30 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 297.6 seconds

RetCode: 0

Status:  OK

CheckDir: muscle.Rcheck

Warnings: 0

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### Running command:
###
###   rm -rf muscle.buildbin-libdir muscle.Rcheck && mkdir muscle.buildbin-libdir muscle.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=muscle.buildbin-libdir muscle_3.12.0.tar.gz >muscle.Rcheck\00install.out 2>&1 && cp muscle.Rcheck\00install.out muscle-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=muscle.buildbin-libdir --install="check:muscle-install.out" --force-multiarch --no-vignettes --timings muscle_3.12.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/muscle.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'muscle' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.2-bioc/meat/muscle.buildbin-libdir/muscle/libs/i386/muscle.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.2-bioc/meat/muscle.buildbin-libdir/muscle/libs/x64/muscle.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [10s] OK
** running examples for arch 'x64' ... [9s] 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: 1 NOTE
See
  'D:/biocbld/bbs-3.2-bioc/meat/muscle.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'muscle' ...
** libs
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -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:186:17: warning: unused variable 'uLengthA' [-Wunused-variable]
aligngivenpath.cpp:187:17: warning: unused variable 'uLengthB' [-Wunused-variable]
aligngivenpath.cpp: In function 'void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)':
aligngivenpath.cpp:335:19: warning: unused variable 'uColA' [-Wunused-variable]
aligngivenpath.cpp:336:19: warning: unused variable 'uColB' [-Wunused-variable]
aligngivenpath.cpp:346:19: warning: unused variable 'uColA' [-Wunused-variable]
aligngivenpath.cpp:354:19: warning: unused variable 'uColB' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -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:58:17: warning: unused variable 'uLengthA' [-Wunused-variable]
aligngivenpathsw.cpp:59:17: warning: unused variable 'uLengthB' [-Wunused-variable]
aligngivenpathsw.cpp: In function 'void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)':
aligngivenpathsw.cpp:204:19: warning: unused variable 'uColA' [-Wunused-variable]
aligngivenpathsw.cpp:205:19: warning: unused variable 'uColB' [-Wunused-variable]
aligngivenpathsw.cpp:215:19: warning: unused variable 'uColA' [-Wunused-variable]
aligngivenpathsw.cpp:223:19: warning: unused variable 'uColB' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c aligntwomsas.cpp -o aligntwomsas.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c aligntwoprofs.cpp -o aligntwoprofs.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c aln.cpp -o aln.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c alpha.cpp -o alpha.o
alpha.cpp: In function 'unsigned int GetAlphaSize(ALPHA)':
alpha.cpp:84:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -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:162:13: warning: unused variable 'uWindowCenter' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
anchors.cpp:53:13: warning: 'void FindBestColsGrade(const SCORE*, unsigned int, double, unsigned int*, unsigned int*)' defined but not used [-Wunused-function]
anchors.cpp:105:13: warning: 'void ListBestCols(const MSA&, const SCORE*, const SCORE*, unsigned int*, unsigned int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c bittraceback.cpp -o bittraceback.o
bittraceback.cpp: In function 'void BitTraceBack(char**, unsigned int, unsigned int, char, PWPath&)':
bittraceback.cpp:146:7: warning: unused variable 'Bits' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
bittraceback.cpp:15:20: warning: 'const char* BitsToStr(char)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c blosum62.cpp -o blosum62.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c blosumla.cpp -o blosumla.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
blosumla.cpp:7:14: warning: 'Blosum62LA' defined but not used [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c clust.cpp -o clust.o
clust.cpp: In member function 'void Clust::ChooseJoin(unsigned int*, unsigned int*, float*, float*)':
clust.cpp:167:9: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
clust.cpp: In member function 'void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)':
clust.cpp:184:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
clust.cpp: In member function 'void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)':
clust.cpp:204:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
clust.cpp: In member function 'float Clust::ComputeDist(unsigned int, unsigned int)':
clust.cpp:295:9: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch]
clust.cpp: In member function 'float Clust::ComputeDistMAFFT(unsigned int, unsigned int)':
clust.cpp:360:14: warning: unused variable 'dDistLR' [-Wunused-variable]
clust.cpp: In member function 'float Clust::ComputeMetric(unsigned int, unsigned int) const':
clust.cpp:611:9: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c cluster.cpp -o cluster.o
cluster.cpp: In member function 'void ClusterTree::Create(const DistFunc&)':
cluster.cpp:284:8: warning: variable 'bFound' set but not used [-Wunused-but-set-variable]
cluster.cpp:267:9: warning: unused variable 'dMaxDist' [-Wunused-variable]
cluster.cpp:308:47: warning: 'uIndexClosest2' may be used uninitialized in this function [-Wuninitialized]
cluster.cpp:307:47: warning: 'uIndexClosest1' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c clwwt.cpp -o clwwt.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c color.cpp -o color.o
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
color.cpp:72:12: warning: 'int BlosumScore(char, char)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c cons.cpp -o cons.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c diaglist.cpp -o diaglist.o
diaglist.cpp: In member function 'void DiagList::FromPath(const PWPath&)':
diaglist.cpp:77:39: warning: 'uStartPosB' may be used uninitialized in this function [-Wuninitialized]
diaglist.cpp:77:39: warning: 'uStartPosA' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c diffobjscore.cpp -o diffobjscore.o
diffobjscore.cpp: In function 'SCORE ScoreLetters(const MSA&, const unsigned int*, unsigned int)':
diffobjscore.cpp:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c diffpaths.cpp -o diffpaths.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c difftrees.cpp -o difftrees.o
difftrees.cpp: In function 'void DiffTrees(const Tree&, const Tree&, Tree&, unsigned int*)':
difftrees.cpp:161:17: warning: unused variable 'uLeafCount2' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c difftreese.cpp -o difftreese.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c distcalc.cpp -o distcalc.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c distfunc.cpp -o distfunc.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c distpwkimura.cpp -o distpwkimura.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c domuscle.cpp -o domuscle.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c dosp.cpp -o dosp.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c dpreglist.cpp -o dpreglist.o
dpreglist.cpp: In function 'void DiagListToDPRegionList(const DiagList&, DPRegionList&, unsigned int, unsigned int)':
dpreglist.cpp:82:19: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c drawtree.cpp -o drawtree.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c edgelist.cpp -o edgelist.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c enumopts.cpp -o enumopts.o
In file included from enumopts.cpp:8:0:
enums.h:15:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:15:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:15:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:15:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:28:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:28:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:28:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:28:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:41:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:41:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:41:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:94:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:94:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:94:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:94:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c enumtostr.cpp -o enumtostr.o
In file included from enumtostr.cpp:16:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c estring.cpp -o estring.o
estring.cpp: In function 'void EstringsToPath(const short int*, const short int*, PWPath&)':
estring.cpp:409:3: warning: 'cType' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
estring.cpp:464:13: warning: 'bool CanMultiplyEstrings(const short int*, const short int*)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fasta.cpp -o fasta.o
fasta.cpp: In member function 'void MSA::FromFASTAFile(TextFile&)':
fasta.cpp:15:11: warning: unused variable 'uSeqCount' [-Wunused-variable]
fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fasta2.cpp -o fasta2.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastclust.cpp -o fastclust.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdist.cpp -o fastdist.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistjones.cpp -o fastdistjones.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistkbit.cpp -o fastdistkbit.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistkmer.cpp -o fastdistkmer.o
fastdistkmer.cpp: In function 'void FastDistKmer(const SeqVect&, DistFunc&)':
fastdistkmer.cpp:235:11: warning: unused variable 'KD' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistmafft.cpp -o fastdistmafft.o
fastdistmafft.cpp: In function 'void DistKmer6_6(const SeqVect&, DistFunc&)':
fastdistmafft.cpp:238:15: warning: unused variable 'pName1' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
fastdistmafft.cpp:104:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistnuc.cpp -o fastdistnuc.o
fastdistnuc.cpp: In function 'void DistKmer4_6(const SeqVect&, DistFunc&)':
fastdistnuc.cpp:223:15: warning: unused variable 'pName1' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
fastdistnuc.cpp:33:17: warning: 'uResidueGroupCount' defined but not used [-Wunused-variable]
fastdistnuc.cpp:85:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastscorepath2.cpp -o fastscorepath2.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c finddiags.cpp -o finddiags.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
finddiags.cpp:11:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c finddiagsn.cpp -o finddiagsn.o
finddiagsn.cpp: In function 'char* TupleToStr(int)':
finddiagsn.cpp:16:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
finddiagsn.cpp:12:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalign.cpp -o glbalign.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalign352.cpp -o glbalign352.o
In file included from glbalign352.cpp:6:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbaligndiag.cpp -o glbaligndiag.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignla.cpp -o glbalignla.o
glbalignla.cpp: In function 'SCORE GlobalAlignLA(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
glbalignla.cpp:424:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
glbalignla.cpp:363:50: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignle.cpp -o glbalignle.o
glbalignle.cpp: In function 'SCORE GlobalAlignLE(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
glbalignle.cpp:427:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignns.cpp -o glbalignns.o
glbalignns.cpp: In function 'SCORE GlobalAlignNS(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
glbalignns.cpp:366:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
glbalignns.cpp:305:50: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignsimple.cpp -o glbalignsimple.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
glbalignsimple.cpp:28:13: warning: 'void ListTB(const char*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
glbalignsimple.cpp:52:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignsp.cpp -o glbalignsp.o
glbalignsp.cpp: In function 'SCORE GlobalAlignSP(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
glbalignsp.cpp:366:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
glbalignsp.cpp:305:50: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignspn.cpp -o glbalignspn.o
glbalignspn.cpp: In function 'SCORE GlobalAlignSPN(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
glbalignspn.cpp:401:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
glbalignspn.cpp:340:50: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignss.cpp -o glbalignss.o
glbalignss.cpp: In function 'SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)':
glbalignss.cpp:177:16: warning: unused variable 'ptrRowA' [-Wunused-variable]
glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable]
glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
glbalignss.cpp:310:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
glbalignss.cpp:252:50: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
glbalignss.cpp:11:14: warning: 'SCORE Subst(const Seq&, const Seq&, unsigned int, unsigned int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalndimer.cpp -o glbalndimer.o
glbalndimer.cpp: In function 'SCORE ScoreProfPosDimer(const ProfPos&, const ProfPos&)':
glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_SPN' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
glbalndimer.cpp:14:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c globals.cpp -o globals.o
In file included from D:/biocbld/BBS-3˜1.2-B/R/include/R.h:50:0,
                 from globals.cpp:17:
D:/biocbld/BBS-3˜1.2-B/R/include/R_ext/RS.h:45:0: warning: "ERROR" redefined [enabled by default]
c:\rtools33\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/wingdi.h:70:0: note: this is the location of the previous definition
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c globalslinux.cpp -o globalslinux.o
In file included from globalslinux.cpp:1:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c globalsosx.cpp -o globalsosx.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c globalsother.cpp -o globalsother.o
In file included from globalsother.cpp:1:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c globalswin32.cpp -o globalswin32.o
globalswin32.cpp: In function 'double GetNAN()':
globalswin32.cpp:24:28: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
globalswin32.cpp: In function 'double GetMemUseMB()':
globalswin32.cpp:59:9: warning: unused variable 'hProc' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c gonnet.cpp -o gonnet.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
gonnet.cpp:137:14: warning: 'Gonnet160' defined but not used [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c gotowt.cpp -o gotowt.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c henikoffweight.cpp -o henikoffweight.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c henikoffweightpb.cpp -o henikoffweightpb.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c html.cpp -o html.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c hydro.cpp -o hydro.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c intmath.cpp -o intmath.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c local.cpp -o local.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c main.cpp -o main.o
In file included from D:/biocbld/BBS-3˜1.2-B/R/include/R.h:50:0,
                 from main.cpp:21:
D:/biocbld/BBS-3˜1.2-B/R/include/R_ext/RS.h:45:0: warning: "ERROR" redefined [enabled by default]
c:\rtools33\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/wingdi.h:70:0: note: this is the location of the previous definition
main.cpp:112:1: warning: missing braces around initializer for 'R_CMethodDef' [-Wmissing-braces]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c makerootmsa.cpp -o makerootmsa.o
makerootmsa.cpp: In function 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)':
makerootmsa.cpp:18:17: warning: unused variable 'uSeqLength' [-Wunused-variable]
makerootmsa.cpp: In function 'short int* MakeRootSeqE(const Seq&, const Tree&, unsigned int, const ProgNode*, Seq&, short int*, short int*)':
makerootmsa.cpp:94:17: warning: unused variable 'Path' [-Wunused-variable]
makerootmsa.cpp: In function 'void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)':
makerootmsa.cpp:168:17: warning: unused variable 'uTreeNodeCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
makerootmsa.cpp:12:13: warning: 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c makerootmsab.cpp -o makerootmsab.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c maketree.cpp -o maketree.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c mhack.cpp -o mhack.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c mpam200.cpp -o mpam200.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c msa.cpp -o msa.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
msa.cpp:385:13: warning: 'void FmtChar(char, unsigned int)' defined but not used [-Wunused-function]
msa.cpp:392:13: warning: 'void FmtInt(unsigned int, unsigned int)' defined but not used [-Wunused-function]
msa.cpp:407:13: warning: 'void FmtInt0(unsigned int, unsigned int)' defined but not used [-Wunused-function]
msa.cpp:419:13: warning: 'void FmtPad(unsigned int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c msa2.cpp -o msa2.o
msa2.cpp: In function 'void SetMSAWeightsMuscle(MSA&)':
msa2.cpp:357:9: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch]
msa2.cpp: In function 'void MSAAppend(MSA&, const MSA&)':
msa2.cpp:476:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c msadistkimura.cpp -o msadistkimura.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c msf.cpp -o msf.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
msf.cpp:24:20: warning: 'const char* strfind(const char*, const char*)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c muscle.cpp -o muscle.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c muscleout.cpp -o muscleout.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nucmx.cpp -o nucmx.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nwdasimple.cpp -o nwdasimple.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nwdasimple2.cpp -o nwdasimple2.o
In file included from nwdasimple2.cpp:3:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nwdasmall.cpp -o nwdasmall.o
In file included from nwdasmall.cpp:4:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nwrec.cpp -o nwrec.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nwsmall.cpp -o nwsmall.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -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:31:9: warning: enumeration value 'OBJSCORE_Undefined' not handled in switch [-Wswitch]
objscore.cpp:31:9: warning: enumeration value 'OBJSCORE_SPM' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c objscore2.cpp -o objscore2.o
objscore2.cpp: In function 'SCORE TermGapScore(bool)':
objscore2.cpp:22:9: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch]
objscore2.cpp: In function 'SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)':
objscore2.cpp:62:8: warning: unused variable 'scoreGaps' [-Wunused-variable]
objscore2.cpp:63:7: warning: unused variable 'bGapping1' [-Wunused-variable]
objscore2.cpp:64:7: warning: unused variable 'bGapping2' [-Wunused-variable]
objscore2.cpp:67:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
objscore2.cpp:82:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
objscore2.cpp: In function 'SCORE ScoreSeqPairGaps(const MSA&, unsigned int, const MSA&, unsigned int)':
objscore2.cpp:140:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
objscore2.cpp:155:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
objscore2.cpp: In function 'SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)':
objscore2.cpp:314:17: warning: unused variable 'uColCount2' [-Wunused-variable]
objscore2.cpp: In function 'SCORE ObjScoreXP(const MSA&, const MSA&)':
objscore2.cpp:493:17: warning: unused variable 'w' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c objscoreda.cpp -o objscoreda.o
In file included from objscoreda.cpp:4:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c onexception.cpp -o onexception.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c optionsR.cpp -o optionsR.o
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c outweights.cpp -o outweights.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c pam200mafft.cpp -o pam200mafft.o
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
pam200mafft.cpp:6:14: warning: 'PAM200' defined but not used [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c params.cpp -o params.o
params.cpp: In function 'void SetPPScore(bool)':
params.cpp:445:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
params.cpp: In function 'void default_params()':
params.cpp:659:18: warning: statement has no effect [-Wunused-value]
params.cpp:652:14: warning: unused variable 'VTML_LA' [-Wunused-variable]
params.cpp:653:14: warning: unused variable 'PAM200' [-Wunused-variable]
params.cpp:654:14: warning: unused variable 'PAM200NoCenter' [-Wunused-variable]
params.cpp:655:14: warning: unused variable 'VTML_SP' [-Wunused-variable]
params.cpp:656:14: warning: unused variable 'VTML_SPNoCenter' [-Wunused-variable]
params.cpp:657:14: warning: unused variable 'NUC_SP' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phy.cpp -o phy.o
phy.cpp: In member function 'void Tree::RootUnrootedTree(ROOT)':
phy.cpp:665:9: warning: unused variable 'dEdgeLength' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phy2.cpp -o phy2.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phy3.cpp -o phy3.o
phy3.cpp: In function 'void CalcInfo(const Tree&, unsigned int, unsigned int, EdgeInfo**)':
phy3.cpp:125:15: warning: unused variable 'dThisDist' [-Wunused-variable]
phy3.cpp: In function 'void FindRoot(const Tree&, unsigned int*, unsigned int*, double*, double*, ROOT)':
phy3.cpp:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable]
phy3.cpp:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable]
phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable]
phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable]
phy3.cpp: In function 'void RootByMidLongestSpan(const Tree&, EdgeInfo**, unsigned int*, unsigned int*, double*, double*)':
phy3.cpp:263:11: warning: variable 'uMostDistantLeaf' set but not used [-Wunused-but-set-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
phy3.cpp:45:13: warning: 'void ListEIs(EdgeInfo**, unsigned int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phy4.cpp -o phy4.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phyfromclust.cpp -o phyfromclust.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phyfromfile.cpp -o phyfromfile.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c physeq.cpp -o physeq.o
physeq.cpp: In member function 'void MSA::ToPhySequentialFile(TextFile&) const':
physeq.cpp:60:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
physeq.cpp:71:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
physeq.cpp: In member function 'void MSA::ToPhyInterleavedFile(TextFile&) const':
physeq.cpp:112:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
physeq.cpp:124:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phytofile.cpp -o phytofile.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c posgap.cpp -o posgap.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c ppscore.cpp -o ppscore.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c profdb.cpp -o profdb.o
In file included from clustsetmsa.h:8:0,
                 from profdb.cpp:9:
msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c profile.cpp -o profile.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c profilefrommsa.cpp -o profilefrommsa.o
profilefrommsa.cpp: In function 'void ListProfile(const ProfPos*, unsigned int, const MSA*)':
profilefrommsa.cpp:131:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
profilefrommsa.cpp: In function 'unsigned int ResidueGroupFromFCounts(const FCOUNT*)':
profilefrommsa.cpp:230:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
profilefrommsa.cpp: In function 'ProfPos* ProfileFromMSA(const MSA&)':
profilefrommsa.cpp:245:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
profilefrommsa.cpp:253:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
profilefrommsa.cpp:15:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c progalign.cpp -o progalign.o
progalign.cpp: In function 'ProgNode* ProgressiveAlignE(const SeqVect&, const Tree&, MSA&)':
progalign.cpp:41:17: warning: unused variable 'uIterCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c progress.cpp -o progress.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c progressivealign.cpp -o progressivealign.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c pwpath.cpp -o pwpath.o
pwpath.cpp: In member function 'void PWPath::Validate() const':
pwpath.cpp:79:16: warning: unused variable 'LastEdge' [-Wunused-variable]
pwpath.cpp: In member function 'void PWPath::FromFile(TextFile&)':
pwpath.cpp:212:11: warning: unused variable 'uEdgeIndex' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c readmx.cpp -o readmx.o
readmx.cpp: In function 'float (* ReadMx(TextFile&))[32][32]':
readmx.cpp:83:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readmx.cpp:84:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
readmx.cpp:30:17: warning: 'unsigned int MxCharToLetter(char)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c realigndiffs.cpp -o realigndiffs.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -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:72:13: warning: unused variable 'uNewRight' [-Wunused-variable]
realigndiffse.cpp:75:13: warning: unused variable 'uOldRight' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c redblack.cpp -o redblack.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refine.cpp -o refine.o
In file included from clustsetmsa.h:8:0,
                 from refine.cpp:9:
msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinehoriz.cpp -o refinehoriz.o
refinehoriz.cpp: In function 'bool RefineHoriz(MSA&, const Tree&, unsigned int, bool, bool)':
refinehoriz.cpp:183:59: warning: 'scoreAfter' may be used uninitialized in this function [-Wuninitialized]
refinehoriz.cpp:170:9: note: 'scoreAfter' was declared here
refinehoriz.cpp:183:59: warning: 'scoreBefore' may be used uninitialized in this function [-Wuninitialized]
refinehoriz.cpp:169:9: note: 'scoreBefore' was declared here
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinesubfams.cpp -o refinesubfams.o
refinesubfams.cpp: In function 'bool RefineSubfams(MSA&, const Tree&, unsigned int)':
refinesubfams.cpp:63:17: warning: unused variable 'uNodeCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinetree.cpp -o refinetree.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinetreee.cpp -o refinetreee.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinevert.cpp -o refinevert.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinew.cpp -o refinew.o
refinew.cpp: In function 'void AppendMSA(MSA&, const MSA&)':
refinew.cpp:26:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
refinew.cpp: In function 'void RefineW(const MSA&, MSA&)':
refinew.cpp:129:13: warning: unused variable 'uOutCols' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c savebest.cpp -o savebest.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c scoredist.cpp -o scoredist.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c scoregaps.cpp -o scoregaps.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
scoregaps.cpp:37:13: warning: 'void FreeGapInfo(GAPINFO*)' defined but not used [-Wunused-function]
scoregaps.cpp:80:14: warning: 'SCORE Penalty(unsigned int, bool)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c scorehistory.cpp -o scorehistory.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c scorepp.cpp -o scorepp.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c seq.cpp -o seq.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c seqvect.cpp -o seqvect.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c setblosumweights.cpp -o setblosumweights.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c setgscweights.cpp -o setgscweights.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c setnewhandler.cpp -o setnewhandler.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c spfast.cpp -o spfast.o
spfast.cpp: In function 'SCORE ObjScoreSPDimer(const MSA&)':
spfast.cpp:252:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
spfast.cpp:14:20: warning: 'const char* GapTypeToStr(int)' defined but not used [-Wunused-function]
spfast.cpp:59:14: warning: 'SCORE SPColBrute(const MSA&, unsigned int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c sptest.cpp -o sptest.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c stabilize.cpp -o stabilize.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c subfam.cpp -o subfam.o
subfam.cpp: In function 'void AlignSubFam(SeqVect&, const Tree&, unsigned int, MSA&)':
subfam.cpp:173:6: warning: unused variable 'NotUsed' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c subfams.cpp -o subfams.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
subfams.cpp:10:13: warning: 'void GetMostDistantPair(DistFunc&, unsigned int*, unsigned int*)' defined but not used [-Wunused-function]
subfams.cpp:40:13: warning: 'void InitializeSingleSource(DistFunc&, unsigned int)' defined but not used [-Wunused-function]
subfams.cpp:52:13: warning: 'void Relax(DistFunc&, unsigned int, unsigned int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c sw.cpp -o sw.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
sw.cpp:20:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c termgaps.cpp -o termgaps.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c textfile.cpp -o textfile.o
textfile.cpp: In member function 'void TextFile::PutChar(char)':
textfile.cpp:104:6: warning: unused variable 'i' [-Wunused-variable]
textfile.cpp: In member function 'void TextFile::PutString(const char*)':
textfile.cpp:117:6: warning: unused variable 'iError' [-Wunused-variable]
textfile.cpp: In member function 'TEXTFILEPOS TextFile::GetPos()':
textfile.cpp:217:6: warning: unused variable 'i' [-Wunused-variable]
textfile.cpp: In member function 'void TextFile::SetPos(TEXTFILEPOS)':
textfile.cpp:230:6: warning: unused variable 'i' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c threewaywt.cpp -o threewaywt.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c tomhydro.cpp -o tomhydro.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -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:21:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
traceback.cpp:59:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c tracebackopt.cpp -o tracebackopt.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -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:22:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
tracebacksw.cpp:29:8: warning: unused variable 'scoreMax' [-Wunused-variable]
tracebacksw.cpp:34:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wuninitialized]
tracebacksw.cpp:47:3: warning: 'cEdgeType' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c treefrommsa.cpp -o treefrommsa.o
In file included from clustsetmsa.h:8:0,
                 from treefrommsa.cpp:5:
msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c typetostr.cpp -o typetostr.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c upgma2.cpp -o upgma2.o
upgma2.cpp: In member function 'virtual void DistCalcTest::CalcDistRange(unsigned int, dist_t*) const':
upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces]
upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces]
upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces]
upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces]
upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces]
upgma2.cpp: In function 'void UPGMA2(const DistCalc&, Tree&, LINKAGE)':
upgma2.cpp:293:4: warning: 'dtNewDist' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
upgma2.cpp:68:13: warning: 'void ListState()' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c usage.cpp -o usage.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c validateids.cpp -o validateids.o
In file included from validateids.cpp:4:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c vtml2.cpp -o vtml2.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c writescorefile.cpp -o writescorefile.o
writescorefile.cpp: In function 'void WriteScoreFile(const MSA&)':
writescorefile.cpp:40:17: warning: 'Score' may be used uninitialized in this function [-Wuninitialized]
writescorefile.cpp:27:11: note: 'Score' was declared here
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -shared -s -static-libgcc -o muscle.dll tmp.def 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 -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/muscle.buildbin-libdir/muscle/libs/i386
** 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

install for x64

* installing *source* package 'muscle' ...
** libs
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -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:186:17: warning: unused variable 'uLengthA' [-Wunused-variable]
aligngivenpath.cpp:187:17: warning: unused variable 'uLengthB' [-Wunused-variable]
aligngivenpath.cpp: In function 'void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)':
aligngivenpath.cpp:335:19: warning: unused variable 'uColA' [-Wunused-variable]
aligngivenpath.cpp:336:19: warning: unused variable 'uColB' [-Wunused-variable]
aligngivenpath.cpp:346:19: warning: unused variable 'uColA' [-Wunused-variable]
aligngivenpath.cpp:354:19: warning: unused variable 'uColB' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -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:58:17: warning: unused variable 'uLengthA' [-Wunused-variable]
aligngivenpathsw.cpp:59:17: warning: unused variable 'uLengthB' [-Wunused-variable]
aligngivenpathsw.cpp: In function 'void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)':
aligngivenpathsw.cpp:204:19: warning: unused variable 'uColA' [-Wunused-variable]
aligngivenpathsw.cpp:205:19: warning: unused variable 'uColB' [-Wunused-variable]
aligngivenpathsw.cpp:215:19: warning: unused variable 'uColA' [-Wunused-variable]
aligngivenpathsw.cpp:223:19: warning: unused variable 'uColB' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c aligntwomsas.cpp -o aligntwomsas.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c aligntwoprofs.cpp -o aligntwoprofs.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c aln.cpp -o aln.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c alpha.cpp -o alpha.o
alpha.cpp: In function 'unsigned int GetAlphaSize(ALPHA)':
alpha.cpp:84:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -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:162:13: warning: unused variable 'uWindowCenter' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
anchors.cpp:53:13: warning: 'void FindBestColsGrade(const SCORE*, unsigned int, double, unsigned int*, unsigned int*)' defined but not used [-Wunused-function]
anchors.cpp:105:13: warning: 'void ListBestCols(const MSA&, const SCORE*, const SCORE*, unsigned int*, unsigned int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c bittraceback.cpp -o bittraceback.o
bittraceback.cpp: In function 'void BitTraceBack(char**, unsigned int, unsigned int, char, PWPath&)':
bittraceback.cpp:146:7: warning: unused variable 'Bits' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
bittraceback.cpp:15:20: warning: 'const char* BitsToStr(char)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c blosum62.cpp -o blosum62.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c blosumla.cpp -o blosumla.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
blosumla.cpp:7:14: warning: 'Blosum62LA' defined but not used [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c clust.cpp -o clust.o
clust.cpp: In member function 'void Clust::ChooseJoin(unsigned int*, unsigned int*, float*, float*)':
clust.cpp:167:9: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
clust.cpp: In member function 'void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)':
clust.cpp:184:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
clust.cpp: In member function 'void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)':
clust.cpp:204:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
clust.cpp: In member function 'float Clust::ComputeDist(unsigned int, unsigned int)':
clust.cpp:295:9: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch]
clust.cpp: In member function 'float Clust::ComputeDistMAFFT(unsigned int, unsigned int)':
clust.cpp:360:14: warning: unused variable 'dDistLR' [-Wunused-variable]
clust.cpp: In member function 'float Clust::ComputeMetric(unsigned int, unsigned int) const':
clust.cpp:611:9: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c cluster.cpp -o cluster.o
cluster.cpp: In member function 'void ClusterTree::Create(const DistFunc&)':
cluster.cpp:284:8: warning: variable 'bFound' set but not used [-Wunused-but-set-variable]
cluster.cpp:267:9: warning: unused variable 'dMaxDist' [-Wunused-variable]
cluster.cpp:308:47: warning: 'uIndexClosest2' may be used uninitialized in this function [-Wuninitialized]
cluster.cpp:307:47: warning: 'uIndexClosest1' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c clwwt.cpp -o clwwt.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c color.cpp -o color.o
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
color.cpp:72:12: warning: 'int BlosumScore(char, char)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c cons.cpp -o cons.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c diaglist.cpp -o diaglist.o
diaglist.cpp: In member function 'void DiagList::FromPath(const PWPath&)':
diaglist.cpp:77:39: warning: 'uStartPosB' may be used uninitialized in this function [-Wuninitialized]
diaglist.cpp:77:39: warning: 'uStartPosA' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c diffobjscore.cpp -o diffobjscore.o
diffobjscore.cpp: In function 'SCORE ScoreLetters(const MSA&, const unsigned int*, unsigned int)':
diffobjscore.cpp:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c diffpaths.cpp -o diffpaths.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c difftrees.cpp -o difftrees.o
difftrees.cpp: In function 'void DiffTrees(const Tree&, const Tree&, Tree&, unsigned int*)':
difftrees.cpp:161:17: warning: unused variable 'uLeafCount2' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c difftreese.cpp -o difftreese.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c distcalc.cpp -o distcalc.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c distfunc.cpp -o distfunc.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c distpwkimura.cpp -o distpwkimura.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c domuscle.cpp -o domuscle.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c dosp.cpp -o dosp.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c dpreglist.cpp -o dpreglist.o
dpreglist.cpp: In function 'void DiagListToDPRegionList(const DiagList&, DPRegionList&, unsigned int, unsigned int)':
dpreglist.cpp:82:19: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c drawtree.cpp -o drawtree.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c edgelist.cpp -o edgelist.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c enumopts.cpp -o enumopts.o
In file included from enumopts.cpp:8:0:
enums.h:15:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:15:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:15:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:15:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:28:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:28:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:28:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:28:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:41:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:41:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:41:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:94:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:94:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:94:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:94:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c enumtostr.cpp -o enumtostr.o
In file included from enumtostr.cpp:16:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c estring.cpp -o estring.o
estring.cpp: In function 'void EstringsToPath(const short int*, const short int*, PWPath&)':
estring.cpp:409:3: warning: 'cType' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
estring.cpp:464:13: warning: 'bool CanMultiplyEstrings(const short int*, const short int*)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fasta.cpp -o fasta.o
fasta.cpp: In member function 'void MSA::FromFASTAFile(TextFile&)':
fasta.cpp:15:11: warning: unused variable 'uSeqCount' [-Wunused-variable]
fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fasta2.cpp -o fasta2.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastclust.cpp -o fastclust.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdist.cpp -o fastdist.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistjones.cpp -o fastdistjones.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistkbit.cpp -o fastdistkbit.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistkmer.cpp -o fastdistkmer.o
fastdistkmer.cpp: In function 'void FastDistKmer(const SeqVect&, DistFunc&)':
fastdistkmer.cpp:235:11: warning: unused variable 'KD' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistmafft.cpp -o fastdistmafft.o
fastdistmafft.cpp: In function 'void DistKmer6_6(const SeqVect&, DistFunc&)':
fastdistmafft.cpp:238:15: warning: unused variable 'pName1' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
fastdistmafft.cpp:104:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistnuc.cpp -o fastdistnuc.o
fastdistnuc.cpp: In function 'void DistKmer4_6(const SeqVect&, DistFunc&)':
fastdistnuc.cpp:223:15: warning: unused variable 'pName1' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
fastdistnuc.cpp:33:17: warning: 'uResidueGroupCount' defined but not used [-Wunused-variable]
fastdistnuc.cpp:85:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastscorepath2.cpp -o fastscorepath2.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c finddiags.cpp -o finddiags.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
finddiags.cpp:11:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c finddiagsn.cpp -o finddiagsn.o
finddiagsn.cpp: In function 'char* TupleToStr(int)':
finddiagsn.cpp:16:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
finddiagsn.cpp:12:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalign.cpp -o glbalign.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalign352.cpp -o glbalign352.o
In file included from glbalign352.cpp:6:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbaligndiag.cpp -o glbaligndiag.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignla.cpp -o glbalignla.o
glbalignla.cpp: In function 'SCORE GlobalAlignLA(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
glbalignla.cpp:424:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
glbalignla.cpp:363:50: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignle.cpp -o glbalignle.o
glbalignle.cpp: In function 'SCORE GlobalAlignLE(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
glbalignle.cpp:427:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignns.cpp -o glbalignns.o
glbalignns.cpp: In function 'SCORE GlobalAlignNS(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
glbalignns.cpp:366:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
glbalignns.cpp:305:50: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignsimple.cpp -o glbalignsimple.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
glbalignsimple.cpp:28:13: warning: 'void ListTB(const char*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
glbalignsimple.cpp:52:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignsp.cpp -o glbalignsp.o
glbalignsp.cpp: In function 'SCORE GlobalAlignSP(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
glbalignsp.cpp:366:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
glbalignsp.cpp:305:50: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignspn.cpp -o glbalignspn.o
glbalignspn.cpp: In function 'SCORE GlobalAlignSPN(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
glbalignspn.cpp:401:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
glbalignspn.cpp:340:50: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignss.cpp -o glbalignss.o
glbalignss.cpp: In function 'SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)':
glbalignss.cpp:177:16: warning: unused variable 'ptrRowA' [-Wunused-variable]
glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable]
glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
glbalignss.cpp:310:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
glbalignss.cpp:252:50: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
glbalignss.cpp:11:14: warning: 'SCORE Subst(const Seq&, const Seq&, unsigned int, unsigned int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalndimer.cpp -o glbalndimer.o
glbalndimer.cpp: In function 'SCORE ScoreProfPosDimer(const ProfPos&, const ProfPos&)':
glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_SPN' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
glbalndimer.cpp:14:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c globals.cpp -o globals.o
In file included from D:/biocbld/BBS-3˜1.2-B/R/include/R.h:50:0,
                 from globals.cpp:17:
D:/biocbld/BBS-3˜1.2-B/R/include/R_ext/RS.h:45:0: warning: "ERROR" redefined [enabled by default]
c:\rtools33\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/wingdi.h:70:0: note: this is the location of the previous definition
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c globalslinux.cpp -o globalslinux.o
In file included from globalslinux.cpp:1:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c globalsosx.cpp -o globalsosx.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c globalsother.cpp -o globalsother.o
In file included from globalsother.cpp:1:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c globalswin32.cpp -o globalswin32.o
globalswin32.cpp: In function 'double GetNAN()':
globalswin32.cpp:24:28: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
globalswin32.cpp: In function 'double GetMemUseMB()':
globalswin32.cpp:59:9: warning: unused variable 'hProc' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c gonnet.cpp -o gonnet.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
gonnet.cpp:137:14: warning: 'Gonnet160' defined but not used [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c gotowt.cpp -o gotowt.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c henikoffweight.cpp -o henikoffweight.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c henikoffweightpb.cpp -o henikoffweightpb.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c html.cpp -o html.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c hydro.cpp -o hydro.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c intmath.cpp -o intmath.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c local.cpp -o local.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c main.cpp -o main.o
In file included from D:/biocbld/BBS-3˜1.2-B/R/include/R.h:50:0,
                 from main.cpp:21:
D:/biocbld/BBS-3˜1.2-B/R/include/R_ext/RS.h:45:0: warning: "ERROR" redefined [enabled by default]
c:\rtools33\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/wingdi.h:70:0: note: this is the location of the previous definition
main.cpp:112:1: warning: missing braces around initializer for 'R_CMethodDef' [-Wmissing-braces]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c makerootmsa.cpp -o makerootmsa.o
makerootmsa.cpp: In function 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)':
makerootmsa.cpp:18:17: warning: unused variable 'uSeqLength' [-Wunused-variable]
makerootmsa.cpp: In function 'short int* MakeRootSeqE(const Seq&, const Tree&, unsigned int, const ProgNode*, Seq&, short int*, short int*)':
makerootmsa.cpp:94:17: warning: unused variable 'Path' [-Wunused-variable]
makerootmsa.cpp: In function 'void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)':
makerootmsa.cpp:168:17: warning: unused variable 'uTreeNodeCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
makerootmsa.cpp:12:13: warning: 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c makerootmsab.cpp -o makerootmsab.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c maketree.cpp -o maketree.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c mhack.cpp -o mhack.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c mpam200.cpp -o mpam200.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c msa.cpp -o msa.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
msa.cpp:385:13: warning: 'void FmtChar(char, unsigned int)' defined but not used [-Wunused-function]
msa.cpp:392:13: warning: 'void FmtInt(unsigned int, unsigned int)' defined but not used [-Wunused-function]
msa.cpp:407:13: warning: 'void FmtInt0(unsigned int, unsigned int)' defined but not used [-Wunused-function]
msa.cpp:419:13: warning: 'void FmtPad(unsigned int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c msa2.cpp -o msa2.o
msa2.cpp: In function 'void SetMSAWeightsMuscle(MSA&)':
msa2.cpp:357:9: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch]
msa2.cpp: In function 'void MSAAppend(MSA&, const MSA&)':
msa2.cpp:476:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c msadistkimura.cpp -o msadistkimura.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c msf.cpp -o msf.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
msf.cpp:24:20: warning: 'const char* strfind(const char*, const char*)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c muscle.cpp -o muscle.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c muscleout.cpp -o muscleout.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nucmx.cpp -o nucmx.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nwdasimple.cpp -o nwdasimple.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nwdasimple2.cpp -o nwdasimple2.o
In file included from nwdasimple2.cpp:3:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nwdasmall.cpp -o nwdasmall.o
In file included from nwdasmall.cpp:4:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nwrec.cpp -o nwrec.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nwsmall.cpp -o nwsmall.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -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:31:9: warning: enumeration value 'OBJSCORE_Undefined' not handled in switch [-Wswitch]
objscore.cpp:31:9: warning: enumeration value 'OBJSCORE_SPM' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c objscore2.cpp -o objscore2.o
objscore2.cpp: In function 'SCORE TermGapScore(bool)':
objscore2.cpp:22:9: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch]
objscore2.cpp: In function 'SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)':
objscore2.cpp:62:8: warning: unused variable 'scoreGaps' [-Wunused-variable]
objscore2.cpp:63:7: warning: unused variable 'bGapping1' [-Wunused-variable]
objscore2.cpp:64:7: warning: unused variable 'bGapping2' [-Wunused-variable]
objscore2.cpp:67:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
objscore2.cpp:82:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
objscore2.cpp: In function 'SCORE ScoreSeqPairGaps(const MSA&, unsigned int, const MSA&, unsigned int)':
objscore2.cpp:140:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
objscore2.cpp:155:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
objscore2.cpp: In function 'SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)':
objscore2.cpp:314:17: warning: unused variable 'uColCount2' [-Wunused-variable]
objscore2.cpp: In function 'SCORE ObjScoreXP(const MSA&, const MSA&)':
objscore2.cpp:493:17: warning: unused variable 'w' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c objscoreda.cpp -o objscoreda.o
In file included from objscoreda.cpp:4:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c onexception.cpp -o onexception.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c optionsR.cpp -o optionsR.o
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:87:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
optionsR.cpp:127:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c outweights.cpp -o outweights.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c pam200mafft.cpp -o pam200mafft.o
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
pam200mafft.cpp:6:14: warning: 'PAM200' defined but not used [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c params.cpp -o params.o
params.cpp: In function 'void SetPPScore(bool)':
params.cpp:445:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
params.cpp: In function 'void default_params()':
params.cpp:659:18: warning: statement has no effect [-Wunused-value]
params.cpp:652:14: warning: unused variable 'VTML_LA' [-Wunused-variable]
params.cpp:653:14: warning: unused variable 'PAM200' [-Wunused-variable]
params.cpp:654:14: warning: unused variable 'PAM200NoCenter' [-Wunused-variable]
params.cpp:655:14: warning: unused variable 'VTML_SP' [-Wunused-variable]
params.cpp:656:14: warning: unused variable 'VTML_SPNoCenter' [-Wunused-variable]
params.cpp:657:14: warning: unused variable 'NUC_SP' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phy.cpp -o phy.o
phy.cpp: In member function 'void Tree::RootUnrootedTree(ROOT)':
phy.cpp:665:9: warning: unused variable 'dEdgeLength' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phy2.cpp -o phy2.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phy3.cpp -o phy3.o
phy3.cpp: In function 'void CalcInfo(const Tree&, unsigned int, unsigned int, EdgeInfo**)':
phy3.cpp:125:15: warning: unused variable 'dThisDist' [-Wunused-variable]
phy3.cpp: In function 'void FindRoot(const Tree&, unsigned int*, unsigned int*, double*, double*, ROOT)':
phy3.cpp:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable]
phy3.cpp:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable]
phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable]
phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable]
phy3.cpp: In function 'void RootByMidLongestSpan(const Tree&, EdgeInfo**, unsigned int*, unsigned int*, double*, double*)':
phy3.cpp:263:11: warning: variable 'uMostDistantLeaf' set but not used [-Wunused-but-set-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
phy3.cpp:45:13: warning: 'void ListEIs(EdgeInfo**, unsigned int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phy4.cpp -o phy4.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phyfromclust.cpp -o phyfromclust.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phyfromfile.cpp -o phyfromfile.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c physeq.cpp -o physeq.o
physeq.cpp: In member function 'void MSA::ToPhySequentialFile(TextFile&) const':
physeq.cpp:60:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
physeq.cpp:71:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
physeq.cpp: In member function 'void MSA::ToPhyInterleavedFile(TextFile&) const':
physeq.cpp:112:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
physeq.cpp:124:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phytofile.cpp -o phytofile.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c posgap.cpp -o posgap.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c ppscore.cpp -o ppscore.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c profdb.cpp -o profdb.o
In file included from clustsetmsa.h:8:0,
                 from profdb.cpp:9:
msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c profile.cpp -o profile.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c profilefrommsa.cpp -o profilefrommsa.o
profilefrommsa.cpp: In function 'void ListProfile(const ProfPos*, unsigned int, const MSA*)':
profilefrommsa.cpp:131:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
profilefrommsa.cpp: In function 'unsigned int ResidueGroupFromFCounts(const FCOUNT*)':
profilefrommsa.cpp:230:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
profilefrommsa.cpp: In function 'ProfPos* ProfileFromMSA(const MSA&)':
profilefrommsa.cpp:245:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
profilefrommsa.cpp:253:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
profilefrommsa.cpp:15:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c progalign.cpp -o progalign.o
progalign.cpp: In function 'ProgNode* ProgressiveAlignE(const SeqVect&, const Tree&, MSA&)':
progalign.cpp:41:17: warning: unused variable 'uIterCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c progress.cpp -o progress.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c progressivealign.cpp -o progressivealign.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c pwpath.cpp -o pwpath.o
pwpath.cpp: In member function 'void PWPath::Validate() const':
pwpath.cpp:79:16: warning: unused variable 'LastEdge' [-Wunused-variable]
pwpath.cpp: In member function 'void PWPath::FromFile(TextFile&)':
pwpath.cpp:212:11: warning: unused variable 'uEdgeIndex' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c readmx.cpp -o readmx.o
readmx.cpp: In function 'float (* ReadMx(TextFile&))[32][32]':
readmx.cpp:83:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readmx.cpp:84:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
readmx.cpp:30:17: warning: 'unsigned int MxCharToLetter(char)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c realigndiffs.cpp -o realigndiffs.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -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:72:13: warning: unused variable 'uNewRight' [-Wunused-variable]
realigndiffse.cpp:75:13: warning: unused variable 'uOldRight' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c redblack.cpp -o redblack.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refine.cpp -o refine.o
In file included from clustsetmsa.h:8:0,
                 from refine.cpp:9:
msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinehoriz.cpp -o refinehoriz.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinesubfams.cpp -o refinesubfams.o
refinesubfams.cpp: In function 'bool RefineSubfams(MSA&, const Tree&, unsigned int)':
refinesubfams.cpp:63:17: warning: unused variable 'uNodeCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinetree.cpp -o refinetree.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinetreee.cpp -o refinetreee.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinevert.cpp -o refinevert.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinew.cpp -o refinew.o
refinew.cpp: In function 'void AppendMSA(MSA&, const MSA&)':
refinew.cpp:26:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
refinew.cpp: In function 'void RefineW(const MSA&, MSA&)':
refinew.cpp:129:13: warning: unused variable 'uOutCols' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c savebest.cpp -o savebest.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c scoredist.cpp -o scoredist.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c scoregaps.cpp -o scoregaps.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
scoregaps.cpp:37:13: warning: 'void FreeGapInfo(GAPINFO*)' defined but not used [-Wunused-function]
scoregaps.cpp:80:14: warning: 'SCORE Penalty(unsigned int, bool)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c scorehistory.cpp -o scorehistory.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c scorepp.cpp -o scorepp.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c seq.cpp -o seq.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c seqvect.cpp -o seqvect.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c setblosumweights.cpp -o setblosumweights.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c setgscweights.cpp -o setgscweights.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c setnewhandler.cpp -o setnewhandler.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c spfast.cpp -o spfast.o
spfast.cpp: In function 'SCORE ObjScoreSPDimer(const MSA&)':
spfast.cpp:252:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
spfast.cpp:14:20: warning: 'const char* GapTypeToStr(int)' defined but not used [-Wunused-function]
spfast.cpp:59:14: warning: 'SCORE SPColBrute(const MSA&, unsigned int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c sptest.cpp -o sptest.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c stabilize.cpp -o stabilize.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c subfam.cpp -o subfam.o
subfam.cpp: In function 'void AlignSubFam(SeqVect&, const Tree&, unsigned int, MSA&)':
subfam.cpp:173:6: warning: unused variable 'NotUsed' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c subfams.cpp -o subfams.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
subfams.cpp:10:13: warning: 'void GetMostDistantPair(DistFunc&, unsigned int*, unsigned int*)' defined but not used [-Wunused-function]
subfams.cpp:40:13: warning: 'void InitializeSingleSource(DistFunc&, unsigned int)' defined but not used [-Wunused-function]
subfams.cpp:52:13: warning: 'void Relax(DistFunc&, unsigned int, unsigned int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c sw.cpp -o sw.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
sw.cpp:20:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c termgaps.cpp -o termgaps.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c textfile.cpp -o textfile.o
textfile.cpp: In member function 'void TextFile::PutChar(char)':
textfile.cpp:104:6: warning: unused variable 'i' [-Wunused-variable]
textfile.cpp: In member function 'void TextFile::PutString(const char*)':
textfile.cpp:117:6: warning: unused variable 'iError' [-Wunused-variable]
textfile.cpp: In member function 'TEXTFILEPOS TextFile::GetPos()':
textfile.cpp:217:6: warning: unused variable 'i' [-Wunused-variable]
textfile.cpp: In member function 'void TextFile::SetPos(TEXTFILEPOS)':
textfile.cpp:230:6: warning: unused variable 'i' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c threewaywt.cpp -o threewaywt.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c tomhydro.cpp -o tomhydro.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -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:21:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
traceback.cpp:59:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wuninitialized]
traceback.cpp:72:3: warning: 'cEdgeType' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c tracebackopt.cpp -o tracebackopt.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -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:22:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
tracebacksw.cpp:29:8: warning: unused variable 'scoreMax' [-Wunused-variable]
tracebacksw.cpp:34:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wuninitialized]
tracebacksw.cpp:47:3: warning: 'cEdgeType' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c treefrommsa.cpp -o treefrommsa.o
In file included from clustsetmsa.h:8:0,
                 from treefrommsa.cpp:5:
msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c typetostr.cpp -o typetostr.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c upgma2.cpp -o upgma2.o
upgma2.cpp: In member function 'virtual void DistCalcTest::CalcDistRange(unsigned int, dist_t*) const':
upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces]
upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces]
upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces]
upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces]
upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces]
upgma2.cpp: In function 'void UPGMA2(const DistCalc&, Tree&, LINKAGE)':
upgma2.cpp:293:4: warning: 'dtNewDist' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
upgma2.cpp:68:13: warning: 'void ListState()' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c usage.cpp -o usage.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c validateids.cpp -o validateids.o
In file included from validateids.cpp:4:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c vtml2.cpp -o vtml2.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c writescorefile.cpp -o writescorefile.o
writescorefile.cpp: In function 'void WriteScoreFile(const MSA&)':
writescorefile.cpp:40:17: warning: 'Score' may be used uninitialized in this function [-Wuninitialized]
writescorefile.cpp:27:11: note: 'Score' was declared here
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -shared -s -static-libgcc -o muscle.dll tmp.def 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 -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/muscle.buildbin-libdir/muscle/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'muscle' as muscle_3.12.0.zip
* DONE (muscle)

name	user	system	elapsed
muscle-package	0.02	0.00	0.02
muscle	3.32	0.03	4.27

name	user	system	elapsed
muscle-package	0	0	0
muscle	2.80	0.03	3.75