BioC 3.5: CHECK report for msa on tokay2

Package: msa

Version: 1.8.0

Command: rm -rf msa.buildbin-libdir msa.Rcheck && mkdir msa.buildbin-libdir msa.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=msa.buildbin-libdir msa_1.8.0.tar.gz >msa.Rcheck\00install.out 2>&1 && cp msa.Rcheck\00install.out msa-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=msa.buildbin-libdir --install="check:msa-install.out" --force-multiarch --no-vignettes --timings msa_1.8.0.tar.gz

StartedAt: 2017-10-18 01:31:48 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:46:11 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 862.8 seconds

RetCode: 0

Status:  OK

CheckDir: msa.Rcheck

Warnings: 0

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###
### Running command:
###
###   rm -rf msa.buildbin-libdir msa.Rcheck && mkdir msa.buildbin-libdir msa.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=msa.buildbin-libdir msa_1.8.0.tar.gz >msa.Rcheck\00install.out 2>&1 && cp msa.Rcheck\00install.out msa-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=msa.buildbin-libdir --install="check:msa-install.out" --force-multiarch --no-vignettes --timings msa_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/msa.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'msa/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'msa' version '1.8.0'
* 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 'msa' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
* 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
* 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 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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 'C:/Users/biocbuild/bbs-3.5-bioc/meat/msa.buildbin-libdir/msa/libs/i386/msa.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)

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' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
msaPrettyPrint 0.45      0    7.89
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
msaPrettyPrint 0.43      0    5.31
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/msa.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'msa' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src"   -O2 -Wall  -mtune=core2 -c R_init_msa.cpp -o R_init_msa.o
In file included from ./Muscle/muscle.h:38:0,
                 from ./Muscle/RMuscle.h:4,
                 from R_init_msa.cpp:3:
./Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src"   -O2 -Wall  -mtune=core2 -c SplitCharVector2List.cpp -o SplitCharVector2List.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src"   -O2 -Wall  -mtune=core2 -c SplitCharVector2Matrix.cpp -o SplitCharVector2Matrix.o
make --file=msaMakefile.win --directory=gc-7.2
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpeaNGby/R.INSTALLbf03a843fd6/msa/src/gc-7.2'
export PKG_LIBS=" -Ilibatomic_ops/src -Iinclude -Iinclude/private"; \
export PKG_CFLAGS=" -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private"; \
export PKG_CXXFLAGS=" -DALL_INTERIOR_POINTERS -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private"; \
C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386/R.exe CMD SHLIB -o gc72.dll *.c; \
C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386/R.exe CMD SHLIB -o gccpp72.dll -L. -lgc72 *.cpp; \
ar rcs libGC.a allchblk.o alloc.o backgraph.o blacklst.o checksums.o darwin_stop_world.o dbg_mlc.o dyn_load.o finalize.o gcj_mlc.o gc_dlopen.o headers.o mach_dep.o malloc.o mallocx.o mark.o mark_rts.o misc.o new_hblk.o obj_map.o os_dep.o pcr_interface.o pthread_start.o pthread_stop_world.o pthread_support.o ptr_chck.o real_malloc.o reclaim.o specific.o stubborn.o thread_local_alloc.o typd_mlc.o win32_threads.o; \
ar rcs libGCcpp.a gc_cpp.o; \
cp libGC*.a ../
make[2]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpeaNGby/R.INSTALLbf03a843fd6/msa/src/gc-7.2'
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c allchblk.c -o allchblk.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c alloc.c -o alloc.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c backgraph.c -o backgraph.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c blacklst.c -o blacklst.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c checksums.c -o checksums.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c darwin_stop_world.c -o darwin_stop_world.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c dbg_mlc.c -o dbg_mlc.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c dyn_load.c -o dyn_load.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c finalize.c -o finalize.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c gc_dlopen.c -o gc_dlopen.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c gcj_mlc.c -o gcj_mlc.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c headers.c -o headers.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c mach_dep.c -o mach_dep.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c malloc.c -o malloc.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c mallocx.c -o mallocx.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c mark.c -o mark.o
mark.c: In function 'GC_mark_some':
mark.c:524:25: warning: assignment from incompatible pointer type
       er.ex_reg.handler = mark_ex_handler;
                         ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c mark_rts.c -o mark_rts.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c misc.c -o misc.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c new_hblk.c -o new_hblk.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c obj_map.c -o obj_map.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c os_dep.c -o os_dep.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c pcr_interface.c -o pcr_interface.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c pthread_start.c -o pthread_start.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c pthread_stop_world.c -o pthread_stop_world.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c pthread_support.c -o pthread_support.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c ptr_chck.c -o ptr_chck.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c real_malloc.c -o real_malloc.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c reclaim.c -o reclaim.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c specific.c -o specific.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c stubborn.c -o stubborn.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c thread_local_alloc.c -o thread_local_alloc.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c typd_mlc.c -o typd_mlc.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O3 -Wall  -std=gnu99 -mtune=core2 -c win32_threads.c -o win32_threads.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o gc72.dll tmp.def allchblk.o alloc.o backgraph.o blacklst.o checksums.o darwin_stop_world.o dbg_mlc.o dyn_load.o finalize.o gc_dlopen.o gcj_mlc.o headers.o mach_dep.o malloc.o mallocx.o mark.o mark_rts.o misc.o new_hblk.o obj_map.o os_dep.o pcr_interface.o pthread_start.o pthread_stop_world.o pthread_support.o ptr_chck.o real_malloc.o reclaim.o specific.o stubborn.o thread_local_alloc.o typd_mlc.o win32_threads.o -Ilibatomic_ops/src -Iinclude -Iinclude/private -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
make[2]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpeaNGby/R.INSTALLbf03a843fd6/msa/src/gc-7.2'
make[2]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpeaNGby/R.INSTALLbf03a843fd6/msa/src/gc-7.2'
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -mtune=core2 -c gc_cpp.cc -o gc_cpp.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o gccpp72.dll tmp.def gc_cpp.o -L. -lgc72 -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
make[2]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpeaNGby/R.INSTALLbf03a843fd6/msa/src/gc-7.2'
make[1]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpeaNGby/R.INSTALLbf03a843fd6/msa/src/gc-7.2'
----------------------------------------
------------------ GC  -----------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile.win --directory=Muscle
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpeaNGby/R.INSTALLbf03a843fd6/msa/src/Muscle'
export PKG_LIBS=" -L"../gc-7.2/" -lgc72 -lgccpp72"
export PKG_CXXFLAGS="-c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1  -I../gc-7.2/include/"
C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386/R.exe CMD SHLIB -o Muscle.dll aligngivenpath.cpp aligngivenpathsw.cpp aligntwomsas.cpp aligntwoprofs.cpp aln.cpp alpha.cpp anchors.cpp bittraceback.cpp blosum62.cpp blosumla.cpp clust.cpp cluster.cpp clwwt.cpp color.cpp cons.cpp diaglist.cpp diffobjscore.cpp diffpaths.cpp difftrees.cpp difftreese.cpp distcalc.cpp distfunc.cpp distpwkimura.cpp domuscle.cpp dosp.cpp dpreglist.cpp drawtree.cpp edgelist.cpp enumopts.cpp enumtostr.cpp estring.cpp fasta.cpp fasta2.cpp fastclust.cpp fastdist.cpp fastdistjones.cpp fastdistkbit.cpp fastdistkmer.cpp fastdistmafft.cpp fastdistnuc.cpp fastscorepath2.cpp finddiags.cpp finddiagsn.cpp glbalign.cpp glbalign352.cpp glbaligndiag.cpp glbalignle.cpp glbalignsimple.cpp glbalignsp.cpp glbalignspn.cpp glbalignss.cpp glbalndimer.cpp globals.cpp globalslinux.cpp globalsosx.cpp globalsother.cpp globalswin32.cpp gonnet.cpp henikoffweight.cpp henikoffweightpb.cpp html.cpp hydro.cpp intmath.cpp local.cpp main.cpp makerootmsa.cpp makerootmsab.cpp maketree.cpp mhack.cpp mpam200.cpp msa.cpp msa2.cpp msadistkimura.cpp msf.cpp muscle.cpp muscleout.cpp nucmx.cpp nwdasimple.cpp nwdasimple2.cpp nwdasmall.cpp nwrec.cpp nwsmall.cpp objscore.cpp objscore2.cpp objscoreda.cpp onexception.cpp options.cpp outweights.cpp pam200mafft.cpp params.cpp phy.cpp phy2.cpp phy3.cpp phy4.cpp phyfromclust.cpp phyfromfile.cpp physeq.cpp phytofile.cpp posgap.cpp ppscore.cpp profdb.cpp profile.cpp profilefrommsa.cpp progalign.cpp progress.cpp progressivealign.cpp pwpath.cpp readmx.cpp realigndiffs.cpp realigndiffse.cpp refine.cpp refinehoriz.cpp refinesubfams.cpp refinetree.cpp refinetreee.cpp refinevert.cpp refinew.cpp savebest.cpp scoredist.cpp scoregaps.cpp scorehistory.cpp scorepp.cpp seq.cpp seqvect.cpp setblosumweights.cpp setgscweights.cpp setnewhandler.cpp spfast.cpp sptest.cpp stabilize.cpp subfam.cpp subfams.cpp sw.cpp termgaps.cpp textfile.cpp threewaywt.cpp tomhydro.cpp traceback.cpp tracebackopt.cpp tracebacksw.cpp treefrommsa.cpp typetostr.cpp upgma2.cpp usage.cpp validateids.cpp vtml2.cpp writescorefile.cpp RMuscle.cpp
make[2]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpeaNGby/R.INSTALLbf03a843fd6/msa/src/Muscle'
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const unsigned uLengthA = msaA.GetColCount();
                 ^
aligngivenpath.cpp:187:17: warning: unused variable 'uLengthB' [-Wunused-variable]
  const unsigned uLengthB = msaB.GetColCount();
                 ^
aligngivenpath.cpp: In function 'void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)':
aligngivenpath.cpp:335:19: warning: unused variable 'uColA' [-Wunused-variable]
    const unsigned uColA = uPrefixLengthA - 1;
                   ^
aligngivenpath.cpp:336:19: warning: unused variable 'uColB' [-Wunused-variable]
    const unsigned uColB = uPrefixLengthB - 1;
                   ^
aligngivenpath.cpp:346:19: warning: unused variable 'uColA' [-Wunused-variable]
    const unsigned uColA = uPrefixLengthA - 1;
                   ^
aligngivenpath.cpp:354:19: warning: unused variable 'uColB' [-Wunused-variable]
    const unsigned uColB = uPrefixLengthB - 1;
                   ^
In file included from muscle.h:38:0,
                 from aligngivenpath.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const unsigned uLengthA = msaA.GetColCount();
                 ^
aligngivenpathsw.cpp:59:17: warning: unused variable 'uLengthB' [-Wunused-variable]
  const unsigned uLengthB = msaB.GetColCount();
                 ^
aligngivenpathsw.cpp: In function 'void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)':
aligngivenpathsw.cpp:204:19: warning: unused variable 'uColA' [-Wunused-variable]
    const unsigned uColA = uPrefixLengthA - 1;
                   ^
aligngivenpathsw.cpp:205:19: warning: unused variable 'uColB' [-Wunused-variable]
    const unsigned uColB = uPrefixLengthB - 1;
                   ^
aligngivenpathsw.cpp:215:19: warning: unused variable 'uColA' [-Wunused-variable]
    const unsigned uColA = uPrefixLengthA - 1;
                   ^
aligngivenpathsw.cpp:223:19: warning: unused variable 'uColB' [-Wunused-variable]
    const unsigned uColB = uPrefixLengthB - 1;
                   ^
In file included from muscle.h:38:0,
                 from aligngivenpathsw.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c aligntwomsas.cpp -o aligntwomsas.o
In file included from aligntwomsas.cpp:6:0:
timing.h:5:0: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(disable:4035)
 ^
In file included from muscle.h:38:0,
                 from aligntwomsas.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
In file included from aligntwomsas.cpp:6:0:
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
 static double TicksToSecs(TICKS t)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c aligntwoprofs.cpp -o aligntwoprofs.o
In file included from muscle.h:38:0,
                 from aligntwoprofs.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c aln.cpp -o aln.o
In file included from muscle.h:38:0,
                 from aln.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  switch (Alpha)
         ^
In file included from muscle.h:38:0,
                 from alpha.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
    unsigned uWindowCenter = uBestColIndex + uWindowLength/2;
             ^
In file included from muscle.h:38:0,
                 from anchors.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
anchors.cpp:53:13: warning: 'void FindBestColsGrade(const SCORE*, unsigned int, double, unsigned int*, unsigned int*)' defined but not used [-Wunused-function]
 static void FindBestColsGrade(const SCORE Score[], unsigned uCount,
             ^
anchors.cpp:105:13: warning: 'void ListBestCols(const MSA&, const SCORE*, const SCORE*, unsigned int*, unsigned int)' defined but not used [-Wunused-function]
 static void ListBestCols(const MSA &msa, const SCORE Score[], const SCORE SmoothScore[],
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  char Bits = TraceBack[uLengthA][uLengthB];
       ^
In file included from muscle.h:38:0,
                 from bittraceback.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
bittraceback.cpp:15:20: warning: 'const char* BitsToStr(char)' defined but not used [-Wunused-function]
 static const char *BitsToStr(char Bits)
                    ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c blosum62.cpp -o blosum62.o
In file included from muscle.h:38:0,
                 from blosum62.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c blosumla.cpp -o blosumla.o
In file included from muscle.h:38:0,
                 from blosumla.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
blosumla.cpp:7:14: warning: 'Blosum62LA' defined but not used [-Wunused-variable]
 static float Blosum62LA[20][20] =
              ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  switch (m_JoinStyle)
         ^
clust.cpp: In member function 'void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)':
clust.cpp:184:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
  const unsigned uClusterCount = GetClusterCount();
                 ^
clust.cpp: In member function 'void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)':
clust.cpp:204:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
  const unsigned uClusterCount = GetClusterCount();
                 ^
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]
  switch (m_CentroidStyle)
         ^
clust.cpp: In member function 'float Clust::ComputeDistMAFFT(unsigned int, unsigned int)':
clust.cpp:360:14: warning: unused variable 'dDistLR' [-Wunused-variable]
  const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex);
              ^
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]
  switch (m_JoinStyle)
         ^
In file included from muscle.h:38:0,
                 from clust.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
   bool bFound = false;
        ^
cluster.cpp:267:9: warning: unused variable 'dMaxDist' [-Wunused-variable]
  double dMaxDist = 0.0;
         ^
cluster.cpp:308:47: warning: 'uIndexClosest2' may be used uninitialized in this function [-Wmaybe-uninitialized]
   ClusterNode &Child2 = m_Nodes[uIndexClosest2];
                                               ^
cluster.cpp:307:47: warning: 'uIndexClosest1' may be used uninitialized in this function [-Wmaybe-uninitialized]
   ClusterNode &Child1 = m_Nodes[uIndexClosest1];
                                               ^
In file included from muscle.h:38:0,
                 from cluster.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c clwwt.cpp -o clwwt.o
In file included from muscle.h:38:0,
                 from clwwt.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c color.cpp -o color.o
In file included from muscle.h:38:0,
                 from color.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
color.cpp:72:12: warning: 'int BlosumScore(char, char)' defined but not used [-Wunused-function]
 static int BlosumScore(char c1, char c2)
            ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c cons.cpp -o cons.o
In file included from muscle.h:38:0,
                 from cons.cpp:7:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c diaglist.cpp -o diaglist.o
diaglist.cpp: In member function 'void DiagList::FromPath(const PWPath&)':
diaglist.cpp:20:29: warning: 'uStartPosB' may be used uninitialized in this function [-Wmaybe-uninitialized]
  d.m_uStartPosB = uStartPosB;
                             ^
diaglist.cpp:52:11: note: 'uStartPosB' was declared here
  unsigned uStartPosB;
           ^
diaglist.cpp:19:29: warning: 'uStartPosA' may be used uninitialized in this function [-Wmaybe-uninitialized]
  d.m_uStartPosA = uStartPosA;
                             ^
diaglist.cpp:51:11: note: 'uStartPosA' was declared here
  unsigned uStartPosA;
           ^
In file included from muscle.h:38:0,
                 from diaglist.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const unsigned uSeqCount = msa.GetSeqCount();
                 ^
diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable]
  const unsigned uColCount = msa.GetColCount();
                 ^
In file included from muscle.h:38:0,
                 from diffobjscore.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c diffpaths.cpp -o diffpaths.o
In file included from muscle.h:38:0,
                 from diffpaths.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const unsigned uLeafCount2 = Tree2.GetLeafCount();
                 ^
In file included from muscle.h:38:0,
                 from difftrees.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c difftreese.cpp -o difftreese.o
In file included from muscle.h:38:0,
                 from difftreese.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c distcalc.cpp -o distcalc.o
In file included from muscle.h:38:0,
                 from distcalc.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c distfunc.cpp -o distfunc.o
In file included from muscle.h:38:0,
                 from distfunc.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c distpwkimura.cpp -o distpwkimura.o
In file included from muscle.h:38:0,
                 from distpwkimura.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c domuscle.cpp -o domuscle.o
In file included from domuscle.cpp:9:0:
timing.h:5:0: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(disable:4035)
 ^
domuscle.cpp: In function 'void DoMuscle(MuscleInput*, MuscleOutput*)':
domuscle.cpp:180:6: warning: unused variable 'PNlength' [-Wunused-variable]
  int PNlength = (msaInput->inputSeqs).Length();
      ^
In file included from muscle.h:38:0,
                 from RMuscle.h:4,
                 from domuscle.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
In file included from domuscle.cpp:9:0:
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
 static double TicksToSecs(TICKS t)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c dosp.cpp -o dosp.o
In file included from muscle.h:38:0,
                 from dosp.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
    const unsigned uDiagLengthMinusCaps = uEndVertexA - uStartVertexA - 1;
                   ^
In file included from muscle.h:38:0,
                 from dpreglist.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c drawtree.cpp -o drawtree.o
In file included from muscle.h:38:0,
                 from drawtree.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c edgelist.cpp -o edgelist.o
In file included from muscle.h:38:0,
                 from edgelist.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c enumopts.cpp -o enumopts.o
In file included from muscle.h:38:0,
                 from enumopts.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c enumtostr.cpp -o enumtostr.o
In file included from muscle.h:38:0,
                 from enumtostr.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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:424:21: warning: 'cType' may be used uninitialized in this function [-Wmaybe-uninitialized]
   Edge.cType = cType;
                     ^
In file included from muscle.h:38:0,
                 from estring.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
estring.cpp:464:13: warning: 'bool CanMultiplyEstrings(const short int*, const short int*)' defined but not used [-Wunused-function]
 static bool CanMultiplyEstrings(const short es1[], const short es2[])
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  unsigned uSeqCount = 0;
           ^
fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable]
  unsigned uColCount = uInsane;
           ^
In file included from muscle.h:38:0,
                 from fasta.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c fasta2.cpp -o fasta2.o
In file included from muscle.h:38:0,
                 from fasta2.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c fastclust.cpp -o fastclust.o
In file included from muscle.h:38:0,
                 from fastclust.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c fastdist.cpp -o fastdist.o
In file included from muscle.h:38:0,
                 from fastdist.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistjones.cpp -o fastdistjones.o
In file included from muscle.h:38:0,
                 from fastdistjones.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistkbit.cpp -o fastdistkbit.o
In file included from muscle.h:38:0,
                 from fastdistkbit.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
    double KD = KimuraDist(EstimatedPctId);
           ^
In file included from muscle.h:38:0,
                 from fastdistkmer.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistmafft.cpp -o fastdistmafft.o
fastdistmafft.cpp: In function 'void DistKmer6_6(const SeqVect&, DistFunc&)':
fastdistmafft.cpp:239:15: warning: unused variable 'pName1' [-Wunused-variable]
   const char *pName1 = s1.GetName();
               ^
In file included from muscle.h:38:0,
                 from fastdistmafft.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
fastdistmafft.cpp:104:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function]
 static void ListCount(const unsigned char Count[])
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
   const char *pName1 = s1.GetName();
               ^
In file included from muscle.h:38:0,
                 from fastdistnuc.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
fastdistnuc.cpp:33:17: warning: 'uResidueGroupCount' defined but not used [-Wunused-variable]
 static unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]);
                 ^
fastdistnuc.cpp:85:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function]
 static void ListCount(const unsigned char Count[])
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c fastscorepath2.cpp -o fastscorepath2.o
In file included from muscle.h:38:0,
                 from fastscorepath2.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c finddiags.cpp -o finddiags.o
In file included from muscle.h:38:0,
                 from finddiags.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
finddiags.cpp:11:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function]
 static char *TupleToStr(int t)
              ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c finddiagsn.cpp -o finddiagsn.o
finddiagsn.cpp: In function 'char* TupleToStr(int)':
finddiagsn.cpp:16:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < K; ++i)
                    ^
In file included from muscle.h:38:0,
                 from finddiagsn.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
finddiagsn.cpp:12:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function]
 static char *TupleToStr(int t)
              ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c glbalign.cpp -o glbalign.o
In file included from glbalign.cpp:3:0:
timing.h:5:0: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(disable:4035)
 ^
In file included from muscle.h:38:0,
                 from glbalign.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
In file included from glbalign.cpp:3:0:
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
 static double TicksToSecs(TICKS t)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c glbalign352.cpp -o glbalign352.o
In file included from glbalign352.cpp:3:0:
timing.h:5:0: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(disable:4035)
 ^
In file included from muscle.h:38:0,
                 from glbalign352.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
In file included from glbalign352.cpp:3:0:
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
 static double TicksToSecs(TICKS t)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c glbaligndiag.cpp -o glbaligndiag.o
In file included from glbaligndiag.cpp:6:0:
timing.h:5:0: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(disable:4035)
 ^
In file included from muscle.h:38:0,
                 from glbaligndiag.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
In file included from glbaligndiag.cpp:6:0:
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
 static double TicksToSecs(TICKS t)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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:431:33: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
   iTraceBack = (int) uInsertPos - (int) uLengthB;
                                 ^
In file included from muscle.h:38:0,
                 from glbalignle.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignsimple.cpp -o glbalignsimple.o
In file included from muscle.h:38:0,
                 from glbalignsimple.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
glbalignsimple.cpp:28:13: warning: 'void ListTB(const char*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static void ListTB(const char *TBM_, const ProfPos *PA, const ProfPos *PB,
             ^
glbalignsimple.cpp:52:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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:366:33: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
   iTraceBack = (int) uInsertPos - (int) uLengthB;
                                 ^
glbalignsp.cpp:305:41: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ptrTraceBack_ij = (int) uInsertPos - (int) j;
                                         ^
In file included from muscle.h:38:0,
                 from glbalignsp.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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:401:33: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
   iTraceBack = (int) uInsertPos - (int) uLengthB;
                                 ^
glbalignspn.cpp:340:41: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ptrTraceBack_ij = (int) uInsertPos - (int) j;
                                         ^
In file included from muscle.h:38:0,
                 from glbalignspn.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
   const SCORE *ptrRowA = MxRowA[i];
                ^
glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable]
  const unsigned uPrefixCountA = uLengthA + 1;
                 ^
glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
  const unsigned uPrefixCountB = uLengthB + 1;
                 ^
glbalignss.cpp:310:33: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
   iTraceBack = (int) uInsertPos - (int) uLengthB;
                                 ^
glbalignss.cpp:252:41: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ptrTraceBack_ij = (int) uInsertPos - (int) j;
                                         ^
In file included from muscle.h:38:0,
                 from glbalignss.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
glbalignss.cpp:11:14: warning: 'SCORE Subst(const Seq&, const Seq&, unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static SCORE Subst(const Seq &seqA, const Seq &seqB, unsigned i, unsigned j)
              ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  switch (g_PPScore)
         ^
glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_SPN' not handled in switch [-Wswitch]
In file included from muscle.h:38:0,
                 from glbalndimer.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
glbalndimer.cpp:14:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function]
 static const char *LocalScoreToStr(SCORE s)
                    ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c globals.cpp -o globals.o
In file included from muscle.h:38:0,
                 from globals.cpp:6:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c globalslinux.cpp -o globalslinux.o
In file included from muscle.h:38:0,
                 from globalslinux.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c globalsosx.cpp -o globalsosx.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c globalsother.cpp -o globalsother.o
In file included from muscle.h:38:0,
                 from globalsother.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c globalswin32.cpp -o globalswin32.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c gonnet.cpp -o gonnet.o
In file included from muscle.h:38:0,
                 from gonnet.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
gonnet.cpp:137:14: warning: 'Gonnet160' defined but not used [-Wunused-variable]
 static SCORE Gonnet160[20][20] =
              ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c henikoffweight.cpp -o henikoffweight.o
In file included from muscle.h:38:0,
                 from henikoffweight.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c henikoffweightpb.cpp -o henikoffweightpb.o
In file included from muscle.h:38:0,
                 from henikoffweightpb.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c html.cpp -o html.o
In file included from muscle.h:38:0,
                 from html.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c hydro.cpp -o hydro.o
In file included from muscle.h:38:0,
                 from hydro.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c intmath.cpp -o intmath.o
In file included from muscle.h:38:0,
                 from intmath.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c local.cpp -o local.o
In file included from muscle.h:38:0,
                 from local.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c main.cpp -o main.o
In file included from muscle.h:38:0,
                 from main.cpp:3:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const unsigned uSeqLength = s.Length();
                 ^
makerootmsa.cpp: In function 'short int* MakeRootSeqE(const Seq&, const Tree&, unsigned int, const ProgNode*, Seq&, short int*, short int*)':
makerootmsa.cpp:94:17: warning: unused variable 'Path' [-Wunused-variable]
   const PWPath &Path = Nodes[uNodeIndex].m_Path;
                 ^
makerootmsa.cpp: In function 'void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)':
makerootmsa.cpp:168:17: warning: unused variable 'uTreeNodeCount' [-Wunused-variable]
  const unsigned uTreeNodeCount = GuideTree.GetNodeCount();
                 ^
In file included from muscle.h:38:0,
                 from makerootmsa.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
makerootmsa.cpp:12:13: warning: 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)' defined but not used [-Wunused-function]
 static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut)
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c makerootmsab.cpp -o makerootmsab.o
In file included from muscle.h:38:0,
                 from makerootmsab.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c maketree.cpp -o maketree.o
In file included from muscle.h:38:0,
                 from maketree.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c mhack.cpp -o mhack.o
In file included from muscle.h:38:0,
                 from mhack.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c mpam200.cpp -o mpam200.o
In file included from muscle.h:38:0,
                 from mpam200.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c msa.cpp -o msa.o
In file included from muscle.h:38:0,
                 from msa.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
msa.cpp:385:13: warning: 'void FmtChar(char, unsigned int)' defined but not used [-Wunused-function]
 static void FmtChar(char c, unsigned uWidth)
             ^
msa.cpp:392:13: warning: 'void FmtInt(unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static void FmtInt(unsigned u, unsigned uWidth)
             ^
msa.cpp:407:13: warning: 'void FmtInt0(unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static void FmtInt0(unsigned u, unsigned uWidth)
             ^
msa.cpp:419:13: warning: 'void FmtPad(unsigned int)' defined but not used [-Wunused-function]
 static void FmtPad(unsigned n)
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  switch (Method)
         ^
msa2.cpp: In function 'void MSAAppend(MSA&, const MSA&)':
msa2.cpp:476:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
  const unsigned uColCountCat = uColCount1 + uColCount2;
                 ^
In file included from muscle.h:38:0,
                 from msa2.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c msadistkimura.cpp -o msadistkimura.o
In file included from muscle.h:38:0,
                 from msadistkimura.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c msf.cpp -o msf.o
In file included from muscle.h:38:0,
                 from msf.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
msf.cpp:24:20: warning: 'const char* strfind(const char*, const char*)' defined but not used [-Wunused-function]
 static const char *strfind(const char *s, const char *t)
                    ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c muscle.cpp -o muscle.o
In file included from muscle.h:38:0,
                 from muscle.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c muscleout.cpp -o muscleout.o
In file included from muscle.h:38:0,
                 from muscleout.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c nucmx.cpp -o nucmx.o
In file included from muscle.h:38:0,
                 from nucmx.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c nwdasimple.cpp -o nwdasimple.o
In file included from muscle.h:38:0,
                 from nwdasimple.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c nwdasimple2.cpp -o nwdasimple2.o
In file included from muscle.h:38:0,
                 from nwdasimple2.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c nwdasmall.cpp -o nwdasmall.o
In file included from muscle.h:38:0,
                 from nwdasmall.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c nwrec.cpp -o nwrec.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c nwsmall.cpp -o nwsmall.o
In file included from muscle.h:38:0,
                 from nwsmall.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c objscore.cpp -o objscore.o
In file included from objscore.cpp:5:0:
timing.h:5:0: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(disable:4035)
 ^
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]
  switch (OS)
         ^
objscore.cpp:31:9: warning: enumeration value 'OBJSCORE_SPM' not handled in switch [-Wswitch]
In file included from muscle.h:38:0,
                 from objscore.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
In file included from objscore.cpp:5:0:
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
 static double TicksToSecs(TICKS t)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  switch (g_TermGaps)
         ^
objscore2.cpp: In function 'SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)':
objscore2.cpp:62:8: warning: unused variable 'scoreGaps' [-Wunused-variable]
  SCORE scoreGaps = 0;
        ^
objscore2.cpp:63:7: warning: unused variable 'bGapping1' [-Wunused-variable]
  bool bGapping1 = false;
       ^
objscore2.cpp:64:7: warning: unused variable 'bGapping2' [-Wunused-variable]
  bool bGapping2 = false;
       ^
objscore2.cpp:67:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
  bool bLeftTermGap = false;
       ^
objscore2.cpp:82:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
  bool bRightTermGap = false;
       ^
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]
  bool bLeftTermGap = false;
       ^
objscore2.cpp:155:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
  bool bRightTermGap = false;
       ^
objscore2.cpp: In function 'SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)':
objscore2.cpp:314:17: warning: unused variable 'uColCount2' [-Wunused-variable]
  const unsigned uColCount2 = msa2.GetColCount();
                 ^
objscore2.cpp: In function 'SCORE ObjScoreXP(const MSA&, const MSA&)':
objscore2.cpp:493:17: warning: unused variable 'w' [-Wunused-variable]
    const WEIGHT w = w1*w2;
                 ^
In file included from muscle.h:38:0,
                 from objscore2.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c objscoreda.cpp -o objscoreda.o
In file included from muscle.h:38:0,
                 from objscoreda.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c onexception.cpp -o onexception.o
In file included from muscle.h:38:0,
                 from onexception.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c options.cpp -o options.o
In file included from muscle.h:38:0,
                 from options.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c outweights.cpp -o outweights.o
In file included from muscle.h:38:0,
                 from outweights.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pam200mafft.cpp -o pam200mafft.o
In file included from muscle.h:38:0,
                 from pam200mafft.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
pam200mafft.cpp:6:14: warning: 'PAM200' defined but not used [-Wunused-variable]
 static float PAM200[23][23] =
              ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c params.cpp -o params.o
params.cpp: In function 'void SetPPScore(bool)':
params.cpp:441:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
  switch (g_PPScore)
         ^
In file included from muscle.h:38:0,
                 from params.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  double dEdgeLength = GetEdgeLength(uNode1, uNode2);
         ^
In file included from muscle.h:38:0,
                 from phy.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c phy2.cpp -o phy2.o
In file included from muscle.h:38:0,
                 from phy2.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const double dThisDist = tree.GetEdgeLength(uNode1, uNode2);
               ^
phy3.cpp: In function 'void FindRoot(const Tree&, unsigned int*, unsigned int*, double*, double*, ROOT)':
phy3.cpp:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable]
  const unsigned uLeafCount = tree.GetLeafCount();
                 ^
phy3.cpp:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable]
  double dAllMaxDist = -1e20;
         ^
phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable]
  unsigned uMaxFrom = NULL_NEIGHBOR;
           ^
phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable]
  unsigned uMaxTo = NULL_NEIGHBOR;
           ^
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]
  unsigned uMostDistantLeaf = NULL_NEIGHBOR;
           ^
In file included from muscle.h:38:0,
                 from phy3.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
phy3.cpp:45:13: warning: 'void ListEIs(EdgeInfo**, unsigned int)' defined but not used [-Wunused-function]
 static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount)
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c phy4.cpp -o phy4.o
In file included from muscle.h:38:0,
                 from phy4.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c phyfromclust.cpp -o phyfromclust.o
In file included from muscle.h:38:0,
                 from phyfromclust.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c phyfromfile.cpp -o phyfromfile.o
In file included from muscle.h:38:0,
                 from phyfromfile.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c physeq.cpp -o physeq.o
physeq.cpp: In member function 'void MSA::ToPhySequentialFile(TextFile&) const':
physeq.cpp:60:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Col == ColCount)
             ^
physeq.cpp:71:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if (Col == ColCount)
            ^
physeq.cpp: In member function 'void MSA::ToPhyInterleavedFile(TextFile&) const':
physeq.cpp:112:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Col == ColCount)
             ^
physeq.cpp:124:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (Col == ColCount)
           ^
In file included from muscle.h:38:0,
                 from physeq.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c phytofile.cpp -o phytofile.o
In file included from muscle.h:38:0,
                 from phytofile.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c posgap.cpp -o posgap.o
In file included from muscle.h:38:0,
                 from posgap.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c ppscore.cpp -o ppscore.o
In file included from muscle.h:38:0,
                 from ppscore.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
   switch(m_Distance)
         ^
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]
In file included from muscle.h:38:0,
                 from profdb.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c profile.cpp -o profile.o
In file included from muscle.h:38:0,
                 from profile.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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:131:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (-1 == PP.m_uResidueGroup)
          ^
profilefrommsa.cpp: In function 'unsigned int ResidueGroupFromFCounts(const FCOUNT*)':
profilefrommsa.cpp:230:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
  switch (g_Alpha)
         ^
profilefrommsa.cpp: In function 'ProfPos* ProfileFromMSA(const MSA&)':
profilefrommsa.cpp:245:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
  const unsigned uSeqCount = a.GetSeqCount();
                 ^
profilefrommsa.cpp:253:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable]
  unsigned uHydrophobicRunLength = 0;
           ^
In file included from muscle.h:38:0,
                 from profilefrommsa.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
profilefrommsa.cpp:15:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function]
 static const char *LocalScoreToStr(SCORE s)
                    ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const unsigned uIterCount = uSeqCount - 1;
                 ^
In file included from muscle.h:38:0,
                 from progalign.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c progress.cpp -o progress.o
In file included from muscle.h:38:0,
                 from progress.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c progressivealign.cpp -o progressivealign.o
In file included from muscle.h:38:0,
                 from progressivealign.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwpath.cpp -o pwpath.o
pwpath.cpp: In member function 'void PWPath::Validate() const':
pwpath.cpp:80:16: warning: unused variable 'LastEdge' [-Wunused-variable]
  const PWEdge &LastEdge = GetEdge(uEdgeCount - 1);
                ^
pwpath.cpp: In member function 'void PWPath::FromFile(TextFile&)':
pwpath.cpp:213:11: warning: unused variable 'uEdgeIndex' [-Wunused-variable]
  unsigned uEdgeIndex = 0;
           ^
In file included from muscle.h:38:0,
                 from pwpath.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c readmx.cpp -o readmx.o
readmx.cpp: In function 'float (* ReadMx(TextFile&))[32][32]':
readmx.cpp:83:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < MAX_ALPHA; ++i)
                    ^
readmx.cpp:84:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int j = 0; j < MAX_ALPHA; ++j)
                     ^
readmx.cpp: In function 'float (* ReadMxFromR(std::vector<std::basic_string<char> >, float (*)[32]))[32][32]':
readmx.cpp:184:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < MAX_ALPHA; ++i)
                    ^
readmx.cpp:185:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int j = 0; j < MAX_ALPHA; ++j)
                     ^
In file included from muscle.h:38:0,
                 from readmx.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
readmx.cpp:30:17: warning: 'unsigned int MxCharToLetter(char)' defined but not used [-Wunused-function]
 static unsigned MxCharToLetter(char c)
                 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c realigndiffs.cpp -o realigndiffs.o
In file included from muscle.h:38:0,
                 from realigndiffs.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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:77:13: warning: unused variable 'uNewRight' [-Wunused-variable]
    unsigned uNewRight = NewTree.GetRight(uNewNodeIndex);
             ^
realigndiffse.cpp:80:13: warning: unused variable 'uOldRight' [-Wunused-variable]
    unsigned uOldRight = OldTree.GetRight(uOld);
             ^
In file included from muscle.h:38:0,
                 from realigndiffse.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
   switch(m_Distance)
         ^
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]
In file included from muscle.h:38:0,
                 from refine.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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:187:59: warning: 'scoreAfter' may be used uninitialized in this function [-Wmaybe-uninitialized]
   SCORE scoreMax = scoreAfter > scoreBefore? scoreAfter : scoreBefore;
                                                           ^
refinehoriz.cpp:174:9: note: 'scoreAfter' was declared here
   SCORE scoreAfter;
         ^
refinehoriz.cpp:187:59: warning: 'scoreBefore' may be used uninitialized in this function [-Wmaybe-uninitialized]
   SCORE scoreMax = scoreAfter > scoreBefore? scoreAfter : scoreBefore;
                                                           ^
refinehoriz.cpp:173:9: note: 'scoreBefore' was declared here
   SCORE scoreBefore;
         ^
In file included from muscle.h:38:0,
                 from refinehoriz.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const unsigned uNodeCount = tree.GetNodeCount();
                 ^
In file included from muscle.h:38:0,
                 from refinesubfams.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c refinetree.cpp -o refinetree.o
In file included from muscle.h:38:0,
                 from refinetree.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c refinetreee.cpp -o refinetreee.o
In file included from muscle.h:38:0,
                 from refinetreee.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c refinevert.cpp -o refinevert.o
In file included from muscle.h:38:0,
                 from refinevert.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c refinew.cpp -o refinew.o
refinew.cpp: In function 'void AppendMSA(MSA&, const MSA&)':
refinew.cpp:22:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
  const unsigned uColCountCat = uColCount1 + uColCount2;
                 ^
refinew.cpp: In function 'void RefineW(const MSA&, MSA&)':
refinew.cpp:125:13: warning: unused variable 'uOutCols' [-Wunused-variable]
    unsigned uOutCols = msaOut.GetColCount();
             ^
In file included from muscle.h:38:0,
                 from refinew.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c savebest.cpp -o savebest.o
In file included from muscle.h:38:0,
                 from savebest.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c scoredist.cpp -o scoredist.o
In file included from muscle.h:38:0,
                 from scoredist.cpp:3:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c scoregaps.cpp -o scoregaps.o
In file included from muscle.h:38:0,
                 from scoregaps.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
scoregaps.cpp:37:13: warning: 'void FreeGapInfo(GAPINFO*)' defined but not used [-Wunused-function]
 static void FreeGapInfo(GAPINFO *GI)
             ^
scoregaps.cpp:80:14: warning: 'SCORE Penalty(unsigned int, bool)' defined but not used [-Wunused-function]
 static SCORE Penalty(unsigned Length, bool Term)
              ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c scorehistory.cpp -o scorehistory.o
In file included from muscle.h:38:0,
                 from scorehistory.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c scorepp.cpp -o scorepp.o
In file included from muscle.h:38:0,
                 from scorepp.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c seq.cpp -o seq.o
In file included from muscle.h:38:0,
                 from seq.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c seqvect.cpp -o seqvect.o
In file included from muscle.h:38:0,
                 from seqvect.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c setblosumweights.cpp -o setblosumweights.o
In file included from muscle.h:38:0,
                 from setblosumweights.cpp:42:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c setgscweights.cpp -o setgscweights.o
In file included from muscle.h:38:0,
                 from setgscweights.cpp:104:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c setnewhandler.cpp -o setnewhandler.o
In file included from muscle.h:38:0,
                 from setnewhandler.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const unsigned uSeqCount = msa.GetSeqCount();
                 ^
In file included from muscle.h:38:0,
                 from spfast.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
spfast.cpp:14:20: warning: 'const char* GapTypeToStr(int)' defined but not used [-Wunused-function]
 static const char *GapTypeToStr(int GapType)
                    ^
spfast.cpp:59:14: warning: 'SCORE SPColBrute(const MSA&, unsigned int)' defined but not used [-Wunused-function]
 static SCORE SPColBrute(const MSA &msa, unsigned uColIndex)
              ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c sptest.cpp -o sptest.o
In file included from muscle.h:38:0,
                 from sptest.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c stabilize.cpp -o stabilize.o
In file included from muscle.h:38:0,
                 from stabilize.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  int NotUsed = system(CmdLine);
      ^
In file included from muscle.h:38:0,
                 from subfam.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c subfams.cpp -o subfams.o
In file included from muscle.h:38:0,
                 from subfams.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
subfams.cpp:10:13: warning: 'void GetMostDistantPair(DistFunc&, unsigned int*, unsigned int*)' defined but not used [-Wunused-function]
 static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2)
             ^
subfams.cpp:40:13: warning: 'void InitializeSingleSource(DistFunc&, unsigned int)' defined but not used [-Wunused-function]
 static void InitializeSingleSource(DistFunc &DF, unsigned uIndex)
             ^
subfams.cpp:52:13: warning: 'void Relax(DistFunc&, unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static void Relax(DistFunc &DF, unsigned u, unsigned v)
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c sw.cpp -o sw.o
In file included from muscle.h:38:0,
                 from sw.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
sw.cpp:20:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c termgaps.cpp -o termgaps.o
In file included from muscle.h:38:0,
                 from termgaps.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c textfile.cpp -o textfile.o
textfile.cpp: In member function 'void TextFile::PutChar(char)':
textfile.cpp:111:6: warning: unused variable 'i' [-Wunused-variable]
  int i = fputc(c, m_ptrFile);
      ^
textfile.cpp: In member function 'void TextFile::PutString(const char*)':
textfile.cpp:124:6: warning: unused variable 'iError' [-Wunused-variable]
  int iError = fputs(szLine, m_ptrFile);
      ^
textfile.cpp: In member function 'TEXTFILEPOS TextFile::GetPos()':
textfile.cpp:224:6: warning: unused variable 'i' [-Wunused-variable]
  int i = fgetpos(m_ptrFile, &p);
      ^
textfile.cpp: In member function 'void TextFile::SetPos(TEXTFILEPOS)':
textfile.cpp:237:6: warning: unused variable 'i' [-Wunused-variable]
  int i = fsetpos(m_ptrFile, &p);
      ^
In file included from muscle.h:38:0,
                 from textfile.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c threewaywt.cpp -o threewaywt.o
In file included from muscle.h:38:0,
                 from threewaywt.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c tomhydro.cpp -o tomhydro.o
In file included from muscle.h:38:0,
                 from tomhydro.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const unsigned uPrefixCountB = uLengthB + 1;
                 ^
traceback.cpp:59:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if ('S' == cEdgeType)
   ^
In file included from muscle.h:38:0,
                 from traceback.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c tracebackopt.cpp -o tracebackopt.o
In file included from muscle.h:38:0,
                 from tracebackopt.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const unsigned uPrefixCountB = uLengthB + 1;
                 ^
tracebacksw.cpp:29:8: warning: unused variable 'scoreMax' [-Wunused-variable]
  SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB);
        ^
tracebacksw.cpp:34:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if ('S' == cEdgeType)
   ^
In file included from muscle.h:38:0,
                 from tracebacksw.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
   switch(m_Distance)
         ^
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]
In file included from muscle.h:38:0,
                 from treefrommsa.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c typetostr.cpp -o typetostr.o
In file included from muscle.h:38:0,
                 from typetostr.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c upgma2.cpp -o upgma2.o
upgma2.cpp: In function 'void UPGMA2(const DistCalc&, Tree&, LINKAGE)':
upgma2.cpp:292:26: warning: 'dtNewDist' may be used uninitialized in this function [-Wmaybe-uninitialized]
    g_Dist[vL] = dtNewDist;
                          ^
In file included from muscle.h:38:0,
                 from upgma2.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
upgma2.cpp:68:13: warning: 'void ListState()' defined but not used [-Wunused-function]
 static void ListState()
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c usage.cpp -o usage.o
In file included from muscle.h:38:0,
                 from usage.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c validateids.cpp -o validateids.o
In file included from muscle.h:38:0,
                 from validateids.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c vtml2.cpp -o vtml2.o
In file included from muscle.h:38:0,
                 from vtml2.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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 [-Wmaybe-uninitialized]
    dSum += Score;
                 ^
writescorefile.cpp:27:11: note: 'Score' was declared here
    double Score;
           ^
In file included from muscle.h:38:0,
                 from writescorefile.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RMuscle.cpp -o RMuscle.o
In file included from muscle.h:38:0,
                 from RMuscle.h:4,
                 from RMuscle.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_32/bin/g++ -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 glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.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 options.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 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 RMuscle.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
make[2]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpeaNGby/R.INSTALLbf03a843fd6/msa/src/Muscle'
ar rcs libMuscle.a 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 glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.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 options.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 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 RMuscle.o
cp libMuscle.a ../
make[1]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpeaNGby/R.INSTALLbf03a843fd6/msa/src/Muscle'
----------------------------------------
---------------- MUSCLE ----------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile.win --directory=ClustalW
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpeaNGby/R.INSTALLbf03a843fd6/msa/src/ClustalW'
cp windows/Makefile .; \
cp windows/m4/Makefile m4/; \
cp windows/src/Makefile src/; \
cp windows/src/clustalw_version.h src/; \
cp windows/src/config.h src/; \
cd src; \
export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. "; \
C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386/R.exe CMD SHLIB -o ClustalW.dll pairwise/FullPairwiseAlign.cpp pairwise/FastPairwiseAlign.cpp fileInput/MSFFileParser.cpp fileInput/FileReader.cpp fileInput/PIRFileParser.cpp fileInput/RSFFileParser.cpp fileInput/GDEFileParser.cpp fileInput/InFileStream.cpp fileInput/ClustalFileParser.cpp fileInput/PearsonFileParser.cpp fileInput/FileParser.cpp fileInput/EMBLFileParser.cpp tree/UPGMA/RootedClusterTree.cpp tree/UPGMA/UPGMAAlgorithm.cpp tree/UPGMA/Node.cpp tree/UPGMA/RootedGuideTree.cpp tree/UPGMA/RootedTreeOutput.cpp tree/Tree.cpp tree/ClusterTree.cpp tree/TreeInterface.cpp tree/UnRootedClusterTree.cpp tree/ClusterTreeOutput.cpp tree/RandomGenerator.cpp tree/NJTree.cpp tree/AlignmentSteps.cpp interface/CommandLineParser.cpp substitutionMatrix/SubMatrix.cpp multipleAlign/Iteration.cpp multipleAlign/MSA.cpp multipleAlign/MyersMillerProfileAlign.cpp multipleAlign/ProfileStandard.cpp multipleAlign/ProfileWithSub.cpp multipleAlign/ProfileBase.cpp multipleAlign/LowScoreSegProfile.cpp general/OutputFile.cpp general/UserParameters.cpp general/Utility.cpp general/InvalidCombination.cpp general/DebugLog.cpp general/ClustalWResources.cpp general/VectorOutOfRange.cpp general/SymMatrix.cpp general/Stats.cpp Help.cpp alignment/Alignment.cpp alignment/AlignmentOutput.cpp alignment/ObjectiveScore.cpp alignment/Sequence.cpp Clustal.cpp RClustalWMain.cpp RClustalW.cpp &&\
ar rcs libClustalW.a pairwise/FullPairwiseAlign.o pairwise/FastPairwiseAlign.o fileInput/MSFFileParser.o fileInput/FileReader.o fileInput/PIRFileParser.o fileInput/RSFFileParser.o fileInput/GDEFileParser.o fileInput/InFileStream.o fileInput/ClustalFileParser.o fileInput/PearsonFileParser.o fileInput/FileParser.o fileInput/EMBLFileParser.o tree/UPGMA/RootedClusterTree.o tree/UPGMA/UPGMAAlgorithm.o tree/UPGMA/Node.o tree/UPGMA/RootedGuideTree.o tree/UPGMA/RootedTreeOutput.o tree/Tree.o tree/ClusterTree.o tree/TreeInterface.o tree/UnRootedClusterTree.o tree/ClusterTreeOutput.o tree/RandomGenerator.o tree/NJTree.o tree/AlignmentSteps.o interface/CommandLineParser.o substitutionMatrix/SubMatrix.o multipleAlign/Iteration.o multipleAlign/MSA.o multipleAlign/MyersMillerProfileAlign.o multipleAlign/ProfileStandard.o multipleAlign/ProfileWithSub.o multipleAlign/ProfileBase.o multipleAlign/LowScoreSegProfile.o general/OutputFile.o general/UserParameters.o general/Utility.o general/InvalidCombination.o general/DebugLog.o general/ClustalWResources.o general/VectorOutOfRange.o general/SymMatrix.o general/Stats.o Help.o alignment/Alignment.o alignment/AlignmentOutput.o alignment/ObjectiveScore.o alignment/Sequence.o Clustal.o RClustalWMain.o RClustalW.o && \
cp libClustalW.a ../../
make[2]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpeaNGby/R.INSTALLbf03a843fd6/msa/src/ClustalW/src'
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c pairwise/FullPairwiseAlign.cpp -o pairwise/FullPairwiseAlign.o
In file included from pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from pairwise/../alignment/Alignment.h:42,
                 from pairwise/PairwiseAlignBase.h:10,
                 from pairwise/FullPairwiseAlign.h:9,
                 from pairwise/FullPairwiseAlign.cpp:9:
pairwise/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
pairwise/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c pairwise/FastPairwiseAlign.cpp -o pairwise/FastPairwiseAlign.o
In file included from pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from pairwise/../alignment/Alignment.h:42,
                 from pairwise/PairwiseAlignBase.h:10,
                 from pairwise/FastPairwiseAlign.h:9,
                 from pairwise/FastPairwiseAlign.cpp:10:
pairwise/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
pairwise/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/MSFFileParser.cpp -o fileInput/MSFFileParser.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/FileReader.cpp -o fileInput/FileReader.o
In file included from fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from fileInput/../alignment/Alignment.h:42,
                 from fileInput/FileReader.h:12,
                 from fileInput/FileReader.cpp:29:
fileInput/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
fileInput/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readCharacterSeqs(clustalw::Alignment*, int, std::string*, ClustalWInput*)':
fileInput/FileReader.cpp:421:10: warning: variable 'maxAlnLength' set but not used [-Wunused-but-set-variable]
      int maxAlnLength; // Get values from the Alignment object.
          ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/PIRFileParser.cpp -o fileInput/PIRFileParser.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/RSFFileParser.cpp -o fileInput/RSFFileParser.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/GDEFileParser.cpp -o fileInput/GDEFileParser.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/InFileStream.cpp -o fileInput/InFileStream.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/ClustalFileParser.cpp -o fileInput/ClustalFileParser.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/PearsonFileParser.cpp -o fileInput/PearsonFileParser.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/FileParser.cpp -o fileInput/FileParser.o
fileInput/FileParser.cpp: In member function 'std::vector<clustalw::Sequence> clustalw::FileParser::getSeqRangeR(int, int, std::string*, ClustalWInput*)':
fileInput/FileParser.cpp:38:7: warning: unused variable 'n' [-Wunused-variable]
   int n = (*input).inputSeqs.size();
       ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/EMBLFileParser.cpp -o fileInput/EMBLFileParser.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UPGMA/RootedClusterTree.cpp -o tree/UPGMA/RootedClusterTree.o
In file included from tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/UPGMA/../../alignment/Alignment.h:42,
                 from tree/UPGMA/../ClusterTree.h:20,
                 from tree/UPGMA/RootedClusterTree.h:8,
                 from tree/UPGMA/RootedClusterTree.cpp:9:
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
In file included from tree/UPGMA/../../alignment/../general/clustalw.h:44:0,
                 from tree/UPGMA/../../alignment/../general/Utility.h:15,
                 from tree/UPGMA/../../alignment/../general/utils.h:8,
                 from tree/UPGMA/../../alignment/../general/UserParameters.h:22,
                 from tree/UPGMA/../../alignment/../general/userparams.h:8,
                 from tree/UPGMA/../../alignment/Sequence.h:20,
                 from tree/UPGMA/../../alignment/Alignment.h:41,
                 from tree/UPGMA/../ClusterTree.h:20,
                 from tree/UPGMA/RootedClusterTree.h:8,
                 from tree/UPGMA/RootedClusterTree.cpp:9:
tree/UPGMA/../../alignment/../general/SymMatrix.h: In member function 'std::auto_ptr<clustalw::AlignmentSteps> clustalw::RootedClusterTree::treeFromDistMatrix(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string&)':
tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
             if (_i > _j) 
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UPGMA/UPGMAAlgorithm.cpp -o tree/UPGMA/UPGMAAlgorithm.o
In file included from tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/UPGMA/../../alignment/Alignment.h:42,
                 from tree/UPGMA/RootedGuideTree.h:17,
                 from tree/UPGMA/UPGMAAlgorithm.h:8,
                 from tree/UPGMA/UPGMAAlgorithm.cpp:4:
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UPGMA/Node.cpp -o tree/UPGMA/Node.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UPGMA/RootedGuideTree.cpp -o tree/UPGMA/RootedGuideTree.o
In file included from tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/UPGMA/../../alignment/Alignment.h:42,
                 from tree/UPGMA/RootedGuideTree.h:17,
                 from tree/UPGMA/RootedGuideTree.cpp:10:
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UPGMA/RootedTreeOutput.cpp -o tree/UPGMA/RootedTreeOutput.o
In file included from tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/UPGMA/../../alignment/Alignment.h:42,
                 from tree/UPGMA/RootedGuideTree.h:17,
                 from tree/UPGMA/RootedTreeOutput.h:15,
                 from tree/UPGMA/RootedTreeOutput.cpp:9:
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
In file included from tree/UPGMA/../../alignment/../general/clustalw.h:44:0,
                 from tree/UPGMA/../../alignment/../general/Utility.h:15,
                 from tree/UPGMA/../../alignment/../general/utils.h:8,
                 from tree/UPGMA/../../alignment/../general/UserParameters.h:22,
                 from tree/UPGMA/../../alignment/../general/userparams.h:8,
                 from tree/UPGMA/../../alignment/Sequence.h:20,
                 from tree/UPGMA/../../alignment/Alignment.h:41,
                 from tree/UPGMA/RootedGuideTree.h:17,
                 from tree/UPGMA/RootedTreeOutput.h:15,
                 from tree/UPGMA/RootedTreeOutput.cpp:9:
tree/UPGMA/../../alignment/../general/SymMatrix.h: In member function 'void clustalw::RootedTreeOutput::printPhylipTree(clustalw::RootedGuideTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*)':
tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
             if (_i > _j) 
             ^
tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
             if (_i > _j) 
             ^
tree/UPGMA/../../alignment/../general/SymMatrix.h: In member function 'void clustalw::RootedTreeOutput::printNexusTree(clustalw::RootedGuideTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*)':
tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
             if (_i > _j) 
             ^
tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
             if (_i > _j) 
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/Tree.cpp -o tree/Tree.o
In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/../alignment/Alignment.h:42,
                 from tree/Tree.h:13,
                 from tree/Tree.cpp:10:
tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/ClusterTree.cpp -o tree/ClusterTree.o
In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/../alignment/Alignment.h:42,
                 from tree/ClusterTree.h:20,
                 from tree/ClusterTree.cpp:9:
tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
tree/ClusterTree.cpp: In member function 'void clustalw::ClusterTree::calcPercIdentity(std::ofstream*, clustalw::Alignment*)':
tree/ClusterTree.cpp:580:9: warning: variable 'rs' set but not used [-Wunused-but-set-variable]
     int rs = 0, rl = 0;
         ^
tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable]
     int rs = 0, rl = 0;
                 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/TreeInterface.cpp -o tree/TreeInterface.o
In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/../alignment/Alignment.h:42,
                 from tree/TreeInterface.h:19,
                 from tree/TreeInterface.cpp:15:
tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UnRootedClusterTree.cpp -o tree/UnRootedClusterTree.o
In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/../alignment/Alignment.h:42,
                 from tree/ClusterTree.h:20,
                 from tree/UnRootedClusterTree.h:8,
                 from tree/UnRootedClusterTree.cpp:9:
tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
In file included from tree/../alignment/../general/clustalw.h:44:0,
                 from tree/../alignment/../general/Utility.h:15,
                 from tree/../alignment/../general/utils.h:8,
                 from tree/../alignment/../general/UserParameters.h:22,
                 from tree/../alignment/../general/userparams.h:8,
                 from tree/../alignment/Sequence.h:20,
                 from tree/../alignment/Alignment.h:41,
                 from tree/ClusterTree.h:20,
                 from tree/UnRootedClusterTree.h:8,
                 from tree/UnRootedClusterTree.cpp:9:
tree/../alignment/../general/SymMatrix.h: In member function 'void clustalw::UnRootedClusterTree::treeFromDistMatrix(clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string&)':
tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
             if (_i > _j) 
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/ClusterTreeOutput.cpp -o tree/ClusterTreeOutput.o
In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/../alignment/Alignment.h:42,
                 from tree/ClusterTreeOutput.h:11,
                 from tree/ClusterTreeOutput.cpp:9:
tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
In file included from tree/../alignment/../general/clustalw.h:44:0,
                 from tree/../alignment/../general/Utility.h:15,
                 from tree/../alignment/../general/utils.h:8,
                 from tree/../alignment/../general/UserParameters.h:22,
                 from tree/../alignment/../general/userparams.h:8,
                 from tree/../alignment/Sequence.h:20,
                 from tree/../alignment/Alignment.h:41,
                 from tree/ClusterTreeOutput.h:11,
                 from tree/ClusterTreeOutput.cpp:9:
tree/../alignment/../general/SymMatrix.h: In member function 'void clustalw::ClusterTreeOutput::printPhylipTree(clustalw::PhyloTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*, std::vector<int>*)':
tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
             if (_i > _j) 
             ^
tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
             if (_i > _j) 
             ^
tree/../alignment/../general/SymMatrix.h: In member function 'void clustalw::ClusterTreeOutput::printNexusTree(clustalw::PhyloTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*, std::vector<int>*)':
tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
             if (_i > _j) 
             ^
tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
             if (_i > _j) 
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/RandomGenerator.cpp -o tree/RandomGenerator.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/NJTree.cpp -o tree/NJTree.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/AlignmentSteps.cpp -o tree/AlignmentSteps.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c interface/CommandLineParser.cpp -o interface/CommandLineParser.o
In file included from interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from interface/../fileInput/../alignment/Alignment.h:42,
                 from interface/../fileInput/FileReader.h:12,
                 from interface/../Clustal.h:18,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c substitutionMatrix/SubMatrix.cpp -o substitutionMatrix/SubMatrix.o
In file included from substitutionMatrix/SubMatrix.cpp:15:0:
substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeriesFromR(Rcpp::NumericMatrix, clustalw::Matrix&, clustalw::Xref&)':
substitutionMatrix/SubMatrix.cpp:1305:10: warning: unused variable 'inline1' [-Wunused-variable]
     char inline1[1024];
          ^
substitutionMatrix/SubMatrix.cpp:1307:9: warning: unused variable 'nmat' [-Wunused-variable]
     int nmat;
         ^
substitutionMatrix/SubMatrix.cpp:1308:9: warning: unused variable 'n' [-Wunused-variable]
     int n, llimit, ulimit;
         ^
substitutionMatrix/SubMatrix.cpp:1308:12: warning: unused variable 'llimit' [-Wunused-variable]
     int n, llimit, ulimit;
            ^
substitutionMatrix/SubMatrix.cpp:1308:20: warning: unused variable 'ulimit' [-Wunused-variable]
     int n, llimit, ulimit;
                    ^
substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readUserMatrixFromR(Rcpp::NumericMatrix, clustalw::Matrix&, clustalw::Xref&)':
substitutionMatrix/SubMatrix.cpp:1361:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (j = 0; j < curline.length(); j++) {
                 ^
substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForHistogram(int (*)[32])':
substitutionMatrix/SubMatrix.cpp:1845:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
     int maxRes;
         ^
substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForLowScoreSeg(int (*)[32])':
substitutionMatrix/SubMatrix.cpp:1905:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
     int maxRes;
         ^
substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeries(const char*, clustalw::Matrix&, clustalw::Xref&)':
substitutionMatrix/SubMatrix.cpp:1023:9: warning: 'n' may be used uninitialized in this function [-Wmaybe-uninitialized]
     int n, llimit, ulimit;
         ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/Iteration.cpp -o multipleAlign/Iteration.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/Iteration.h:8,
                 from multipleAlign/Iteration.cpp:13:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)':
multipleAlign/Iteration.cpp:170:9: warning: variable 'count' set but not used [-Wunused-but-set-variable]
     int count;
         ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/MSA.cpp -o multipleAlign/MSA.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/ProfileBase.h:14,
                 from multipleAlign/MSA.h:10,
                 from multipleAlign/MSA.cpp:16:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
multipleAlign/MSA.cpp: In member function 'int clustalw::MSA::multiSeqAlign(clustalw::Alignment*, clustalw::DistMatrix*, std::vector<int>*, clustalw::AlignmentSteps*, int)':
multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable]
       int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18
           ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/MyersMillerProfileAlign.cpp -o multipleAlign/MyersMillerProfileAlign.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/ProfileAlignAlgorithm.h:10,
                 from multipleAlign/MyersMillerProfileAlign.h:10,
                 from multipleAlign/MyersMillerProfileAlign.cpp:10:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/ProfileStandard.cpp -o multipleAlign/ProfileStandard.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/ProfileStandard.h:9,
                 from multipleAlign/ProfileStandard.cpp:9:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/ProfileWithSub.cpp -o multipleAlign/ProfileWithSub.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/ProfileWithSub.h:9,
                 from multipleAlign/ProfileWithSub.cpp:9:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/ProfileBase.cpp -o multipleAlign/ProfileBase.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/ProfileBase.h:14,
                 from multipleAlign/ProfileBase.cpp:9:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/LowScoreSegProfile.cpp -o multipleAlign/LowScoreSegProfile.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/LowScoreSegProfile.h:13,
                 from multipleAlign/LowScoreSegProfile.cpp:9:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/OutputFile.cpp -o general/OutputFile.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/UserParameters.cpp -o general/UserParameters.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/Utility.cpp -o general/Utility.o
general/Utility.cpp: In member function 'bool clustalw::Utility::lineType(char*, const char*)':
general/Utility.cpp:251:8: warning: variable 'n' set but not used [-Wunused-but-set-variable]
    int n;
        ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/InvalidCombination.cpp -o general/InvalidCombination.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/DebugLog.cpp -o general/DebugLog.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/ClustalWResources.cpp -o general/ClustalWResources.o
general/ClustalWResources.cpp: In member function 'std::string clustalw::ClustalWResources::findFile(std::string, clustalw::ClustalWResourcePathType) const':
general/ClustalWResources.cpp:106:12: warning: array subscript is above array bounds [-Warray-bounds]
     delim[1] = 0;
            ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/VectorOutOfRange.cpp -o general/VectorOutOfRange.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/SymMatrix.cpp -o general/SymMatrix.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/Stats.cpp -o general/Stats.o
In file included from general/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from general/../alignment/Alignment.h:42,
                 from general/Stats.cpp:15:
general/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
general/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c Help.cpp -o Help.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c alignment/Alignment.cpp -o alignment/Alignment.o
In file included from alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from alignment/Alignment.h:42,
                 from alignment/Alignment.cpp:25:
alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c alignment/AlignmentOutput.cpp -o alignment/AlignmentOutput.o
In file included from alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from alignment/Alignment.h:42,
                 from alignment/AlignmentOutput.h:24,
                 from alignment/AlignmentOutput.cpp:27:
alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c alignment/ObjectiveScore.cpp -o alignment/ObjectiveScore.o
In file included from alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from alignment/ObjectiveScore.h:15,
                 from alignment/ObjectiveScore.cpp:10:
alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c alignment/Sequence.cpp -o alignment/Sequence.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c Clustal.cpp -o Clustal.o
In file included from fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from fileInput/../alignment/Alignment.h:42,
                 from fileInput/FileReader.h:12,
                 from Clustal.h:18,
                 from Clustal.cpp:27:
fileInput/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
fileInput/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c RClustalWMain.cpp -o RClustalWMain.o
In file included from alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from alignment/Alignment.h:42,
                 from RClustalWMain.cpp:5:
alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c RClustalW.cpp -o RClustalW.o
RClustalW.cpp: In function 'SEXPREC* RClustalW(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
RClustalW.cpp:513:31: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
             if (!(firstvalue2 == -1 | secondvalue2 == -1)) {
                               ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ClustalW.dll tmp.def pairwise/FullPairwiseAlign.o pairwise/FastPairwiseAlign.o fileInput/MSFFileParser.o fileInput/FileReader.o fileInput/PIRFileParser.o fileInput/RSFFileParser.o fileInput/GDEFileParser.o fileInput/InFileStream.o fileInput/ClustalFileParser.o fileInput/PearsonFileParser.o fileInput/FileParser.o fileInput/EMBLFileParser.o tree/UPGMA/RootedClusterTree.o tree/UPGMA/UPGMAAlgorithm.o tree/UPGMA/Node.o tree/UPGMA/RootedGuideTree.o tree/UPGMA/RootedTreeOutput.o tree/Tree.o tree/ClusterTree.o tree/TreeInterface.o tree/UnRootedClusterTree.o tree/ClusterTreeOutput.o tree/RandomGenerator.o tree/NJTree.o tree/AlignmentSteps.o interface/CommandLineParser.o substitutionMatrix/SubMatrix.o multipleAlign/Iteration.o multipleAlign/MSA.o multipleAlign/MyersMillerProfileAlign.o multipleAlign/ProfileStandard.o multipleAlign/ProfileWithSub.o multipleAlign/ProfileBase.o multipleAlign/LowScoreSegProfile.o general/OutputFile.o general/UserParameters.o general/Utility.o general/InvalidCombination.o general/DebugLog.o general/ClustalWResources.o general/VectorOutOfRange.o general/SymMatrix.o general/Stats.o Help.o alignment/Alignment.o alignment/AlignmentOutput.o alignment/ObjectiveScore.o alignment/Sequence.o Clustal.o RClustalWMain.o RClustalW.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
make[2]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpeaNGby/R.INSTALLbf03a843fd6/msa/src/ClustalW/src'
make[1]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpeaNGby/R.INSTALLbf03a843fd6/msa/src/ClustalW'
----------------------------------------
--------------- ClustalW ---------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile.win --directory=ClustalOmega
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpeaNGby/R.INSTALLbf03a843fd6/msa/src/ClustalOmega'
cp windows/src/config.h src/; \
cp windows/src/clustal-omega-config.h src/; \
export PKG_LIBS=" -L"../../gc-7.2" -lgccpp72 -lgc72"; \
export PKG_CXXFLAGS=" -std=c++98 -DMATH_H_CLIB -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
export PKG_CFLAGS=" -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc"; \
cd src; \
C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386/R.exe CMD SHLIB -o ClustalOmega.dll exceptions4c/e4c_lite.c argtable2/argtable2.c argtable2/arg_end.c argtable2/arg_rem.c argtable2/arg_lit.c argtable2/arg_int.c argtable2/arg_dbl.c argtable2/arg_str.c argtable2/arg_file.c kmpp/KMeans.cpp kmpp/KmTree.cpp kmpp/KmUtils.cpp clustal/hhalign_wrapper.c clustal/ktuple_pair.c clustal/list.c clustal/log.c clustal/muscle_upgma.c clustal/muscle_tree.c clustal/mbed.c clustal/pair_dist.c clustal/progress.c clustal/seq.c clustal/symmatrix.c clustal/tree.c clustal/util.c clustal/weights.c squid/a2m.c squid/aligneval.c squid/alignio.c squid/clustal.c squid/cluster.c squid/dayhoff.c squid/eps.c squid/file.c squid/getopt.c squid/gki.c squid/gsi.c squid/gsi64.c squid/hsregex.c squid/iupac.c squid/msa.c squid/msf.c squid/phylip.c squid/revcomp.c squid/rk.c squid/selex.c squid/seqencode.c squid/shuffle.c squid/sqerror.c squid/sqio.c squid/squidcore.c squid/sre_ctype.c squid/sre_math.c squid/sre_random.c squid/sre_string.c squid/ssi.c squid/stack.c squid/stockholm.c squid/stopwatch.c squid/translate.c squid/types.c squid/vectorops.c squid/weight.c hhalign/hhalign.cpp RClustalOmega.cpp mymain.c clustal-omega.c && \
ar rcs libClustalOmega.a exceptions4c/e4c_lite.o argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o clustal/tree.o clustal/util.o clustal/weights.o squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o squid/types.o squid/vectorops.o squid/weight.o hhalign/hhalign.o RClustalOmega.o mymain.o clustal-omega.o && \
cp libClustalOmega.a ../../
make[2]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpeaNGby/R.INSTALLbf03a843fd6/msa/src/ClustalOmega/src'
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c exceptions4c/e4c_lite.c -o exceptions4c/e4c_lite.o
exceptions4c/e4c_lite.c:16:8: warning: missing braces around initializer [-Wmissing-braces]
 struct e4c_context e4c = {0};
        ^
exceptions4c/e4c_lite.c:16:8: warning: (near initialization for 'e4c.jump') [-Wmissing-braces]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c argtable2/argtable2.c -o argtable2/argtable2.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c argtable2/arg_end.c -o argtable2/arg_end.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c argtable2/arg_rem.c -o argtable2/arg_rem.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c argtable2/arg_lit.c -o argtable2/arg_lit.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c argtable2/arg_int.c -o argtable2/arg_int.o
argtable2/arg_int.c: In function 'strtol0X':
argtable2/arg_int.c:60:5: warning: implicit declaration of function 'isspace' [-Wimplicit-function-declaration]
     while (isspace(*ptr))
     ^
argtable2/arg_int.c:89:4: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration]
    if (toupper(*ptr++)!=toupper(X))
    ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c argtable2/arg_dbl.c -o argtable2/arg_dbl.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c argtable2/arg_str.c -o argtable2/arg_str.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c argtable2/arg_file.c -o argtable2/arg_file.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -std=c++98 -DMATH_H_CLIB -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include   -O2 -Wall  -mtune=core2 -c kmpp/KMeans.cpp -o kmpp/KMeans.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -std=c++98 -DMATH_H_CLIB -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include   -O2 -Wall  -mtune=core2 -c kmpp/KmTree.cpp -o kmpp/KmTree.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -std=c++98 -DMATH_H_CLIB -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include   -O2 -Wall  -mtune=core2 -c kmpp/KmUtils.cpp -o kmpp/KmUtils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c clustal/hhalign_wrapper.c -o clustal/hhalign_wrapper.o
In file included from clustal/hhalign_wrapper.c:22:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
clustal/hhalign_wrapper.c: In function 'SanitiseUnknown':
clustal/hhalign_wrapper.c:85:9: warning: unused variable 'iLen' [-Wunused-variable]
     int iLen; /* length of sequence */
         ^
clustal/hhalign_wrapper.c:84:9: warning: unused variable 'iR' [-Wunused-variable]
     int iR; /* iterator for residue */
         ^
clustal/hhalign_wrapper.c: In function 'ReAttachLeadingGaps':
clustal/hhalign_wrapper.c:239:9: warning: variable 'iSize2' set but not used [-Wunused-but-set-variable]
     int iSize2 = 0; /* #seqs in 2nd profile */
         ^
clustal/hhalign_wrapper.c:238:9: warning: variable 'iSize1' set but not used [-Wunused-but-set-variable]
     int iSize1 = 0; /* #seqs in 1st profile */
         ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c clustal/ktuple_pair.c -o clustal/ktuple_pair.o
In file included from clustal/ktuple_pair.c:29:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
clustal/ktuple_pair.c: In function 'KTuplePairDist':
clustal/ktuple_pair.c:758:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
         #pragma omp critical(ktuple)
 ^
clustal/ktuple_pair.c:801:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
             #pragma omp critical(ktuple)
 ^
clustal/ktuple_pair.c:822:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
     #pragma omp critical(ktuple)
 ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c clustal/list.c -o clustal/list.o
In file included from clustal/list.c:32:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
clustal/list.c: In function 'IntListRemoveNext':
clustal/list.c:248:5: warning: 'piData' may be used uninitialized in this function [-Wmaybe-uninitialized]
     prList->destroy(piData);
     ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c clustal/log.c -o clustal/log.o
In file included from clustal/log.c:22:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c clustal/muscle_upgma.c -o clustal/muscle_upgma.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c clustal/muscle_tree.c -o clustal/muscle_tree.o
clustal/muscle_tree.c:519:1: warning: 'IsEdge' defined but not used [-Wunused-function]
 IsEdge(unsigned uNodeIndex1, unsigned uNodeIndex2, tree_t *tree)
 ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c clustal/mbed.c -o clustal/mbed.o
In file included from clustal/mbed.c:28:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
clustal/mbed.c: In function 'BisectingKmeans':
clustal/mbed.c:786:16: warning: variable 'dCost' set but not used [-Wunused-but-set-variable]
         double dCost = -1.0;
                ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c clustal/pair_dist.c -o clustal/pair_dist.o
In file included from clustal/pair_dist.c:22:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
clustal/pair_dist.c: In function 'SquidIdPairDist':
clustal/pair_dist.c:206:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
         #pragma omp critical(squidid)
 ^
clustal/pair_dist.c:218:0: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
         #pragma omp atomic
 ^
clustal/pair_dist.c:228:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
             #pragma omp critical(squidid)
 ^
clustal/pair_dist.c:177:10: warning: unused variable 'bPrintCR' [-Wunused-variable]
     bool bPrintCR = (rLog.iLogLevelEnabled<=LOG_VERBOSE) ? FALSE : TRUE;
          ^
clustal/pair_dist.c: In function 'PairDistances':
clustal/pair_dist.c:336:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
             #pragma omp parallel for private(iChunk) schedule(dynamic)
 ^
clustal/pair_dist.c:359:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
             #pragma omp parallel for private(iChunk) schedule(dynamic)
 ^
clustal/pair_dist.c:376:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
             #pragma omp parallel for private(iChunk) schedule(dynamic)
 ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c clustal/progress.c -o clustal/progress.o
In file included from clustal/progress.c:22:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c clustal/seq.c -o clustal/seq.o
In file included from clustal/seq.c:30:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
clustal/seq.c: In function 'AliStat':
clustal/seq.c:68:9: warning: unused variable 'iAux' [-Wunused-variable]
     int iAux;
         ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c clustal/symmatrix.c -o clustal/symmatrix.o
In file included from clustal/symmatrix.c:30:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c clustal/tree.c -o clustal/tree.o
In file included from clustal/tree.c:22:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c clustal/util.c -o clustal/util.o
In file included from clustal/util.c:22:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c clustal/weights.c -o clustal/weights.o
In file included from clustal/weights.c:72:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/a2m.c -o squid/a2m.o
In file included from squid/squid.h:32:0,
                 from squid/a2m.c:20:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/aligneval.c -o squid/aligneval.o
In file included from squid/squid.h:32:0,
                 from squid/aligneval.c:59:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/alignio.c -o squid/alignio.o
In file included from squid/squid.h:32:0,
                 from squid/alignio.c:21:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/clustal.c -o squid/clustal.o
In file included from squid/squid.h:32:0,
                 from squid/clustal.c:24:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
squid/clustal.c: In function 'WriteClustal':
squid/clustal.c:214:7: warning: unused variable 'cons' [-Wunused-variable]
   int cons;
       ^
squid/clustal.c: In function 'WriteClustalForR':
squid/clustal.c:438:6: warning: unused variable 'cons' [-Wunused-variable]
  int cons;
      ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/cluster.c -o squid/cluster.o
In file included from squid/squid.h:32:0,
                 from squid/cluster.c:124:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/dayhoff.c -o squid/dayhoff.o
In file included from squid/squid.h:32:0,
                 from squid/dayhoff.c:28:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/eps.c -o squid/eps.o
In file included from squid/squid.h:32:0,
                 from squid/eps.c:23:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/file.c -o squid/file.o
In file included from squid/squid.h:32:0,
                 from squid/file.c:28:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/getopt.c -o squid/getopt.o
In file included from squid/squid.h:32:0,
                 from squid/getopt.c:17:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/gki.c -o squid/gki.o
In file included from squid/squid.h:32:0,
                 from squid/gki.c:82:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/gsi.c -o squid/gsi.o
In file included from squid/squid.h:32:0,
                 from squid/gsi.c:35:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/gsi64.c -o squid/gsi64.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/hsregex.c -o squid/hsregex.o
In file included from squid/squid.h:32:0,
                 from squid/hsregex.c:33:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
squid/hsregex.c: In function 'regbranch':
squid/hsregex.c:499:6: warning: 'flags' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int flags;
      ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/iupac.c -o squid/iupac.o
In file included from squid/squid.h:32:0,
                 from squid/iupac.c:17:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/msa.c -o squid/msa.o
In file included from squid/squid.h:32:0,
                 from squid/msa.c:22:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/msf.c -o squid/msf.o
In file included from squid/squid.h:32:0,
                 from squid/msf.c:25:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
squid/msf.c: In function 'ReadMSF':
squid/msf.c:87:11: warning: variable 'alleged_checksum' set but not used [-Wunused-but-set-variable]
   int     alleged_checksum;
           ^
squid/msf.c:85:11: warning: variable 'alleged_alen' set but not used [-Wunused-but-set-variable]
   int     alleged_alen;
           ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/phylip.c -o squid/phylip.o
In file included from squid/squid.h:32:0,
                 from squid/phylip.c:23:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
squid/phylip.c: In function 'ReadPhylip':
squid/phylip.c:80:15: warning: variable 'alen' set but not used [-Wunused-but-set-variable]
   int   nseq, alen;
               ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/revcomp.c -o squid/revcomp.o
In file included from squid/squid.h:32:0,
                 from squid/revcomp.c:19:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/rk.c -o squid/rk.o
In file included from squid/squid.h:32:0,
                 from squid/rk.c:26:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/selex.c -o squid/selex.o
In file included from squid/squid.h:32:0,
                 from squid/selex.c:43:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/seqencode.c -o squid/seqencode.o
In file included from squid/squid.h:32:0,
                 from squid/seqencode.c:18:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/shuffle.c -o squid/shuffle.o
In file included from squid/squid.h:32:0,
                 from squid/shuffle.c:42:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/sqerror.c -o squid/sqerror.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/sqio.c -o squid/sqio.o
In file included from squid/squid.h:32:0,
                 from squid/sqio.c:57:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/squidcore.c -o squid/squidcore.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/sre_ctype.c -o squid/sre_ctype.o
In file included from squid/squid.h:32:0,
                 from squid/sre_ctype.c:19:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/sre_math.c -o squid/sre_math.o
In file included from squid/squid.h:32:0,
                 from squid/sre_math.c:19:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/sre_random.c -o squid/sre_random.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/sre_string.c -o squid/sre_string.o
In file included from squid/squid.h:32:0,
                 from squid/sre_string.c:23:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/ssi.c -o squid/ssi.o
In file included from squid/squid.h:32:0,
                 from squid/ssi.c:16:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/stack.c -o squid/stack.o
In file included from squid/squid.h:32:0,
                 from squid/stack.c:18:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/stockholm.c -o squid/stockholm.o
In file included from squid/squid.h:32:0,
                 from squid/stockholm.c:31:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/stopwatch.c -o squid/stopwatch.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/translate.c -o squid/translate.o
In file included from squid/squid.h:32:0,
                 from squid/translate.c:19:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/types.c -o squid/types.o
In file included from squid/squid.h:32:0,
                 from squid/types.c:20:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/vectorops.c -o squid/vectorops.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c squid/weight.c -o squid/weight.o
In file included from squid/squid.h:32:0,
                 from squid/weight.c:19:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -std=c++98 -DMATH_H_CLIB -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include   -O2 -Wall  -mtune=core2 -c hhalign/hhalign.cpp -o hhalign/hhalign.o
In file included from hhalign/hhalign.cpp:62:0:
hhalign/util-C.h: In function 'float fast_log2(float)':
hhalign/util-C.h:94:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   int a = (((*((int *)&x)) & 0x7F800000) >>23 )-0x7f;
                         ^
hhalign/util-C.h:95:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   int b =  ((*((int *)&x)) & 0x007FE000) >>13;
                         ^
hhalign/util-C.h:96:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   int c =  ((*((int *)&x)) & 0x00001FFF);
                         ^
hhalign/util-C.h: In function 'float fpow2(float)':
hhalign/util-C.h:111:23: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   int lx = *((int*)&tx) - 0x4b400000;   // integer value of x
                       ^
hhalign/util-C.h: In function 'float fast_pow2(float)':
hhalign/util-C.h:158:35: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
    pow2[b]=(*((unsigned int *)(&f)) & 0x7FFFFF); // store the mantisse of 2^(1+b/1024)
                                   ^
hhalign/util-C.h:202:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   return *((float*)&y);
                      ^
In file included from hhalign/hhalign.cpp:76:0:
hhalign/hhhmm-C.h: In member function 'int HMM::ReadHMMer3(FILE*, char*)':
hhalign/hhhmm-C.h:1141:12: warning: variable 'dAlphaInv' set but not used [-Wunused-but-set-variable]
     double dAlphaInv = 1.00 / (double)(iAlpha); /* weight of AA */
            ^
In file included from hhalign/hhalign.cpp:77:0:
hhalign/hhalignment-C.h: In member function 'void Alignment::Read(FILE*, char*, char*)':
hhalign/hhalignment-C.h:245:32: warning: variable 'ptr2' set but not used [-Wunused-but-set-variable]
                   char *ptr1, *ptr2;
                                ^
hhalign/hhalignment-C.h: In member function 'int Alignment::FilterWithCoreHMM(char*, float, HMM&)':
hhalign/hhalignment-C.h:1429:19: warning: variable 'score_M' set but not used [-Wunused-but-set-variable]
             float score_M=0.0;
                   ^
hhalign/hhalignment-C.h:1430:19: warning: variable 'score_prev' set but not used [-Wunused-but-set-variable]
             float score_prev=0.0;
                   ^
In file included from hhalign/hhalign.cpp:81:0:
hhalign/hhhitlist-C.h: In member function 'void HitList::TransitiveScoring()':
hhalign/hhhitlist-C.h:1259:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
   size_t unused; /* disable fread gcc warning */
          ^
hhalign/hhhitlist-C.h: In member function 'void HitList::TransitiveScoring2()':
hhalign/hhhitlist-C.h:1624:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
   size_t unused; /* disable fread gcc warning */
          ^
hhalign/hhhitlist-C.h: In member function 'void HitList::TransitiveScoring3()':
hhalign/hhhitlist-C.h:1994:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
   size_t unused; /* disable fread gcc warning */
          ^
hhalign/hhhitlist-C.h: In member function 'void HitList::TransitiveScoring4()':
hhalign/hhhitlist-C.h:2359:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
   size_t unused; /* disable fread gcc warning */
          ^
In file included from hhalign/hhalign.cpp:82:0:
hhalign/hhfunc-C.h: In function 'void AddBackgroundFrequencies(float**, float**, float**, int, hmm_light*, char**, char*, int, char*)':
hhalign/hhfunc-C.h:74:9: warning: unused variable 'iT' [-Wunused-variable]
     int iT; /* transition state iterator */
         ^
In file included from hhalign/hhalign.cpp:82:0:
hhalign/hhfunc-C.h:80:11: warning: unused variable 'fGThgiew' [-Wunused-variable]
     float fGThgiew = UNITY - fGWeight; /* weight of 'true' transitions */
           ^
hhalign/hhfunc-C.h:85:11: warning: unused variable 'zf1SeqTrans' [-Wunused-variable]
     float zf1SeqTrans[] = {0.98, 0.01, 0.01, 0.25, 0.75, 0.25, 0.75};
           ^
hhalign/hhfunc-C.h:86:11: warning: unused variable 'zf1SeqInit' [-Wunused-variable]
     float zf1SeqInit[]  = {0.98, 0.01, 0.01, 0.99, 0.01, 0.99, 0.01};
           ^
hhalign/hhfunc-C.h:87:11: warning: unused variable 'zf1SeqDel' [-Wunused-variable]
     float zf1SeqDel[]   = {0.24, 0.01, 0.75, 0.01, 0.01, 0.01, 0.01};
           ^
hhalign/hhfunc-C.h:88:11: warning: unused variable 'zf1SeqRevrt' [-Wunused-variable]
     float zf1SeqRevrt[] = {0.98, 0.01, 0.01, 0.01, 0.01, 0.99, 0.01};
           ^
hhalign/hhfunc-C.h: In function 'int ReadAndPrepare(int, char**, int, hmm_light*, char*, char*, double*, char*, HMM&, Alignment*)':
hhalign/hhfunc-C.h:328:17: warning: unused variable 'NEFF_SCORE' [-Wunused-variable]
       const int NEFF_SCORE = 10; /* FIXME: Magic Number */
                 ^
hhalign/hhfunc-C.h:511:17: warning: unused variable 'NEFF_SCORE' [-Wunused-variable]
       const int NEFF_SCORE = 10; /* FIXME: Magic Number */
                 ^
hhalign/hhalign.cpp: In function 'int hhalign(char**, int, double*, char**, int, double*, double*, hmm_light*, char*, char*, char*, char*, hhalign_para, hhalign_scores*, int, int, char*, char*)':
hhalign/hhalign.cpp:721:9: warning: variable 'Nali' set but not used [-Wunused-but-set-variable]
     int Nali;                    /* number of normally backtraced alignments 
         ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -std=c++98 -DMATH_H_CLIB -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include   -O2 -Wall  -mtune=core2 -c RClustalOmega.cpp -o RClustalOmega.o
In file included from RClustalOmega.cpp:27:0:
config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c mymain.c -o mymain.o
In file included from mymain.c:22:0:
config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O3 -Wall  -std=gnu99 -mtune=core2 -c clustal-omega.c -o clustal-omega.o
In file included from clustal-omega.c:22:0:
config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ClustalOmega.dll tmp.def exceptions4c/e4c_lite.o argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o clustal/tree.o clustal/util.o clustal/weights.o squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o squid/types.o squid/vectorops.o squid/weight.o hhalign/hhalign.o RClustalOmega.o mymain.o clustal-omega.o -L../../gc-7.2 -lgccpp72 -lgc72 -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
make[2]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpeaNGby/R.INSTALLbf03a843fd6/msa/src/ClustalOmega/src'
make[1]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpeaNGby/R.INSTALLbf03a843fd6/msa/src/ClustalOmega'
----------------------------------------
------------- ClustalOmega -------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o msa.dll tmp.def R_init_msa.o SplitCharVector2List.o SplitCharVector2Matrix.o -Wl,--whole-archive ./libGC.a ./libMuscle.a ./libClustalW.a ./libClustalOmega.a -Wl,--no-whole-archive -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/msa.buildbin-libdir/msa/libs/i386
** R
** 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 'msa' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src"   -O2 -Wall  -mtune=core2 -c R_init_msa.cpp -o R_init_msa.o
In file included from ./Muscle/muscle.h:38:0,
                 from ./Muscle/RMuscle.h:4,
                 from R_init_msa.cpp:3:
./Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src"   -O2 -Wall  -mtune=core2 -c SplitCharVector2List.cpp -o SplitCharVector2List.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src"   -O2 -Wall  -mtune=core2 -c SplitCharVector2Matrix.cpp -o SplitCharVector2Matrix.o
make --file=msaMakefile.win --directory=gc-7.2
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpqkfLZc/R.INSTALL219820462db7/msa/src/gc-7.2'
export PKG_LIBS=" -Ilibatomic_ops/src -Iinclude -Iinclude/private"; \
export PKG_CFLAGS=" -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private"; \
export PKG_CXXFLAGS=" -DALL_INTERIOR_POINTERS -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private"; \
C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64/R.exe CMD SHLIB -o gc72.dll *.c; \
C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64/R.exe CMD SHLIB -o gccpp72.dll -L. -lgc72 *.cpp; \
ar rcs libGC.a allchblk.o alloc.o backgraph.o blacklst.o checksums.o darwin_stop_world.o dbg_mlc.o dyn_load.o finalize.o gcj_mlc.o gc_dlopen.o headers.o mach_dep.o malloc.o mallocx.o mark.o mark_rts.o misc.o new_hblk.o obj_map.o os_dep.o pcr_interface.o pthread_start.o pthread_stop_world.o pthread_support.o ptr_chck.o real_malloc.o reclaim.o specific.o stubborn.o thread_local_alloc.o typd_mlc.o win32_threads.o; \
ar rcs libGCcpp.a gc_cpp.o; \
cp libGC*.a ../
make[2]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpqkfLZc/R.INSTALL219820462db7/msa/src/gc-7.2'
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c allchblk.c -o allchblk.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c alloc.c -o alloc.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c backgraph.c -o backgraph.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c blacklst.c -o blacklst.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c checksums.c -o checksums.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c darwin_stop_world.c -o darwin_stop_world.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c dbg_mlc.c -o dbg_mlc.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c dyn_load.c -o dyn_load.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c finalize.c -o finalize.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c gc_dlopen.c -o gc_dlopen.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c gcj_mlc.c -o gcj_mlc.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c headers.c -o headers.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c mach_dep.c -o mach_dep.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c malloc.c -o malloc.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c mallocx.c -o mallocx.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c mark.c -o mark.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c mark_rts.c -o mark_rts.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c misc.c -o misc.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c new_hblk.c -o new_hblk.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c obj_map.c -o obj_map.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c os_dep.c -o os_dep.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c pcr_interface.c -o pcr_interface.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c pthread_start.c -o pthread_start.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c pthread_stop_world.c -o pthread_stop_world.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c pthread_support.c -o pthread_support.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c ptr_chck.c -o ptr_chck.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c real_malloc.c -o real_malloc.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c reclaim.c -o reclaim.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c specific.c -o specific.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c stubborn.c -o stubborn.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c thread_local_alloc.c -o thread_local_alloc.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c typd_mlc.c -o typd_mlc.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -std=gnu99 -mtune=core2 -c win32_threads.c -o win32_threads.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o gc72.dll tmp.def allchblk.o alloc.o backgraph.o blacklst.o checksums.o darwin_stop_world.o dbg_mlc.o dyn_load.o finalize.o gc_dlopen.o gcj_mlc.o headers.o mach_dep.o malloc.o mallocx.o mark.o mark_rts.o misc.o new_hblk.o obj_map.o os_dep.o pcr_interface.o pthread_start.o pthread_stop_world.o pthread_support.o ptr_chck.o real_malloc.o reclaim.o specific.o stubborn.o thread_local_alloc.o typd_mlc.o win32_threads.o -Ilibatomic_ops/src -Iinclude -Iinclude/private -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
make[2]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpqkfLZc/R.INSTALL219820462db7/msa/src/gc-7.2'
make[2]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpqkfLZc/R.INSTALL219820462db7/msa/src/gc-7.2'
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DALL_INTERIOR_POINTERS -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -Ilibatomic_ops/src -Iinclude -Iinclude/private   -O2 -Wall  -mtune=core2 -c gc_cpp.cc -o gc_cpp.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o gccpp72.dll tmp.def gc_cpp.o -L. -lgc72 -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
make[2]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpqkfLZc/R.INSTALL219820462db7/msa/src/gc-7.2'
make[1]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpqkfLZc/R.INSTALL219820462db7/msa/src/gc-7.2'
----------------------------------------
------------------ GC  -----------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile.win --directory=Muscle
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpqkfLZc/R.INSTALL219820462db7/msa/src/Muscle'
export PKG_LIBS=" -L"../gc-7.2/" -lgc72 -lgccpp72"
export PKG_CXXFLAGS="-c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1  -I../gc-7.2/include/"
C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64/R.exe CMD SHLIB -o Muscle.dll aligngivenpath.cpp aligngivenpathsw.cpp aligntwomsas.cpp aligntwoprofs.cpp aln.cpp alpha.cpp anchors.cpp bittraceback.cpp blosum62.cpp blosumla.cpp clust.cpp cluster.cpp clwwt.cpp color.cpp cons.cpp diaglist.cpp diffobjscore.cpp diffpaths.cpp difftrees.cpp difftreese.cpp distcalc.cpp distfunc.cpp distpwkimura.cpp domuscle.cpp dosp.cpp dpreglist.cpp drawtree.cpp edgelist.cpp enumopts.cpp enumtostr.cpp estring.cpp fasta.cpp fasta2.cpp fastclust.cpp fastdist.cpp fastdistjones.cpp fastdistkbit.cpp fastdistkmer.cpp fastdistmafft.cpp fastdistnuc.cpp fastscorepath2.cpp finddiags.cpp finddiagsn.cpp glbalign.cpp glbalign352.cpp glbaligndiag.cpp glbalignle.cpp glbalignsimple.cpp glbalignsp.cpp glbalignspn.cpp glbalignss.cpp glbalndimer.cpp globals.cpp globalslinux.cpp globalsosx.cpp globalsother.cpp globalswin32.cpp gonnet.cpp henikoffweight.cpp henikoffweightpb.cpp html.cpp hydro.cpp intmath.cpp local.cpp main.cpp makerootmsa.cpp makerootmsab.cpp maketree.cpp mhack.cpp mpam200.cpp msa.cpp msa2.cpp msadistkimura.cpp msf.cpp muscle.cpp muscleout.cpp nucmx.cpp nwdasimple.cpp nwdasimple2.cpp nwdasmall.cpp nwrec.cpp nwsmall.cpp objscore.cpp objscore2.cpp objscoreda.cpp onexception.cpp options.cpp outweights.cpp pam200mafft.cpp params.cpp phy.cpp phy2.cpp phy3.cpp phy4.cpp phyfromclust.cpp phyfromfile.cpp physeq.cpp phytofile.cpp posgap.cpp ppscore.cpp profdb.cpp profile.cpp profilefrommsa.cpp progalign.cpp progress.cpp progressivealign.cpp pwpath.cpp readmx.cpp realigndiffs.cpp realigndiffse.cpp refine.cpp refinehoriz.cpp refinesubfams.cpp refinetree.cpp refinetreee.cpp refinevert.cpp refinew.cpp savebest.cpp scoredist.cpp scoregaps.cpp scorehistory.cpp scorepp.cpp seq.cpp seqvect.cpp setblosumweights.cpp setgscweights.cpp setnewhandler.cpp spfast.cpp sptest.cpp stabilize.cpp subfam.cpp subfams.cpp sw.cpp termgaps.cpp textfile.cpp threewaywt.cpp tomhydro.cpp traceback.cpp tracebackopt.cpp tracebacksw.cpp treefrommsa.cpp typetostr.cpp upgma2.cpp usage.cpp validateids.cpp vtml2.cpp writescorefile.cpp RMuscle.cpp
make[2]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpqkfLZc/R.INSTALL219820462db7/msa/src/Muscle'
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const unsigned uLengthA = msaA.GetColCount();
                 ^
aligngivenpath.cpp:187:17: warning: unused variable 'uLengthB' [-Wunused-variable]
  const unsigned uLengthB = msaB.GetColCount();
                 ^
aligngivenpath.cpp: In function 'void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)':
aligngivenpath.cpp:335:19: warning: unused variable 'uColA' [-Wunused-variable]
    const unsigned uColA = uPrefixLengthA - 1;
                   ^
aligngivenpath.cpp:336:19: warning: unused variable 'uColB' [-Wunused-variable]
    const unsigned uColB = uPrefixLengthB - 1;
                   ^
aligngivenpath.cpp:346:19: warning: unused variable 'uColA' [-Wunused-variable]
    const unsigned uColA = uPrefixLengthA - 1;
                   ^
aligngivenpath.cpp:354:19: warning: unused variable 'uColB' [-Wunused-variable]
    const unsigned uColB = uPrefixLengthB - 1;
                   ^
In file included from muscle.h:38:0,
                 from aligngivenpath.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const unsigned uLengthA = msaA.GetColCount();
                 ^
aligngivenpathsw.cpp:59:17: warning: unused variable 'uLengthB' [-Wunused-variable]
  const unsigned uLengthB = msaB.GetColCount();
                 ^
aligngivenpathsw.cpp: In function 'void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)':
aligngivenpathsw.cpp:204:19: warning: unused variable 'uColA' [-Wunused-variable]
    const unsigned uColA = uPrefixLengthA - 1;
                   ^
aligngivenpathsw.cpp:205:19: warning: unused variable 'uColB' [-Wunused-variable]
    const unsigned uColB = uPrefixLengthB - 1;
                   ^
aligngivenpathsw.cpp:215:19: warning: unused variable 'uColA' [-Wunused-variable]
    const unsigned uColA = uPrefixLengthA - 1;
                   ^
aligngivenpathsw.cpp:223:19: warning: unused variable 'uColB' [-Wunused-variable]
    const unsigned uColB = uPrefixLengthB - 1;
                   ^
In file included from muscle.h:38:0,
                 from aligngivenpathsw.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c aligntwomsas.cpp -o aligntwomsas.o
In file included from aligntwomsas.cpp:6:0:
timing.h:5:0: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(disable:4035)
 ^
In file included from muscle.h:38:0,
                 from aligntwomsas.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
In file included from aligntwomsas.cpp:6:0:
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
 static double TicksToSecs(TICKS t)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c aligntwoprofs.cpp -o aligntwoprofs.o
In file included from muscle.h:38:0,
                 from aligntwoprofs.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c aln.cpp -o aln.o
In file included from muscle.h:38:0,
                 from aln.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  switch (Alpha)
         ^
In file included from muscle.h:38:0,
                 from alpha.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
    unsigned uWindowCenter = uBestColIndex + uWindowLength/2;
             ^
In file included from muscle.h:38:0,
                 from anchors.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
anchors.cpp:53:13: warning: 'void FindBestColsGrade(const SCORE*, unsigned int, double, unsigned int*, unsigned int*)' defined but not used [-Wunused-function]
 static void FindBestColsGrade(const SCORE Score[], unsigned uCount,
             ^
anchors.cpp:105:13: warning: 'void ListBestCols(const MSA&, const SCORE*, const SCORE*, unsigned int*, unsigned int)' defined but not used [-Wunused-function]
 static void ListBestCols(const MSA &msa, const SCORE Score[], const SCORE SmoothScore[],
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  char Bits = TraceBack[uLengthA][uLengthB];
       ^
In file included from muscle.h:38:0,
                 from bittraceback.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
bittraceback.cpp:15:20: warning: 'const char* BitsToStr(char)' defined but not used [-Wunused-function]
 static const char *BitsToStr(char Bits)
                    ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c blosum62.cpp -o blosum62.o
In file included from muscle.h:38:0,
                 from blosum62.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c blosumla.cpp -o blosumla.o
In file included from muscle.h:38:0,
                 from blosumla.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
blosumla.cpp:7:14: warning: 'Blosum62LA' defined but not used [-Wunused-variable]
 static float Blosum62LA[20][20] =
              ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  switch (m_JoinStyle)
         ^
clust.cpp: In member function 'void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)':
clust.cpp:184:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
  const unsigned uClusterCount = GetClusterCount();
                 ^
clust.cpp: In member function 'void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)':
clust.cpp:204:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
  const unsigned uClusterCount = GetClusterCount();
                 ^
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]
  switch (m_CentroidStyle)
         ^
clust.cpp: In member function 'float Clust::ComputeDistMAFFT(unsigned int, unsigned int)':
clust.cpp:360:14: warning: unused variable 'dDistLR' [-Wunused-variable]
  const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex);
              ^
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]
  switch (m_JoinStyle)
         ^
In file included from muscle.h:38:0,
                 from clust.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
   bool bFound = false;
        ^
cluster.cpp:267:9: warning: unused variable 'dMaxDist' [-Wunused-variable]
  double dMaxDist = 0.0;
         ^
cluster.cpp:308:47: warning: 'uIndexClosest2' may be used uninitialized in this function [-Wmaybe-uninitialized]
   ClusterNode &Child2 = m_Nodes[uIndexClosest2];
                                               ^
cluster.cpp:307:47: warning: 'uIndexClosest1' may be used uninitialized in this function [-Wmaybe-uninitialized]
   ClusterNode &Child1 = m_Nodes[uIndexClosest1];
                                               ^
In file included from muscle.h:38:0,
                 from cluster.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c clwwt.cpp -o clwwt.o
In file included from muscle.h:38:0,
                 from clwwt.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c color.cpp -o color.o
In file included from muscle.h:38:0,
                 from color.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
color.cpp:72:12: warning: 'int BlosumScore(char, char)' defined but not used [-Wunused-function]
 static int BlosumScore(char c1, char c2)
            ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c cons.cpp -o cons.o
In file included from muscle.h:38:0,
                 from cons.cpp:7:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c diaglist.cpp -o diaglist.o
diaglist.cpp: In member function 'void DiagList::FromPath(const PWPath&)':
diaglist.cpp:20:29: warning: 'uStartPosB' may be used uninitialized in this function [-Wmaybe-uninitialized]
  d.m_uStartPosB = uStartPosB;
                             ^
diaglist.cpp:52:11: note: 'uStartPosB' was declared here
  unsigned uStartPosB;
           ^
diaglist.cpp:19:29: warning: 'uStartPosA' may be used uninitialized in this function [-Wmaybe-uninitialized]
  d.m_uStartPosA = uStartPosA;
                             ^
diaglist.cpp:51:11: note: 'uStartPosA' was declared here
  unsigned uStartPosA;
           ^
In file included from muscle.h:38:0,
                 from diaglist.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const unsigned uSeqCount = msa.GetSeqCount();
                 ^
diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable]
  const unsigned uColCount = msa.GetColCount();
                 ^
In file included from muscle.h:38:0,
                 from diffobjscore.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c diffpaths.cpp -o diffpaths.o
In file included from muscle.h:38:0,
                 from diffpaths.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const unsigned uLeafCount2 = Tree2.GetLeafCount();
                 ^
In file included from muscle.h:38:0,
                 from difftrees.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c difftreese.cpp -o difftreese.o
In file included from muscle.h:38:0,
                 from difftreese.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c distcalc.cpp -o distcalc.o
In file included from muscle.h:38:0,
                 from distcalc.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c distfunc.cpp -o distfunc.o
In file included from muscle.h:38:0,
                 from distfunc.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c distpwkimura.cpp -o distpwkimura.o
In file included from muscle.h:38:0,
                 from distpwkimura.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c domuscle.cpp -o domuscle.o
In file included from domuscle.cpp:9:0:
timing.h:5:0: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(disable:4035)
 ^
domuscle.cpp: In function 'void DoMuscle(MuscleInput*, MuscleOutput*)':
domuscle.cpp:180:6: warning: unused variable 'PNlength' [-Wunused-variable]
  int PNlength = (msaInput->inputSeqs).Length();
      ^
In file included from muscle.h:38:0,
                 from RMuscle.h:4,
                 from domuscle.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
In file included from domuscle.cpp:9:0:
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
 static double TicksToSecs(TICKS t)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c dosp.cpp -o dosp.o
In file included from muscle.h:38:0,
                 from dosp.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
    const unsigned uDiagLengthMinusCaps = uEndVertexA - uStartVertexA - 1;
                   ^
In file included from muscle.h:38:0,
                 from dpreglist.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c drawtree.cpp -o drawtree.o
In file included from muscle.h:38:0,
                 from drawtree.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c edgelist.cpp -o edgelist.o
In file included from muscle.h:38:0,
                 from edgelist.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c enumopts.cpp -o enumopts.o
In file included from muscle.h:38:0,
                 from enumopts.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c enumtostr.cpp -o enumtostr.o
In file included from muscle.h:38:0,
                 from enumtostr.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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:424:21: warning: 'cType' may be used uninitialized in this function [-Wmaybe-uninitialized]
   Edge.cType = cType;
                     ^
In file included from muscle.h:38:0,
                 from estring.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
estring.cpp:464:13: warning: 'bool CanMultiplyEstrings(const short int*, const short int*)' defined but not used [-Wunused-function]
 static bool CanMultiplyEstrings(const short es1[], const short es2[])
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  unsigned uSeqCount = 0;
           ^
fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable]
  unsigned uColCount = uInsane;
           ^
In file included from muscle.h:38:0,
                 from fasta.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c fasta2.cpp -o fasta2.o
In file included from muscle.h:38:0,
                 from fasta2.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c fastclust.cpp -o fastclust.o
In file included from muscle.h:38:0,
                 from fastclust.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c fastdist.cpp -o fastdist.o
In file included from muscle.h:38:0,
                 from fastdist.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistjones.cpp -o fastdistjones.o
In file included from muscle.h:38:0,
                 from fastdistjones.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistkbit.cpp -o fastdistkbit.o
In file included from muscle.h:38:0,
                 from fastdistkbit.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
    double KD = KimuraDist(EstimatedPctId);
           ^
In file included from muscle.h:38:0,
                 from fastdistkmer.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistmafft.cpp -o fastdistmafft.o
fastdistmafft.cpp: In function 'void DistKmer6_6(const SeqVect&, DistFunc&)':
fastdistmafft.cpp:239:15: warning: unused variable 'pName1' [-Wunused-variable]
   const char *pName1 = s1.GetName();
               ^
In file included from muscle.h:38:0,
                 from fastdistmafft.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
fastdistmafft.cpp:104:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function]
 static void ListCount(const unsigned char Count[])
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
   const char *pName1 = s1.GetName();
               ^
In file included from muscle.h:38:0,
                 from fastdistnuc.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
fastdistnuc.cpp:33:17: warning: 'uResidueGroupCount' defined but not used [-Wunused-variable]
 static unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]);
                 ^
fastdistnuc.cpp:85:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function]
 static void ListCount(const unsigned char Count[])
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c fastscorepath2.cpp -o fastscorepath2.o
In file included from muscle.h:38:0,
                 from fastscorepath2.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c finddiags.cpp -o finddiags.o
In file included from muscle.h:38:0,
                 from finddiags.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
finddiags.cpp:11:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function]
 static char *TupleToStr(int t)
              ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c finddiagsn.cpp -o finddiagsn.o
finddiagsn.cpp: In function 'char* TupleToStr(int)':
finddiagsn.cpp:16:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < K; ++i)
                    ^
In file included from muscle.h:38:0,
                 from finddiagsn.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
finddiagsn.cpp:12:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function]
 static char *TupleToStr(int t)
              ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c glbalign.cpp -o glbalign.o
In file included from glbalign.cpp:3:0:
timing.h:5:0: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(disable:4035)
 ^
In file included from muscle.h:38:0,
                 from glbalign.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
In file included from glbalign.cpp:3:0:
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
 static double TicksToSecs(TICKS t)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c glbalign352.cpp -o glbalign352.o
In file included from glbalign352.cpp:3:0:
timing.h:5:0: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(disable:4035)
 ^
In file included from muscle.h:38:0,
                 from glbalign352.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
In file included from glbalign352.cpp:3:0:
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
 static double TicksToSecs(TICKS t)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c glbaligndiag.cpp -o glbaligndiag.o
In file included from glbaligndiag.cpp:6:0:
timing.h:5:0: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(disable:4035)
 ^
In file included from muscle.h:38:0,
                 from glbaligndiag.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
In file included from glbaligndiag.cpp:6:0:
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
 static double TicksToSecs(TICKS t)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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:431:33: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
   iTraceBack = (int) uInsertPos - (int) uLengthB;
                                 ^
In file included from muscle.h:38:0,
                 from glbalignle.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignsimple.cpp -o glbalignsimple.o
In file included from muscle.h:38:0,
                 from glbalignsimple.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
glbalignsimple.cpp:28:13: warning: 'void ListTB(const char*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static void ListTB(const char *TBM_, const ProfPos *PA, const ProfPos *PB,
             ^
glbalignsimple.cpp:52:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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:366:33: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
   iTraceBack = (int) uInsertPos - (int) uLengthB;
                                 ^
glbalignsp.cpp:305:41: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ptrTraceBack_ij = (int) uInsertPos - (int) j;
                                         ^
In file included from muscle.h:38:0,
                 from glbalignsp.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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:401:33: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
   iTraceBack = (int) uInsertPos - (int) uLengthB;
                                 ^
glbalignspn.cpp:340:41: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ptrTraceBack_ij = (int) uInsertPos - (int) j;
                                         ^
In file included from muscle.h:38:0,
                 from glbalignspn.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
   const SCORE *ptrRowA = MxRowA[i];
                ^
glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable]
  const unsigned uPrefixCountA = uLengthA + 1;
                 ^
glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
  const unsigned uPrefixCountB = uLengthB + 1;
                 ^
glbalignss.cpp:310:33: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
   iTraceBack = (int) uInsertPos - (int) uLengthB;
                                 ^
glbalignss.cpp:252:41: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ptrTraceBack_ij = (int) uInsertPos - (int) j;
                                         ^
In file included from muscle.h:38:0,
                 from glbalignss.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
glbalignss.cpp:11:14: warning: 'SCORE Subst(const Seq&, const Seq&, unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static SCORE Subst(const Seq &seqA, const Seq &seqB, unsigned i, unsigned j)
              ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  switch (g_PPScore)
         ^
glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_SPN' not handled in switch [-Wswitch]
In file included from muscle.h:38:0,
                 from glbalndimer.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
glbalndimer.cpp:14:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function]
 static const char *LocalScoreToStr(SCORE s)
                    ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c globals.cpp -o globals.o
In file included from muscle.h:38:0,
                 from globals.cpp:6:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c globalslinux.cpp -o globalslinux.o
In file included from muscle.h:38:0,
                 from globalslinux.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c globalsosx.cpp -o globalsosx.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c globalsother.cpp -o globalsother.o
In file included from muscle.h:38:0,
                 from globalsother.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c globalswin32.cpp -o globalswin32.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c gonnet.cpp -o gonnet.o
In file included from muscle.h:38:0,
                 from gonnet.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
gonnet.cpp:137:14: warning: 'Gonnet160' defined but not used [-Wunused-variable]
 static SCORE Gonnet160[20][20] =
              ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c henikoffweight.cpp -o henikoffweight.o
In file included from muscle.h:38:0,
                 from henikoffweight.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c henikoffweightpb.cpp -o henikoffweightpb.o
In file included from muscle.h:38:0,
                 from henikoffweightpb.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c html.cpp -o html.o
In file included from muscle.h:38:0,
                 from html.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c hydro.cpp -o hydro.o
In file included from muscle.h:38:0,
                 from hydro.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c intmath.cpp -o intmath.o
In file included from muscle.h:38:0,
                 from intmath.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c local.cpp -o local.o
In file included from muscle.h:38:0,
                 from local.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c main.cpp -o main.o
In file included from muscle.h:38:0,
                 from main.cpp:3:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const unsigned uSeqLength = s.Length();
                 ^
makerootmsa.cpp: In function 'short int* MakeRootSeqE(const Seq&, const Tree&, unsigned int, const ProgNode*, Seq&, short int*, short int*)':
makerootmsa.cpp:94:17: warning: unused variable 'Path' [-Wunused-variable]
   const PWPath &Path = Nodes[uNodeIndex].m_Path;
                 ^
makerootmsa.cpp: In function 'void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)':
makerootmsa.cpp:168:17: warning: unused variable 'uTreeNodeCount' [-Wunused-variable]
  const unsigned uTreeNodeCount = GuideTree.GetNodeCount();
                 ^
In file included from muscle.h:38:0,
                 from makerootmsa.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
makerootmsa.cpp:12:13: warning: 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)' defined but not used [-Wunused-function]
 static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut)
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c makerootmsab.cpp -o makerootmsab.o
In file included from muscle.h:38:0,
                 from makerootmsab.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c maketree.cpp -o maketree.o
In file included from muscle.h:38:0,
                 from maketree.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c mhack.cpp -o mhack.o
In file included from muscle.h:38:0,
                 from mhack.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c mpam200.cpp -o mpam200.o
In file included from muscle.h:38:0,
                 from mpam200.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c msa.cpp -o msa.o
In file included from muscle.h:38:0,
                 from msa.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
msa.cpp:385:13: warning: 'void FmtChar(char, unsigned int)' defined but not used [-Wunused-function]
 static void FmtChar(char c, unsigned uWidth)
             ^
msa.cpp:392:13: warning: 'void FmtInt(unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static void FmtInt(unsigned u, unsigned uWidth)
             ^
msa.cpp:407:13: warning: 'void FmtInt0(unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static void FmtInt0(unsigned u, unsigned uWidth)
             ^
msa.cpp:419:13: warning: 'void FmtPad(unsigned int)' defined but not used [-Wunused-function]
 static void FmtPad(unsigned n)
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  switch (Method)
         ^
msa2.cpp: In function 'void MSAAppend(MSA&, const MSA&)':
msa2.cpp:476:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
  const unsigned uColCountCat = uColCount1 + uColCount2;
                 ^
In file included from muscle.h:38:0,
                 from msa2.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c msadistkimura.cpp -o msadistkimura.o
In file included from muscle.h:38:0,
                 from msadistkimura.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c msf.cpp -o msf.o
In file included from muscle.h:38:0,
                 from msf.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
msf.cpp:24:20: warning: 'const char* strfind(const char*, const char*)' defined but not used [-Wunused-function]
 static const char *strfind(const char *s, const char *t)
                    ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c muscle.cpp -o muscle.o
In file included from muscle.h:38:0,
                 from muscle.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c muscleout.cpp -o muscleout.o
In file included from muscle.h:38:0,
                 from muscleout.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c nucmx.cpp -o nucmx.o
In file included from muscle.h:38:0,
                 from nucmx.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c nwdasimple.cpp -o nwdasimple.o
In file included from muscle.h:38:0,
                 from nwdasimple.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c nwdasimple2.cpp -o nwdasimple2.o
In file included from muscle.h:38:0,
                 from nwdasimple2.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c nwdasmall.cpp -o nwdasmall.o
In file included from muscle.h:38:0,
                 from nwdasmall.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c nwrec.cpp -o nwrec.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c nwsmall.cpp -o nwsmall.o
In file included from muscle.h:38:0,
                 from nwsmall.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c objscore.cpp -o objscore.o
In file included from objscore.cpp:5:0:
timing.h:5:0: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(disable:4035)
 ^
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]
  switch (OS)
         ^
objscore.cpp:31:9: warning: enumeration value 'OBJSCORE_SPM' not handled in switch [-Wswitch]
In file included from muscle.h:38:0,
                 from objscore.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
In file included from objscore.cpp:5:0:
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
 static double TicksToSecs(TICKS t)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  switch (g_TermGaps)
         ^
objscore2.cpp: In function 'SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)':
objscore2.cpp:62:8: warning: unused variable 'scoreGaps' [-Wunused-variable]
  SCORE scoreGaps = 0;
        ^
objscore2.cpp:63:7: warning: unused variable 'bGapping1' [-Wunused-variable]
  bool bGapping1 = false;
       ^
objscore2.cpp:64:7: warning: unused variable 'bGapping2' [-Wunused-variable]
  bool bGapping2 = false;
       ^
objscore2.cpp:67:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
  bool bLeftTermGap = false;
       ^
objscore2.cpp:82:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
  bool bRightTermGap = false;
       ^
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]
  bool bLeftTermGap = false;
       ^
objscore2.cpp:155:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
  bool bRightTermGap = false;
       ^
objscore2.cpp: In function 'SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)':
objscore2.cpp:314:17: warning: unused variable 'uColCount2' [-Wunused-variable]
  const unsigned uColCount2 = msa2.GetColCount();
                 ^
objscore2.cpp: In function 'SCORE ObjScoreXP(const MSA&, const MSA&)':
objscore2.cpp:493:17: warning: unused variable 'w' [-Wunused-variable]
    const WEIGHT w = w1*w2;
                 ^
In file included from muscle.h:38:0,
                 from objscore2.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c objscoreda.cpp -o objscoreda.o
In file included from muscle.h:38:0,
                 from objscoreda.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c onexception.cpp -o onexception.o
In file included from muscle.h:38:0,
                 from onexception.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c options.cpp -o options.o
In file included from muscle.h:38:0,
                 from options.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c outweights.cpp -o outweights.o
In file included from muscle.h:38:0,
                 from outweights.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pam200mafft.cpp -o pam200mafft.o
In file included from muscle.h:38:0,
                 from pam200mafft.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
pam200mafft.cpp:6:14: warning: 'PAM200' defined but not used [-Wunused-variable]
 static float PAM200[23][23] =
              ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c params.cpp -o params.o
params.cpp: In function 'void SetPPScore(bool)':
params.cpp:441:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
  switch (g_PPScore)
         ^
In file included from muscle.h:38:0,
                 from params.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  double dEdgeLength = GetEdgeLength(uNode1, uNode2);
         ^
In file included from muscle.h:38:0,
                 from phy.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c phy2.cpp -o phy2.o
In file included from muscle.h:38:0,
                 from phy2.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const double dThisDist = tree.GetEdgeLength(uNode1, uNode2);
               ^
phy3.cpp: In function 'void FindRoot(const Tree&, unsigned int*, unsigned int*, double*, double*, ROOT)':
phy3.cpp:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable]
  const unsigned uLeafCount = tree.GetLeafCount();
                 ^
phy3.cpp:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable]
  double dAllMaxDist = -1e20;
         ^
phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable]
  unsigned uMaxFrom = NULL_NEIGHBOR;
           ^
phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable]
  unsigned uMaxTo = NULL_NEIGHBOR;
           ^
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]
  unsigned uMostDistantLeaf = NULL_NEIGHBOR;
           ^
In file included from muscle.h:38:0,
                 from phy3.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
phy3.cpp:45:13: warning: 'void ListEIs(EdgeInfo**, unsigned int)' defined but not used [-Wunused-function]
 static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount)
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c phy4.cpp -o phy4.o
In file included from muscle.h:38:0,
                 from phy4.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c phyfromclust.cpp -o phyfromclust.o
In file included from muscle.h:38:0,
                 from phyfromclust.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c phyfromfile.cpp -o phyfromfile.o
In file included from muscle.h:38:0,
                 from phyfromfile.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c physeq.cpp -o physeq.o
physeq.cpp: In member function 'void MSA::ToPhySequentialFile(TextFile&) const':
physeq.cpp:60:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Col == ColCount)
             ^
physeq.cpp:71:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if (Col == ColCount)
            ^
physeq.cpp: In member function 'void MSA::ToPhyInterleavedFile(TextFile&) const':
physeq.cpp:112:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Col == ColCount)
             ^
physeq.cpp:124:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (Col == ColCount)
           ^
In file included from muscle.h:38:0,
                 from physeq.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c phytofile.cpp -o phytofile.o
In file included from muscle.h:38:0,
                 from phytofile.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c posgap.cpp -o posgap.o
In file included from muscle.h:38:0,
                 from posgap.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c ppscore.cpp -o ppscore.o
In file included from muscle.h:38:0,
                 from ppscore.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
   switch(m_Distance)
         ^
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]
In file included from muscle.h:38:0,
                 from profdb.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c profile.cpp -o profile.o
In file included from muscle.h:38:0,
                 from profile.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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:131:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (-1 == PP.m_uResidueGroup)
          ^
profilefrommsa.cpp: In function 'unsigned int ResidueGroupFromFCounts(const FCOUNT*)':
profilefrommsa.cpp:230:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
  switch (g_Alpha)
         ^
profilefrommsa.cpp: In function 'ProfPos* ProfileFromMSA(const MSA&)':
profilefrommsa.cpp:245:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
  const unsigned uSeqCount = a.GetSeqCount();
                 ^
profilefrommsa.cpp:253:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable]
  unsigned uHydrophobicRunLength = 0;
           ^
In file included from muscle.h:38:0,
                 from profilefrommsa.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
profilefrommsa.cpp:15:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function]
 static const char *LocalScoreToStr(SCORE s)
                    ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const unsigned uIterCount = uSeqCount - 1;
                 ^
In file included from muscle.h:38:0,
                 from progalign.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c progress.cpp -o progress.o
In file included from muscle.h:38:0,
                 from progress.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c progressivealign.cpp -o progressivealign.o
In file included from muscle.h:38:0,
                 from progressivealign.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwpath.cpp -o pwpath.o
pwpath.cpp: In member function 'void PWPath::Validate() const':
pwpath.cpp:80:16: warning: unused variable 'LastEdge' [-Wunused-variable]
  const PWEdge &LastEdge = GetEdge(uEdgeCount - 1);
                ^
pwpath.cpp: In member function 'void PWPath::FromFile(TextFile&)':
pwpath.cpp:213:11: warning: unused variable 'uEdgeIndex' [-Wunused-variable]
  unsigned uEdgeIndex = 0;
           ^
In file included from muscle.h:38:0,
                 from pwpath.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c readmx.cpp -o readmx.o
readmx.cpp: In function 'float (* ReadMx(TextFile&))[32][32]':
readmx.cpp:83:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < MAX_ALPHA; ++i)
                    ^
readmx.cpp:84:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int j = 0; j < MAX_ALPHA; ++j)
                     ^
readmx.cpp: In function 'float (* ReadMxFromR(std::vector<std::basic_string<char> >, float (*)[32]))[32][32]':
readmx.cpp:184:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < MAX_ALPHA; ++i)
                    ^
readmx.cpp:185:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int j = 0; j < MAX_ALPHA; ++j)
                     ^
In file included from muscle.h:38:0,
                 from readmx.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
readmx.cpp:30:17: warning: 'unsigned int MxCharToLetter(char)' defined but not used [-Wunused-function]
 static unsigned MxCharToLetter(char c)
                 ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c realigndiffs.cpp -o realigndiffs.o
In file included from muscle.h:38:0,
                 from realigndiffs.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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:77:13: warning: unused variable 'uNewRight' [-Wunused-variable]
    unsigned uNewRight = NewTree.GetRight(uNewNodeIndex);
             ^
realigndiffse.cpp:80:13: warning: unused variable 'uOldRight' [-Wunused-variable]
    unsigned uOldRight = OldTree.GetRight(uOld);
             ^
In file included from muscle.h:38:0,
                 from realigndiffse.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
   switch(m_Distance)
         ^
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]
In file included from muscle.h:38:0,
                 from refine.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c refinehoriz.cpp -o refinehoriz.o
In file included from muscle.h:38:0,
                 from refinehoriz.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const unsigned uNodeCount = tree.GetNodeCount();
                 ^
In file included from muscle.h:38:0,
                 from refinesubfams.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c refinetree.cpp -o refinetree.o
In file included from muscle.h:38:0,
                 from refinetree.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c refinetreee.cpp -o refinetreee.o
In file included from muscle.h:38:0,
                 from refinetreee.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c refinevert.cpp -o refinevert.o
In file included from muscle.h:38:0,
                 from refinevert.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c refinew.cpp -o refinew.o
refinew.cpp: In function 'void AppendMSA(MSA&, const MSA&)':
refinew.cpp:22:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
  const unsigned uColCountCat = uColCount1 + uColCount2;
                 ^
refinew.cpp: In function 'void RefineW(const MSA&, MSA&)':
refinew.cpp:125:13: warning: unused variable 'uOutCols' [-Wunused-variable]
    unsigned uOutCols = msaOut.GetColCount();
             ^
In file included from muscle.h:38:0,
                 from refinew.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c savebest.cpp -o savebest.o
In file included from muscle.h:38:0,
                 from savebest.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c scoredist.cpp -o scoredist.o
In file included from muscle.h:38:0,
                 from scoredist.cpp:3:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c scoregaps.cpp -o scoregaps.o
In file included from muscle.h:38:0,
                 from scoregaps.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
scoregaps.cpp:37:13: warning: 'void FreeGapInfo(GAPINFO*)' defined but not used [-Wunused-function]
 static void FreeGapInfo(GAPINFO *GI)
             ^
scoregaps.cpp:80:14: warning: 'SCORE Penalty(unsigned int, bool)' defined but not used [-Wunused-function]
 static SCORE Penalty(unsigned Length, bool Term)
              ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c scorehistory.cpp -o scorehistory.o
In file included from muscle.h:38:0,
                 from scorehistory.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c scorepp.cpp -o scorepp.o
In file included from muscle.h:38:0,
                 from scorepp.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c seq.cpp -o seq.o
In file included from muscle.h:38:0,
                 from seq.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c seqvect.cpp -o seqvect.o
In file included from muscle.h:38:0,
                 from seqvect.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c setblosumweights.cpp -o setblosumweights.o
In file included from muscle.h:38:0,
                 from setblosumweights.cpp:42:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c setgscweights.cpp -o setgscweights.o
In file included from muscle.h:38:0,
                 from setgscweights.cpp:104:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c setnewhandler.cpp -o setnewhandler.o
In file included from muscle.h:38:0,
                 from setnewhandler.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const unsigned uSeqCount = msa.GetSeqCount();
                 ^
In file included from muscle.h:38:0,
                 from spfast.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
spfast.cpp:14:20: warning: 'const char* GapTypeToStr(int)' defined but not used [-Wunused-function]
 static const char *GapTypeToStr(int GapType)
                    ^
spfast.cpp:59:14: warning: 'SCORE SPColBrute(const MSA&, unsigned int)' defined but not used [-Wunused-function]
 static SCORE SPColBrute(const MSA &msa, unsigned uColIndex)
              ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c sptest.cpp -o sptest.o
In file included from muscle.h:38:0,
                 from sptest.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c stabilize.cpp -o stabilize.o
In file included from muscle.h:38:0,
                 from stabilize.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  int NotUsed = system(CmdLine);
      ^
In file included from muscle.h:38:0,
                 from subfam.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c subfams.cpp -o subfams.o
In file included from muscle.h:38:0,
                 from subfams.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
subfams.cpp:10:13: warning: 'void GetMostDistantPair(DistFunc&, unsigned int*, unsigned int*)' defined but not used [-Wunused-function]
 static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2)
             ^
subfams.cpp:40:13: warning: 'void InitializeSingleSource(DistFunc&, unsigned int)' defined but not used [-Wunused-function]
 static void InitializeSingleSource(DistFunc &DF, unsigned uIndex)
             ^
subfams.cpp:52:13: warning: 'void Relax(DistFunc&, unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static void Relax(DistFunc &DF, unsigned u, unsigned v)
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c sw.cpp -o sw.o
In file included from muscle.h:38:0,
                 from sw.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
sw.cpp:20:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
 static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c termgaps.cpp -o termgaps.o
In file included from muscle.h:38:0,
                 from termgaps.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c textfile.cpp -o textfile.o
textfile.cpp: In member function 'void TextFile::PutChar(char)':
textfile.cpp:111:6: warning: unused variable 'i' [-Wunused-variable]
  int i = fputc(c, m_ptrFile);
      ^
textfile.cpp: In member function 'void TextFile::PutString(const char*)':
textfile.cpp:124:6: warning: unused variable 'iError' [-Wunused-variable]
  int iError = fputs(szLine, m_ptrFile);
      ^
textfile.cpp: In member function 'TEXTFILEPOS TextFile::GetPos()':
textfile.cpp:224:6: warning: unused variable 'i' [-Wunused-variable]
  int i = fgetpos(m_ptrFile, &p);
      ^
textfile.cpp: In member function 'void TextFile::SetPos(TEXTFILEPOS)':
textfile.cpp:237:6: warning: unused variable 'i' [-Wunused-variable]
  int i = fsetpos(m_ptrFile, &p);
      ^
In file included from muscle.h:38:0,
                 from textfile.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c threewaywt.cpp -o threewaywt.o
In file included from muscle.h:38:0,
                 from threewaywt.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c tomhydro.cpp -o tomhydro.o
In file included from muscle.h:38:0,
                 from tomhydro.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const unsigned uPrefixCountB = uLengthB + 1;
                 ^
traceback.cpp:59:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if ('S' == cEdgeType)
   ^
In file included from muscle.h:38:0,
                 from traceback.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c tracebackopt.cpp -o tracebackopt.o
In file included from muscle.h:38:0,
                 from tracebackopt.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
  const unsigned uPrefixCountB = uLengthB + 1;
                 ^
tracebacksw.cpp:29:8: warning: unused variable 'scoreMax' [-Wunused-variable]
  SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB);
        ^
tracebacksw.cpp:34:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if ('S' == cEdgeType)
   ^
In file included from muscle.h:38:0,
                 from tracebacksw.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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]
   switch(m_Distance)
         ^
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]
In file included from muscle.h:38:0,
                 from treefrommsa.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c typetostr.cpp -o typetostr.o
In file included from muscle.h:38:0,
                 from typetostr.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c upgma2.cpp -o upgma2.o
upgma2.cpp: In function 'void UPGMA2(const DistCalc&, Tree&, LINKAGE)':
upgma2.cpp:292:26: warning: 'dtNewDist' may be used uninitialized in this function [-Wmaybe-uninitialized]
    g_Dist[vL] = dtNewDist;
                          ^
In file included from muscle.h:38:0,
                 from upgma2.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
upgma2.cpp:68:13: warning: 'void ListState()' defined but not used [-Wunused-function]
 static void ListState()
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c usage.cpp -o usage.o
In file included from muscle.h:38:0,
                 from usage.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c validateids.cpp -o validateids.o
In file included from muscle.h:38:0,
                 from validateids.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c vtml2.cpp -o vtml2.o
In file included from muscle.h:38:0,
                 from vtml2.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/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 [-Wmaybe-uninitialized]
    dSum += Score;
                 ^
writescorefile.cpp:27:11: note: 'Score' was declared here
    double Score;
           ^
In file included from muscle.h:38:0,
                 from writescorefile.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RMuscle.cpp -o RMuscle.o
In file included from muscle.h:38:0,
                 from RMuscle.h:4,
                 from RMuscle.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
 static double ScoreToDouble(SCORE Score)
               ^
C:/Rtools/mingw_64/bin/g++ -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 glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.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 options.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 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 RMuscle.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
make[2]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpqkfLZc/R.INSTALL219820462db7/msa/src/Muscle'
ar rcs libMuscle.a 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 glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.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 options.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 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 RMuscle.o
cp libMuscle.a ../
make[1]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpqkfLZc/R.INSTALL219820462db7/msa/src/Muscle'
----------------------------------------
---------------- MUSCLE ----------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile.win --directory=ClustalW
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpqkfLZc/R.INSTALL219820462db7/msa/src/ClustalW'
cp windows/Makefile .; \
cp windows/m4/Makefile m4/; \
cp windows/src/Makefile src/; \
cp windows/src/clustalw_version.h src/; \
cp windows/src/config.h src/; \
cd src; \
export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. "; \
C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64/R.exe CMD SHLIB -o ClustalW.dll pairwise/FullPairwiseAlign.cpp pairwise/FastPairwiseAlign.cpp fileInput/MSFFileParser.cpp fileInput/FileReader.cpp fileInput/PIRFileParser.cpp fileInput/RSFFileParser.cpp fileInput/GDEFileParser.cpp fileInput/InFileStream.cpp fileInput/ClustalFileParser.cpp fileInput/PearsonFileParser.cpp fileInput/FileParser.cpp fileInput/EMBLFileParser.cpp tree/UPGMA/RootedClusterTree.cpp tree/UPGMA/UPGMAAlgorithm.cpp tree/UPGMA/Node.cpp tree/UPGMA/RootedGuideTree.cpp tree/UPGMA/RootedTreeOutput.cpp tree/Tree.cpp tree/ClusterTree.cpp tree/TreeInterface.cpp tree/UnRootedClusterTree.cpp tree/ClusterTreeOutput.cpp tree/RandomGenerator.cpp tree/NJTree.cpp tree/AlignmentSteps.cpp interface/CommandLineParser.cpp substitutionMatrix/SubMatrix.cpp multipleAlign/Iteration.cpp multipleAlign/MSA.cpp multipleAlign/MyersMillerProfileAlign.cpp multipleAlign/ProfileStandard.cpp multipleAlign/ProfileWithSub.cpp multipleAlign/ProfileBase.cpp multipleAlign/LowScoreSegProfile.cpp general/OutputFile.cpp general/UserParameters.cpp general/Utility.cpp general/InvalidCombination.cpp general/DebugLog.cpp general/ClustalWResources.cpp general/VectorOutOfRange.cpp general/SymMatrix.cpp general/Stats.cpp Help.cpp alignment/Alignment.cpp alignment/AlignmentOutput.cpp alignment/ObjectiveScore.cpp alignment/Sequence.cpp Clustal.cpp RClustalWMain.cpp RClustalW.cpp &&\
ar rcs libClustalW.a pairwise/FullPairwiseAlign.o pairwise/FastPairwiseAlign.o fileInput/MSFFileParser.o fileInput/FileReader.o fileInput/PIRFileParser.o fileInput/RSFFileParser.o fileInput/GDEFileParser.o fileInput/InFileStream.o fileInput/ClustalFileParser.o fileInput/PearsonFileParser.o fileInput/FileParser.o fileInput/EMBLFileParser.o tree/UPGMA/RootedClusterTree.o tree/UPGMA/UPGMAAlgorithm.o tree/UPGMA/Node.o tree/UPGMA/RootedGuideTree.o tree/UPGMA/RootedTreeOutput.o tree/Tree.o tree/ClusterTree.o tree/TreeInterface.o tree/UnRootedClusterTree.o tree/ClusterTreeOutput.o tree/RandomGenerator.o tree/NJTree.o tree/AlignmentSteps.o interface/CommandLineParser.o substitutionMatrix/SubMatrix.o multipleAlign/Iteration.o multipleAlign/MSA.o multipleAlign/MyersMillerProfileAlign.o multipleAlign/ProfileStandard.o multipleAlign/ProfileWithSub.o multipleAlign/ProfileBase.o multipleAlign/LowScoreSegProfile.o general/OutputFile.o general/UserParameters.o general/Utility.o general/InvalidCombination.o general/DebugLog.o general/ClustalWResources.o general/VectorOutOfRange.o general/SymMatrix.o general/Stats.o Help.o alignment/Alignment.o alignment/AlignmentOutput.o alignment/ObjectiveScore.o alignment/Sequence.o Clustal.o RClustalWMain.o RClustalW.o && \
cp libClustalW.a ../../
make[2]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpqkfLZc/R.INSTALL219820462db7/msa/src/ClustalW/src'
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c pairwise/FullPairwiseAlign.cpp -o pairwise/FullPairwiseAlign.o
In file included from pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from pairwise/../alignment/Alignment.h:42,
                 from pairwise/PairwiseAlignBase.h:10,
                 from pairwise/FullPairwiseAlign.h:9,
                 from pairwise/FullPairwiseAlign.cpp:9:
pairwise/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
pairwise/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c pairwise/FastPairwiseAlign.cpp -o pairwise/FastPairwiseAlign.o
In file included from pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from pairwise/../alignment/Alignment.h:42,
                 from pairwise/PairwiseAlignBase.h:10,
                 from pairwise/FastPairwiseAlign.h:9,
                 from pairwise/FastPairwiseAlign.cpp:10:
pairwise/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
pairwise/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/MSFFileParser.cpp -o fileInput/MSFFileParser.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/FileReader.cpp -o fileInput/FileReader.o
In file included from fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from fileInput/../alignment/Alignment.h:42,
                 from fileInput/FileReader.h:12,
                 from fileInput/FileReader.cpp:29:
fileInput/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
fileInput/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readCharacterSeqs(clustalw::Alignment*, int, std::string*, ClustalWInput*)':
fileInput/FileReader.cpp:421:10: warning: variable 'maxAlnLength' set but not used [-Wunused-but-set-variable]
      int maxAlnLength; // Get values from the Alignment object.
          ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/PIRFileParser.cpp -o fileInput/PIRFileParser.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/RSFFileParser.cpp -o fileInput/RSFFileParser.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/GDEFileParser.cpp -o fileInput/GDEFileParser.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/InFileStream.cpp -o fileInput/InFileStream.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/ClustalFileParser.cpp -o fileInput/ClustalFileParser.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/PearsonFileParser.cpp -o fileInput/PearsonFileParser.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/FileParser.cpp -o fileInput/FileParser.o
fileInput/FileParser.cpp: In member function 'std::vector<clustalw::Sequence> clustalw::FileParser::getSeqRangeR(int, int, std::string*, ClustalWInput*)':
fileInput/FileParser.cpp:38:7: warning: unused variable 'n' [-Wunused-variable]
   int n = (*input).inputSeqs.size();
       ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/EMBLFileParser.cpp -o fileInput/EMBLFileParser.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UPGMA/RootedClusterTree.cpp -o tree/UPGMA/RootedClusterTree.o
In file included from tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/UPGMA/../../alignment/Alignment.h:42,
                 from tree/UPGMA/../ClusterTree.h:20,
                 from tree/UPGMA/RootedClusterTree.h:8,
                 from tree/UPGMA/RootedClusterTree.cpp:9:
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
In file included from tree/UPGMA/../../alignment/../general/clustalw.h:44:0,
                 from tree/UPGMA/../../alignment/../general/Utility.h:15,
                 from tree/UPGMA/../../alignment/../general/utils.h:8,
                 from tree/UPGMA/../../alignment/../general/UserParameters.h:22,
                 from tree/UPGMA/../../alignment/../general/userparams.h:8,
                 from tree/UPGMA/../../alignment/Sequence.h:20,
                 from tree/UPGMA/../../alignment/Alignment.h:41,
                 from tree/UPGMA/../ClusterTree.h:20,
                 from tree/UPGMA/RootedClusterTree.h:8,
                 from tree/UPGMA/RootedClusterTree.cpp:9:
tree/UPGMA/../../alignment/../general/SymMatrix.h: In member function 'std::auto_ptr<clustalw::AlignmentSteps> clustalw::RootedClusterTree::treeFromDistMatrix(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string&)':
tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
             if (_i > _j) 
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UPGMA/UPGMAAlgorithm.cpp -o tree/UPGMA/UPGMAAlgorithm.o
In file included from tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/UPGMA/../../alignment/Alignment.h:42,
                 from tree/UPGMA/RootedGuideTree.h:17,
                 from tree/UPGMA/UPGMAAlgorithm.h:8,
                 from tree/UPGMA/UPGMAAlgorithm.cpp:4:
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UPGMA/Node.cpp -o tree/UPGMA/Node.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UPGMA/RootedGuideTree.cpp -o tree/UPGMA/RootedGuideTree.o
In file included from tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/UPGMA/../../alignment/Alignment.h:42,
                 from tree/UPGMA/RootedGuideTree.h:17,
                 from tree/UPGMA/RootedGuideTree.cpp:10:
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UPGMA/RootedTreeOutput.cpp -o tree/UPGMA/RootedTreeOutput.o
In file included from tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/UPGMA/../../alignment/Alignment.h:42,
                 from tree/UPGMA/RootedGuideTree.h:17,
                 from tree/UPGMA/RootedTreeOutput.h:15,
                 from tree/UPGMA/RootedTreeOutput.cpp:9:
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
In file included from tree/UPGMA/../../alignment/../general/clustalw.h:44:0,
                 from tree/UPGMA/../../alignment/../general/Utility.h:15,
                 from tree/UPGMA/../../alignment/../general/utils.h:8,
                 from tree/UPGMA/../../alignment/../general/UserParameters.h:22,
                 from tree/UPGMA/../../alignment/../general/userparams.h:8,
                 from tree/UPGMA/../../alignment/Sequence.h:20,
                 from tree/UPGMA/../../alignment/Alignment.h:41,
                 from tree/UPGMA/RootedGuideTree.h:17,
                 from tree/UPGMA/RootedTreeOutput.h:15,
                 from tree/UPGMA/RootedTreeOutput.cpp:9:
tree/UPGMA/../../alignment/../general/SymMatrix.h: In member function 'void clustalw::RootedTreeOutput::printPhylipTree(clustalw::RootedGuideTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*)':
tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
             if (_i > _j) 
             ^
tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
             if (_i > _j) 
             ^
tree/UPGMA/../../alignment/../general/SymMatrix.h: In member function 'void clustalw::RootedTreeOutput::printNexusTree(clustalw::RootedGuideTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*)':
tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
             if (_i > _j) 
             ^
tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
             if (_i > _j) 
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/Tree.cpp -o tree/Tree.o
In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/../alignment/Alignment.h:42,
                 from tree/Tree.h:13,
                 from tree/Tree.cpp:10:
tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/ClusterTree.cpp -o tree/ClusterTree.o
In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/../alignment/Alignment.h:42,
                 from tree/ClusterTree.h:20,
                 from tree/ClusterTree.cpp:9:
tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
tree/ClusterTree.cpp: In member function 'void clustalw::ClusterTree::calcPercIdentity(std::ofstream*, clustalw::Alignment*)':
tree/ClusterTree.cpp:580:9: warning: variable 'rs' set but not used [-Wunused-but-set-variable]
     int rs = 0, rl = 0;
         ^
tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable]
     int rs = 0, rl = 0;
                 ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/TreeInterface.cpp -o tree/TreeInterface.o
In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/../alignment/Alignment.h:42,
                 from tree/TreeInterface.h:19,
                 from tree/TreeInterface.cpp:15:
tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UnRootedClusterTree.cpp -o tree/UnRootedClusterTree.o
In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/../alignment/Alignment.h:42,
                 from tree/ClusterTree.h:20,
                 from tree/UnRootedClusterTree.h:8,
                 from tree/UnRootedClusterTree.cpp:9:
tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
In file included from tree/../alignment/../general/clustalw.h:44:0,
                 from tree/../alignment/../general/Utility.h:15,
                 from tree/../alignment/../general/utils.h:8,
                 from tree/../alignment/../general/UserParameters.h:22,
                 from tree/../alignment/../general/userparams.h:8,
                 from tree/../alignment/Sequence.h:20,
                 from tree/../alignment/Alignment.h:41,
                 from tree/ClusterTree.h:20,
                 from tree/UnRootedClusterTree.h:8,
                 from tree/UnRootedClusterTree.cpp:9:
tree/../alignment/../general/SymMatrix.h: In member function 'void clustalw::UnRootedClusterTree::treeFromDistMatrix(clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string&)':
tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
             if (_i > _j) 
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/ClusterTreeOutput.cpp -o tree/ClusterTreeOutput.o
In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from tree/../alignment/Alignment.h:42,
                 from tree/ClusterTreeOutput.h:11,
                 from tree/ClusterTreeOutput.cpp:9:
tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
In file included from tree/../alignment/../general/clustalw.h:44:0,
                 from tree/../alignment/../general/Utility.h:15,
                 from tree/../alignment/../general/utils.h:8,
                 from tree/../alignment/../general/UserParameters.h:22,
                 from tree/../alignment/../general/userparams.h:8,
                 from tree/../alignment/Sequence.h:20,
                 from tree/../alignment/Alignment.h:41,
                 from tree/ClusterTreeOutput.h:11,
                 from tree/ClusterTreeOutput.cpp:9:
tree/../alignment/../general/SymMatrix.h: In member function 'void clustalw::ClusterTreeOutput::printPhylipTree(clustalw::PhyloTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*, std::vector<int>*)':
tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
             if (_i > _j) 
             ^
tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
             if (_i > _j) 
             ^
tree/../alignment/../general/SymMatrix.h: In member function 'void clustalw::ClusterTreeOutput::printNexusTree(clustalw::PhyloTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*, std::vector<int>*)':
tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
             if (_i > _j) 
             ^
tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
             if (_i > _j) 
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/RandomGenerator.cpp -o tree/RandomGenerator.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/NJTree.cpp -o tree/NJTree.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/AlignmentSteps.cpp -o tree/AlignmentSteps.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c interface/CommandLineParser.cpp -o interface/CommandLineParser.o
In file included from interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from interface/../fileInput/../alignment/Alignment.h:42,
                 from interface/../fileInput/FileReader.h:12,
                 from interface/../Clustal.h:18,
                 from interface/CommandLineParser.h:18,
                 from interface/CommandLineParser.cpp:13:
interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c substitutionMatrix/SubMatrix.cpp -o substitutionMatrix/SubMatrix.o
In file included from substitutionMatrix/SubMatrix.cpp:15:0:
substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeriesFromR(Rcpp::NumericMatrix, clustalw::Matrix&, clustalw::Xref&)':
substitutionMatrix/SubMatrix.cpp:1305:10: warning: unused variable 'inline1' [-Wunused-variable]
     char inline1[1024];
          ^
substitutionMatrix/SubMatrix.cpp:1307:9: warning: unused variable 'nmat' [-Wunused-variable]
     int nmat;
         ^
substitutionMatrix/SubMatrix.cpp:1308:9: warning: unused variable 'n' [-Wunused-variable]
     int n, llimit, ulimit;
         ^
substitutionMatrix/SubMatrix.cpp:1308:12: warning: unused variable 'llimit' [-Wunused-variable]
     int n, llimit, ulimit;
            ^
substitutionMatrix/SubMatrix.cpp:1308:20: warning: unused variable 'ulimit' [-Wunused-variable]
     int n, llimit, ulimit;
                    ^
substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readUserMatrixFromR(Rcpp::NumericMatrix, clustalw::Matrix&, clustalw::Xref&)':
substitutionMatrix/SubMatrix.cpp:1361:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (j = 0; j < curline.length(); j++) {
                 ^
substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForHistogram(int (*)[32])':
substitutionMatrix/SubMatrix.cpp:1845:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
     int maxRes;
         ^
substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForLowScoreSeg(int (*)[32])':
substitutionMatrix/SubMatrix.cpp:1905:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
     int maxRes;
         ^
substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeries(const char*, clustalw::Matrix&, clustalw::Xref&)':
substitutionMatrix/SubMatrix.cpp:1023:9: warning: 'n' may be used uninitialized in this function [-Wmaybe-uninitialized]
     int n, llimit, ulimit;
         ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/Iteration.cpp -o multipleAlign/Iteration.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/Iteration.h:8,
                 from multipleAlign/Iteration.cpp:13:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)':
multipleAlign/Iteration.cpp:170:9: warning: variable 'count' set but not used [-Wunused-but-set-variable]
     int count;
         ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/MSA.cpp -o multipleAlign/MSA.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/ProfileBase.h:14,
                 from multipleAlign/MSA.h:10,
                 from multipleAlign/MSA.cpp:16:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
multipleAlign/MSA.cpp: In member function 'int clustalw::MSA::multiSeqAlign(clustalw::Alignment*, clustalw::DistMatrix*, std::vector<int>*, clustalw::AlignmentSteps*, int)':
multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable]
       int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18
           ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/MyersMillerProfileAlign.cpp -o multipleAlign/MyersMillerProfileAlign.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/ProfileAlignAlgorithm.h:10,
                 from multipleAlign/MyersMillerProfileAlign.h:10,
                 from multipleAlign/MyersMillerProfileAlign.cpp:10:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/ProfileStandard.cpp -o multipleAlign/ProfileStandard.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/ProfileStandard.h:9,
                 from multipleAlign/ProfileStandard.cpp:9:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/ProfileWithSub.cpp -o multipleAlign/ProfileWithSub.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/ProfileWithSub.h:9,
                 from multipleAlign/ProfileWithSub.cpp:9:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/ProfileBase.cpp -o multipleAlign/ProfileBase.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/ProfileBase.h:14,
                 from multipleAlign/ProfileBase.cpp:9:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/LowScoreSegProfile.cpp -o multipleAlign/LowScoreSegProfile.o
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from multipleAlign/../alignment/Alignment.h:42,
                 from multipleAlign/LowScoreSegProfile.h:13,
                 from multipleAlign/LowScoreSegProfile.cpp:9:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/OutputFile.cpp -o general/OutputFile.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/UserParameters.cpp -o general/UserParameters.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/Utility.cpp -o general/Utility.o
general/Utility.cpp: In member function 'bool clustalw::Utility::lineType(char*, const char*)':
general/Utility.cpp:251:8: warning: variable 'n' set but not used [-Wunused-but-set-variable]
    int n;
        ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/InvalidCombination.cpp -o general/InvalidCombination.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/DebugLog.cpp -o general/DebugLog.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/ClustalWResources.cpp -o general/ClustalWResources.o
general/ClustalWResources.cpp: In member function 'std::string clustalw::ClustalWResources::findFile(std::string, clustalw::ClustalWResourcePathType) const':
general/ClustalWResources.cpp:106:12: warning: array subscript is above array bounds [-Warray-bounds]
     delim[1] = 0;
            ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/VectorOutOfRange.cpp -o general/VectorOutOfRange.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/SymMatrix.cpp -o general/SymMatrix.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/Stats.cpp -o general/Stats.o
In file included from general/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from general/../alignment/Alignment.h:42,
                 from general/Stats.cpp:15:
general/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
general/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c Help.cpp -o Help.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c alignment/Alignment.cpp -o alignment/Alignment.o
In file included from alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from alignment/Alignment.h:42,
                 from alignment/Alignment.cpp:25:
alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c alignment/AlignmentOutput.cpp -o alignment/AlignmentOutput.o
In file included from alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from alignment/Alignment.h:42,
                 from alignment/AlignmentOutput.h:24,
                 from alignment/AlignmentOutput.cpp:27:
alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c alignment/ObjectiveScore.cpp -o alignment/ObjectiveScore.o
In file included from alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from alignment/ObjectiveScore.h:15,
                 from alignment/ObjectiveScore.cpp:10:
alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c alignment/Sequence.cpp -o alignment/Sequence.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c Clustal.cpp -o Clustal.o
In file included from fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from fileInput/../alignment/Alignment.h:42,
                 from fileInput/FileReader.h:12,
                 from Clustal.h:18,
                 from Clustal.cpp:27:
fileInput/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
fileInput/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c RClustalWMain.cpp -o RClustalWMain.o
In file included from alignment/../substitutionMatrix/globalmatrix.h:8:0,
                 from alignment/Alignment.h:42,
                 from RClustalWMain.cpp:5:
alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
                                                              ^
alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
                                                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c RClustalW.cpp -o RClustalW.o
RClustalW.cpp: In function 'SEXPREC* RClustalW(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
RClustalW.cpp:513:31: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
             if (!(firstvalue2 == -1 | secondvalue2 == -1)) {
                               ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ClustalW.dll tmp.def pairwise/FullPairwiseAlign.o pairwise/FastPairwiseAlign.o fileInput/MSFFileParser.o fileInput/FileReader.o fileInput/PIRFileParser.o fileInput/RSFFileParser.o fileInput/GDEFileParser.o fileInput/InFileStream.o fileInput/ClustalFileParser.o fileInput/PearsonFileParser.o fileInput/FileParser.o fileInput/EMBLFileParser.o tree/UPGMA/RootedClusterTree.o tree/UPGMA/UPGMAAlgorithm.o tree/UPGMA/Node.o tree/UPGMA/RootedGuideTree.o tree/UPGMA/RootedTreeOutput.o tree/Tree.o tree/ClusterTree.o tree/TreeInterface.o tree/UnRootedClusterTree.o tree/ClusterTreeOutput.o tree/RandomGenerator.o tree/NJTree.o tree/AlignmentSteps.o interface/CommandLineParser.o substitutionMatrix/SubMatrix.o multipleAlign/Iteration.o multipleAlign/MSA.o multipleAlign/MyersMillerProfileAlign.o multipleAlign/ProfileStandard.o multipleAlign/ProfileWithSub.o multipleAlign/ProfileBase.o multipleAlign/LowScoreSegProfile.o general/OutputFile.o general/UserParameters.o general/Utility.o general/InvalidCombination.o general/DebugLog.o general/ClustalWResources.o general/VectorOutOfRange.o general/SymMatrix.o general/Stats.o Help.o alignment/Alignment.o alignment/AlignmentOutput.o alignment/ObjectiveScore.o alignment/Sequence.o Clustal.o RClustalWMain.o RClustalW.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
make[2]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpqkfLZc/R.INSTALL219820462db7/msa/src/ClustalW/src'
make[1]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpqkfLZc/R.INSTALL219820462db7/msa/src/ClustalW'
----------------------------------------
--------------- ClustalW ---------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile.win --directory=ClustalOmega
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpqkfLZc/R.INSTALL219820462db7/msa/src/ClustalOmega'
cp windows/src/config.h src/; \
cp windows/src/clustal-omega-config.h src/; \
export PKG_LIBS=" -L"../../gc-7.2" -lgccpp72 -lgc72"; \
export PKG_CXXFLAGS=" -std=c++98 -DMATH_H_CLIB -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
export PKG_CFLAGS=" -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc"; \
cd src; \
C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64/R.exe CMD SHLIB -o ClustalOmega.dll exceptions4c/e4c_lite.c argtable2/argtable2.c argtable2/arg_end.c argtable2/arg_rem.c argtable2/arg_lit.c argtable2/arg_int.c argtable2/arg_dbl.c argtable2/arg_str.c argtable2/arg_file.c kmpp/KMeans.cpp kmpp/KmTree.cpp kmpp/KmUtils.cpp clustal/hhalign_wrapper.c clustal/ktuple_pair.c clustal/list.c clustal/log.c clustal/muscle_upgma.c clustal/muscle_tree.c clustal/mbed.c clustal/pair_dist.c clustal/progress.c clustal/seq.c clustal/symmatrix.c clustal/tree.c clustal/util.c clustal/weights.c squid/a2m.c squid/aligneval.c squid/alignio.c squid/clustal.c squid/cluster.c squid/dayhoff.c squid/eps.c squid/file.c squid/getopt.c squid/gki.c squid/gsi.c squid/gsi64.c squid/hsregex.c squid/iupac.c squid/msa.c squid/msf.c squid/phylip.c squid/revcomp.c squid/rk.c squid/selex.c squid/seqencode.c squid/shuffle.c squid/sqerror.c squid/sqio.c squid/squidcore.c squid/sre_ctype.c squid/sre_math.c squid/sre_random.c squid/sre_string.c squid/ssi.c squid/stack.c squid/stockholm.c squid/stopwatch.c squid/translate.c squid/types.c squid/vectorops.c squid/weight.c hhalign/hhalign.cpp RClustalOmega.cpp mymain.c clustal-omega.c && \
ar rcs libClustalOmega.a exceptions4c/e4c_lite.o argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o clustal/tree.o clustal/util.o clustal/weights.o squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o squid/types.o squid/vectorops.o squid/weight.o hhalign/hhalign.o RClustalOmega.o mymain.o clustal-omega.o && \
cp libClustalOmega.a ../../
make[2]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpqkfLZc/R.INSTALL219820462db7/msa/src/ClustalOmega/src'
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c exceptions4c/e4c_lite.c -o exceptions4c/e4c_lite.o
exceptions4c/e4c_lite.c:16:8: warning: missing braces around initializer [-Wmissing-braces]
 struct e4c_context e4c = {0};
        ^
exceptions4c/e4c_lite.c:16:8: warning: (near initialization for 'e4c.jump') [-Wmissing-braces]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c argtable2/argtable2.c -o argtable2/argtable2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c argtable2/arg_end.c -o argtable2/arg_end.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c argtable2/arg_rem.c -o argtable2/arg_rem.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c argtable2/arg_lit.c -o argtable2/arg_lit.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c argtable2/arg_int.c -o argtable2/arg_int.o
argtable2/arg_int.c: In function 'strtol0X':
argtable2/arg_int.c:60:5: warning: implicit declaration of function 'isspace' [-Wimplicit-function-declaration]
     while (isspace(*ptr))
     ^
argtable2/arg_int.c:89:4: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration]
    if (toupper(*ptr++)!=toupper(X))
    ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c argtable2/arg_dbl.c -o argtable2/arg_dbl.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c argtable2/arg_str.c -o argtable2/arg_str.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c argtable2/arg_file.c -o argtable2/arg_file.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -std=c++98 -DMATH_H_CLIB -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include   -O2 -Wall  -mtune=core2 -c kmpp/KMeans.cpp -o kmpp/KMeans.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -std=c++98 -DMATH_H_CLIB -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include   -O2 -Wall  -mtune=core2 -c kmpp/KmTree.cpp -o kmpp/KmTree.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -std=c++98 -DMATH_H_CLIB -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include   -O2 -Wall  -mtune=core2 -c kmpp/KmUtils.cpp -o kmpp/KmUtils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c clustal/hhalign_wrapper.c -o clustal/hhalign_wrapper.o
In file included from clustal/hhalign_wrapper.c:22:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
clustal/hhalign_wrapper.c: In function 'SanitiseUnknown':
clustal/hhalign_wrapper.c:85:9: warning: unused variable 'iLen' [-Wunused-variable]
     int iLen; /* length of sequence */
         ^
clustal/hhalign_wrapper.c:84:9: warning: unused variable 'iR' [-Wunused-variable]
     int iR; /* iterator for residue */
         ^
clustal/hhalign_wrapper.c: In function 'ReAttachLeadingGaps':
clustal/hhalign_wrapper.c:239:9: warning: variable 'iSize2' set but not used [-Wunused-but-set-variable]
     int iSize2 = 0; /* #seqs in 2nd profile */
         ^
clustal/hhalign_wrapper.c:238:9: warning: variable 'iSize1' set but not used [-Wunused-but-set-variable]
     int iSize1 = 0; /* #seqs in 1st profile */
         ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c clustal/ktuple_pair.c -o clustal/ktuple_pair.o
In file included from clustal/ktuple_pair.c:29:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
clustal/ktuple_pair.c: In function 'KTuplePairDist':
clustal/ktuple_pair.c:758:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
         #pragma omp critical(ktuple)
 ^
clustal/ktuple_pair.c:801:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
             #pragma omp critical(ktuple)
 ^
clustal/ktuple_pair.c:822:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
     #pragma omp critical(ktuple)
 ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c clustal/list.c -o clustal/list.o
In file included from clustal/list.c:32:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c clustal/log.c -o clustal/log.o
In file included from clustal/log.c:22:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c clustal/muscle_upgma.c -o clustal/muscle_upgma.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c clustal/muscle_tree.c -o clustal/muscle_tree.o
clustal/muscle_tree.c:519:1: warning: 'IsEdge' defined but not used [-Wunused-function]
 IsEdge(unsigned uNodeIndex1, unsigned uNodeIndex2, tree_t *tree)
 ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c clustal/mbed.c -o clustal/mbed.o
In file included from clustal/mbed.c:28:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
clustal/mbed.c: In function 'BisectingKmeans':
clustal/mbed.c:786:16: warning: variable 'dCost' set but not used [-Wunused-but-set-variable]
         double dCost = -1.0;
                ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c clustal/pair_dist.c -o clustal/pair_dist.o
In file included from clustal/pair_dist.c:22:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
clustal/pair_dist.c: In function 'SquidIdPairDist':
clustal/pair_dist.c:206:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
         #pragma omp critical(squidid)
 ^
clustal/pair_dist.c:218:0: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
         #pragma omp atomic
 ^
clustal/pair_dist.c:228:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
             #pragma omp critical(squidid)
 ^
clustal/pair_dist.c:177:10: warning: unused variable 'bPrintCR' [-Wunused-variable]
     bool bPrintCR = (rLog.iLogLevelEnabled<=LOG_VERBOSE) ? FALSE : TRUE;
          ^
clustal/pair_dist.c: In function 'PairDistances':
clustal/pair_dist.c:336:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
             #pragma omp parallel for private(iChunk) schedule(dynamic)
 ^
clustal/pair_dist.c:359:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
             #pragma omp parallel for private(iChunk) schedule(dynamic)
 ^
clustal/pair_dist.c:376:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
             #pragma omp parallel for private(iChunk) schedule(dynamic)
 ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c clustal/progress.c -o clustal/progress.o
In file included from clustal/progress.c:22:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c clustal/seq.c -o clustal/seq.o
In file included from clustal/seq.c:30:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
clustal/seq.c: In function 'AliStat':
clustal/seq.c:68:9: warning: unused variable 'iAux' [-Wunused-variable]
     int iAux;
         ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c clustal/symmatrix.c -o clustal/symmatrix.o
In file included from clustal/symmatrix.c:30:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c clustal/tree.c -o clustal/tree.o
In file included from clustal/tree.c:22:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c clustal/util.c -o clustal/util.o
In file included from clustal/util.c:22:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c clustal/weights.c -o clustal/weights.o
In file included from clustal/weights.c:72:0:
./config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/a2m.c -o squid/a2m.o
In file included from squid/squid.h:32:0,
                 from squid/a2m.c:20:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/aligneval.c -o squid/aligneval.o
In file included from squid/squid.h:32:0,
                 from squid/aligneval.c:59:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/alignio.c -o squid/alignio.o
In file included from squid/squid.h:32:0,
                 from squid/alignio.c:21:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/clustal.c -o squid/clustal.o
In file included from squid/squid.h:32:0,
                 from squid/clustal.c:24:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
squid/clustal.c: In function 'WriteClustal':
squid/clustal.c:214:7: warning: unused variable 'cons' [-Wunused-variable]
   int cons;
       ^
squid/clustal.c: In function 'WriteClustalForR':
squid/clustal.c:438:6: warning: unused variable 'cons' [-Wunused-variable]
  int cons;
      ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/cluster.c -o squid/cluster.o
In file included from squid/squid.h:32:0,
                 from squid/cluster.c:124:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/dayhoff.c -o squid/dayhoff.o
In file included from squid/squid.h:32:0,
                 from squid/dayhoff.c:28:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/eps.c -o squid/eps.o
In file included from squid/squid.h:32:0,
                 from squid/eps.c:23:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/file.c -o squid/file.o
In file included from squid/squid.h:32:0,
                 from squid/file.c:28:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/getopt.c -o squid/getopt.o
In file included from squid/squid.h:32:0,
                 from squid/getopt.c:17:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/gki.c -o squid/gki.o
In file included from squid/squid.h:32:0,
                 from squid/gki.c:82:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/gsi.c -o squid/gsi.o
In file included from squid/squid.h:32:0,
                 from squid/gsi.c:35:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/gsi64.c -o squid/gsi64.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/hsregex.c -o squid/hsregex.o
In file included from squid/squid.h:32:0,
                 from squid/hsregex.c:33:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
squid/hsregex.c: In function 'regbranch':
squid/hsregex.c:499:6: warning: 'flags' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int flags;
      ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/iupac.c -o squid/iupac.o
In file included from squid/squid.h:32:0,
                 from squid/iupac.c:17:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/msa.c -o squid/msa.o
In file included from squid/squid.h:32:0,
                 from squid/msa.c:22:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/msf.c -o squid/msf.o
In file included from squid/squid.h:32:0,
                 from squid/msf.c:25:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
squid/msf.c: In function 'ReadMSF':
squid/msf.c:87:11: warning: variable 'alleged_checksum' set but not used [-Wunused-but-set-variable]
   int     alleged_checksum;
           ^
squid/msf.c:85:11: warning: variable 'alleged_alen' set but not used [-Wunused-but-set-variable]
   int     alleged_alen;
           ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/phylip.c -o squid/phylip.o
In file included from squid/squid.h:32:0,
                 from squid/phylip.c:23:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
squid/phylip.c: In function 'ReadPhylip':
squid/phylip.c:80:15: warning: variable 'alen' set but not used [-Wunused-but-set-variable]
   int   nseq, alen;
               ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/revcomp.c -o squid/revcomp.o
In file included from squid/squid.h:32:0,
                 from squid/revcomp.c:19:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/rk.c -o squid/rk.o
In file included from squid/squid.h:32:0,
                 from squid/rk.c:26:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/selex.c -o squid/selex.o
In file included from squid/squid.h:32:0,
                 from squid/selex.c:43:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/seqencode.c -o squid/seqencode.o
In file included from squid/squid.h:32:0,
                 from squid/seqencode.c:18:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/shuffle.c -o squid/shuffle.o
In file included from squid/squid.h:32:0,
                 from squid/shuffle.c:42:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/sqerror.c -o squid/sqerror.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/sqio.c -o squid/sqio.o
In file included from squid/squid.h:32:0,
                 from squid/sqio.c:57:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/squidcore.c -o squid/squidcore.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/sre_ctype.c -o squid/sre_ctype.o
In file included from squid/squid.h:32:0,
                 from squid/sre_ctype.c:19:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/sre_math.c -o squid/sre_math.o
In file included from squid/squid.h:32:0,
                 from squid/sre_math.c:19:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/sre_random.c -o squid/sre_random.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/sre_string.c -o squid/sre_string.o
In file included from squid/squid.h:32:0,
                 from squid/sre_string.c:23:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/ssi.c -o squid/ssi.o
In file included from squid/squid.h:32:0,
                 from squid/ssi.c:16:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/stack.c -o squid/stack.o
In file included from squid/squid.h:32:0,
                 from squid/stack.c:18:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/stockholm.c -o squid/stockholm.o
In file included from squid/squid.h:32:0,
                 from squid/stockholm.c:31:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/stopwatch.c -o squid/stopwatch.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/translate.c -o squid/translate.o
In file included from squid/squid.h:32:0,
                 from squid/translate.c:19:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/types.c -o squid/types.o
In file included from squid/squid.h:32:0,
                 from squid/types.c:20:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/vectorops.c -o squid/vectorops.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c squid/weight.c -o squid/weight.o
In file included from squid/squid.h:32:0,
                 from squid/weight.c:19:
squid/../config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -std=c++98 -DMATH_H_CLIB -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include   -O2 -Wall  -mtune=core2 -c hhalign/hhalign.cpp -o hhalign/hhalign.o
In file included from hhalign/hhalign.cpp:62:0:
hhalign/util-C.h: In function 'float fast_log2(float)':
hhalign/util-C.h:94:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   int a = (((*((int *)&x)) & 0x7F800000) >>23 )-0x7f;
                         ^
hhalign/util-C.h:95:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   int b =  ((*((int *)&x)) & 0x007FE000) >>13;
                         ^
hhalign/util-C.h:96:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   int c =  ((*((int *)&x)) & 0x00001FFF);
                         ^
hhalign/util-C.h: In function 'float fpow2(float)':
hhalign/util-C.h:111:23: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   int lx = *((int*)&tx) - 0x4b400000;   // integer value of x
                       ^
hhalign/util-C.h: In function 'float fast_pow2(float)':
hhalign/util-C.h:158:35: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
    pow2[b]=(*((unsigned int *)(&f)) & 0x7FFFFF); // store the mantisse of 2^(1+b/1024)
                                   ^
hhalign/util-C.h:202:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   return *((float*)&y);
                      ^
In file included from hhalign/hhalign.cpp:76:0:
hhalign/hhhmm-C.h: In member function 'int HMM::ReadHMMer3(FILE*, char*)':
hhalign/hhhmm-C.h:1141:12: warning: variable 'dAlphaInv' set but not used [-Wunused-but-set-variable]
     double dAlphaInv = 1.00 / (double)(iAlpha); /* weight of AA */
            ^
In file included from hhalign/hhalign.cpp:77:0:
hhalign/hhalignment-C.h: In member function 'void Alignment::Read(FILE*, char*, char*)':
hhalign/hhalignment-C.h:245:32: warning: variable 'ptr2' set but not used [-Wunused-but-set-variable]
                   char *ptr1, *ptr2;
                                ^
hhalign/hhalignment-C.h: In member function 'int Alignment::FilterWithCoreHMM(char*, float, HMM&)':
hhalign/hhalignment-C.h:1429:19: warning: variable 'score_M' set but not used [-Wunused-but-set-variable]
             float score_M=0.0;
                   ^
hhalign/hhalignment-C.h:1430:19: warning: variable 'score_prev' set but not used [-Wunused-but-set-variable]
             float score_prev=0.0;
                   ^
In file included from hhalign/hhalign.cpp:81:0:
hhalign/hhhitlist-C.h: In member function 'void HitList::TransitiveScoring()':
hhalign/hhhitlist-C.h:1259:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
   size_t unused; /* disable fread gcc warning */
          ^
hhalign/hhhitlist-C.h: In member function 'void HitList::TransitiveScoring2()':
hhalign/hhhitlist-C.h:1624:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
   size_t unused; /* disable fread gcc warning */
          ^
hhalign/hhhitlist-C.h: In member function 'void HitList::TransitiveScoring3()':
hhalign/hhhitlist-C.h:1994:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
   size_t unused; /* disable fread gcc warning */
          ^
hhalign/hhhitlist-C.h: In member function 'void HitList::TransitiveScoring4()':
hhalign/hhhitlist-C.h:2359:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
   size_t unused; /* disable fread gcc warning */
          ^
In file included from hhalign/hhalign.cpp:82:0:
hhalign/hhfunc-C.h: In function 'void AddBackgroundFrequencies(float**, float**, float**, int, hmm_light*, char**, char*, int, char*)':
hhalign/hhfunc-C.h:74:9: warning: unused variable 'iT' [-Wunused-variable]
     int iT; /* transition state iterator */
         ^
In file included from hhalign/hhalign.cpp:82:0:
hhalign/hhfunc-C.h:80:11: warning: unused variable 'fGThgiew' [-Wunused-variable]
     float fGThgiew = UNITY - fGWeight; /* weight of 'true' transitions */
           ^
hhalign/hhfunc-C.h:85:11: warning: unused variable 'zf1SeqTrans' [-Wunused-variable]
     float zf1SeqTrans[] = {0.98, 0.01, 0.01, 0.25, 0.75, 0.25, 0.75};
           ^
hhalign/hhfunc-C.h:86:11: warning: unused variable 'zf1SeqInit' [-Wunused-variable]
     float zf1SeqInit[]  = {0.98, 0.01, 0.01, 0.99, 0.01, 0.99, 0.01};
           ^
hhalign/hhfunc-C.h:87:11: warning: unused variable 'zf1SeqDel' [-Wunused-variable]
     float zf1SeqDel[]   = {0.24, 0.01, 0.75, 0.01, 0.01, 0.01, 0.01};
           ^
hhalign/hhfunc-C.h:88:11: warning: unused variable 'zf1SeqRevrt' [-Wunused-variable]
     float zf1SeqRevrt[] = {0.98, 0.01, 0.01, 0.01, 0.01, 0.99, 0.01};
           ^
hhalign/hhfunc-C.h: In function 'int ReadAndPrepare(int, char**, int, hmm_light*, char*, char*, double*, char*, HMM&, Alignment*)':
hhalign/hhfunc-C.h:328:17: warning: unused variable 'NEFF_SCORE' [-Wunused-variable]
       const int NEFF_SCORE = 10; /* FIXME: Magic Number */
                 ^
hhalign/hhfunc-C.h:511:17: warning: unused variable 'NEFF_SCORE' [-Wunused-variable]
       const int NEFF_SCORE = 10; /* FIXME: Magic Number */
                 ^
hhalign/hhalign.cpp: In function 'int hhalign(char**, int, double*, char**, int, double*, double*, hmm_light*, char*, char*, char*, char*, hhalign_para, hhalign_scores*, int, int, char*, char*)':
hhalign/hhalign.cpp:721:9: warning: variable 'Nali' set but not used [-Wunused-but-set-variable]
     int Nali;                    /* number of normally backtraced alignments 
         ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -std=c++98 -DMATH_H_CLIB -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include   -O2 -Wall  -mtune=core2 -c RClustalOmega.cpp -o RClustalOmega.o
In file included from RClustalOmega.cpp:27:0:
config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c mymain.c -o mymain.o
In file included from mymain.c:22:0:
config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc   -O2 -Wall  -std=gnu99 -mtune=core2 -c clustal-omega.c -o clustal-omega.o
In file included from clustal-omega.c:22:0:
config.h:132:0: warning: "NDEBUG" redefined
 #define NDEBUG /**/
 ^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ClustalOmega.dll tmp.def exceptions4c/e4c_lite.o argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o clustal/tree.o clustal/util.o clustal/weights.o squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o squid/types.o squid/vectorops.o squid/weight.o hhalign/hhalign.o RClustalOmega.o mymain.o clustal-omega.o -L../../gc-7.2 -lgccpp72 -lgc72 -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
make[2]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpqkfLZc/R.INSTALL219820462db7/msa/src/ClustalOmega/src'
make[1]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.5-bioc/tmpdir/RtmpqkfLZc/R.INSTALL219820462db7/msa/src/ClustalOmega'
----------------------------------------
------------- ClustalOmega -------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o msa.dll tmp.def R_init_msa.o SplitCharVector2List.o SplitCharVector2Matrix.o -Wl,--whole-archive ./libGC.a ./libMuscle.a ./libClustalW.a ./libClustalOmega.a -Wl,--no-whole-archive -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/msa.buildbin-libdir/msa/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'msa' as msa_1.8.0.zip
* DONE (msa)

name	user	system	elapsed
MsaMetaData-class	0.81	0.03	0.95
MsaMultipleAlignmentClasses	0.72	0.03	0.75
msa-package	0.21	0.00	0.22
msa	0.91	0.02	0.92
msaCheckNames	0.03	0.00	0.03
msaClustalOmega	0.47	0.02	0.48
msaClustalW	0.34	0.01	0.36
msaConsensusSequence-methods	0.13	0.00	0.13
msaConservationScore-methods	1.39	0.02	1.40
msaConvert	0.19	0.00	0.19
msaMuscle	0.84	0.01	0.86
msaPrettyPrint	0.45	0.00	7.89

name	user	system	elapsed
MsaMetaData-class	0.86	0.00	0.86
MsaMultipleAlignmentClasses	0.57	0.02	0.59
msa-package	0.18	0.00	0.17
msa	0.84	0.03	0.87
msaCheckNames	0.03	0.00	0.03
msaClustalOmega	0.31	0.07	0.38
msaClustalW	0.35	0.01	0.36
msaConsensusSequence-methods	0.12	0.00	0.12
msaConservationScore-methods	1.19	0.02	1.21
msaConvert	0.16	0.00	0.15
msaMuscle	0.78	0.01	0.80
msaPrettyPrint	0.43	0.00	5.31