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BioC 3.2: CHECK report for msa on moscato1

This page was generated on 2016-04-23 10:21:55 -0700 (Sat, 23 Apr 2016).

Package 675/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
msa 1.2.1
Ulrich Bodenhofer
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/msa
Last Changed Rev: 111668 / Revision: 116712
Last Changed Date: 2015-12-19 11:20:23 -0800 (Sat, 19 Dec 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: msa
Version: 1.2.1
Command: rm -rf msa.buildbin-libdir msa.Rcheck && mkdir msa.buildbin-libdir msa.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=msa.buildbin-libdir msa_1.2.1.tar.gz >msa.Rcheck\00install.out 2>&1 && cp msa.Rcheck\00install.out msa-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=msa.buildbin-libdir --install="check:msa-install.out" --force-multiarch --no-vignettes --timings msa_1.2.1.tar.gz
StartedAt: 2016-04-23 05:02:22 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 05:22:26 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 1204.2 seconds
RetCode: 0
Status:  OK  
CheckDir: msa.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf msa.buildbin-libdir msa.Rcheck && mkdir msa.buildbin-libdir msa.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=msa.buildbin-libdir msa_1.2.1.tar.gz >msa.Rcheck\00install.out 2>&1 && cp msa.Rcheck\00install.out msa-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=msa.buildbin-libdir --install="check:msa-install.out" --force-multiarch --no-vignettes --timings msa_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/msa.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'msa/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'msa' version '1.2.1'
* 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   5.5Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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 'D:/biocbld/bbs-3.2-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)
File 'D:/biocbld/bbs-3.2-bioc/meat/msa.buildbin-libdir/msa/libs/x64/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' ... [21s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
msaPrettyPrint 0.42      0    7.24
** running examples for arch 'x64' ... [16s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
msaPrettyPrint 0.33      0    5.17
* 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
  'D:/biocbld/bbs-3.2-bioc/meat/msa.Rcheck/00check.log'
for details.

msa.Rcheck/00install.out:


install for i386

* installing *source* package 'msa' ...
** libs
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
./Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
make --file=msaMakefile.win --directory=gc-7.2
make[1]: Entering directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/RtmpCUgzyL/R.INSTALLab0513b4995/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"; \
D:/biocbld/BBS-3˜1.2-B/R/bin/i386/R.exe CMD SHLIB -o gc72.dll *.c; \
D:/biocbld/BBS-3˜1.2-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/d/biocbld/bbs-3.2-bioc/tmpdir/RtmpCUgzyL/R.INSTALLab0513b4995/msa/src/gc-7.2'
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
g++ -m32 -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 -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
make[2]: Leaving directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/RtmpCUgzyL/R.INSTALLab0513b4995/msa/src/gc-7.2'
make[2]: Entering directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/RtmpCUgzyL/R.INSTALLab0513b4995/msa/src/gc-7.2'
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
g++ -m32 -shared -s -static-libgcc -o gccpp72.dll tmp.def gc_cpp.o -L. -lgc72 -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
make[2]: Leaving directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/RtmpCUgzyL/R.INSTALLab0513b4995/msa/src/gc-7.2'
make[1]: Leaving directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/RtmpCUgzyL/R.INSTALLab0513b4995/msa/src/gc-7.2'
----------------------------------------
------------------ GC  -----------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile.win --directory=Muscle
make[1]: Entering directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/RtmpCUgzyL/R.INSTALLab0513b4995/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/"
D:/biocbld/BBS-3˜1.2-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/d/biocbld/bbs-3.2-bioc/tmpdir/RtmpCUgzyL/R.INSTALLab0513b4995/msa/src/Muscle'
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c aligngivenpath.cpp -o aligngivenpath.o
aligngivenpath.cpp: In function 'void AppendTplInserts(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)':
aligngivenpath.cpp:186:17: warning: unused variable 'uLengthA' [-Wunused-variable]
aligngivenpath.cpp:187:17: warning: unused variable 'uLengthB' [-Wunused-variable]
aligngivenpath.cpp: In function 'void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)':
aligngivenpath.cpp:335:19: warning: unused variable 'uColA' [-Wunused-variable]
aligngivenpath.cpp:336:19: warning: unused variable 'uColB' [-Wunused-variable]
aligngivenpath.cpp:346:19: warning: unused variable 'uColA' [-Wunused-variable]
aligngivenpath.cpp:354:19: warning: unused variable 'uColB' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c aligngivenpathsw.cpp -o aligngivenpathsw.o
aligngivenpathsw.cpp: In function 'void AppendUnalignedTerminals(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)':
aligngivenpathsw.cpp:58:17: warning: unused variable 'uLengthA' [-Wunused-variable]
aligngivenpathsw.cpp:59:17: warning: unused variable 'uLengthB' [-Wunused-variable]
aligngivenpathsw.cpp: In function 'void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)':
aligngivenpathsw.cpp:204:19: warning: unused variable 'uColA' [-Wunused-variable]
aligngivenpathsw.cpp:205:19: warning: unused variable 'uColB' [-Wunused-variable]
aligngivenpathsw.cpp:215:19: warning: unused variable 'uColA' [-Wunused-variable]
aligngivenpathsw.cpp:223:19: warning: unused variable 'uColB' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c aligntwoprofs.cpp -o aligntwoprofs.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c aln.cpp -o aln.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c alpha.cpp -o alpha.o
alpha.cpp: In function 'unsigned int GetAlphaSize(ALPHA)':
alpha.cpp:84:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c anchors.cpp -o anchors.o
anchors.cpp: In function 'void MergeBestCols(const SCORE*, const unsigned int*, unsigned int, unsigned int, unsigned int*, unsigned int*)':
anchors.cpp:162:13: warning: unused variable 'uWindowCenter' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
anchors.cpp:53:13: warning: 'void FindBestColsGrade(const SCORE*, unsigned int, double, unsigned int*, unsigned int*)' defined but not used [-Wunused-function]
anchors.cpp:105:13: warning: 'void ListBestCols(const MSA&, const SCORE*, const SCORE*, unsigned int*, unsigned int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c bittraceback.cpp -o bittraceback.o
bittraceback.cpp: In function 'void BitTraceBack(char**, unsigned int, unsigned int, char, PWPath&)':
bittraceback.cpp:146:7: warning: unused variable 'Bits' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
bittraceback.cpp:15:20: warning: 'const char* BitsToStr(char)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c blosum62.cpp -o blosum62.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c blosumla.cpp -o blosumla.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
blosumla.cpp:7:14: warning: 'Blosum62LA' defined but not used [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c clust.cpp -o clust.o
clust.cpp: In member function 'void Clust::ChooseJoin(unsigned int*, unsigned int*, float*, float*)':
clust.cpp:167:9: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
clust.cpp: In member function 'void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)':
clust.cpp:184:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
clust.cpp: In member function 'void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)':
clust.cpp:204:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
clust.cpp: In member function 'float Clust::ComputeDist(unsigned int, unsigned int)':
clust.cpp:295:9: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch]
clust.cpp: In member function 'float Clust::ComputeDistMAFFT(unsigned int, unsigned int)':
clust.cpp:360:14: warning: unused variable 'dDistLR' [-Wunused-variable]
clust.cpp: In member function 'float Clust::ComputeMetric(unsigned int, unsigned int) const':
clust.cpp:611:9: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c cluster.cpp -o cluster.o
cluster.cpp: In member function 'void ClusterTree::Create(const DistFunc&)':
cluster.cpp:284:8: warning: variable 'bFound' set but not used [-Wunused-but-set-variable]
cluster.cpp:267:9: warning: unused variable 'dMaxDist' [-Wunused-variable]
cluster.cpp:308:47: warning: 'uIndexClosest2' may be used uninitialized in this function [-Wuninitialized]
cluster.cpp:307:47: warning: 'uIndexClosest1' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c clwwt.cpp -o clwwt.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c color.cpp -o color.o
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
color.cpp:72:12: warning: 'int BlosumScore(char, char)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c cons.cpp -o cons.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c diaglist.cpp -o diaglist.o
diaglist.cpp: In member function 'void DiagList::FromPath(const PWPath&)':
diaglist.cpp:77:39: warning: 'uStartPosB' may be used uninitialized in this function [-Wuninitialized]
diaglist.cpp:77:39: warning: 'uStartPosA' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c diffobjscore.cpp -o diffobjscore.o
diffobjscore.cpp: In function 'SCORE ScoreLetters(const MSA&, const unsigned int*, unsigned int)':
diffobjscore.cpp:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c diffpaths.cpp -o diffpaths.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c difftrees.cpp -o difftrees.o
difftrees.cpp: In function 'void DiffTrees(const Tree&, const Tree&, Tree&, unsigned int*)':
difftrees.cpp:161:17: warning: unused variable 'uLeafCount2' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c difftreese.cpp -o difftreese.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c distcalc.cpp -o distcalc.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c distfunc.cpp -o distfunc.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c distpwkimura.cpp -o distpwkimura.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
domuscle.cpp: In function 'void DoMuscle(MuscleInput*, MuscleOutput*)':
domuscle.cpp:180:6: warning: unused variable 'PNlength' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c dosp.cpp -o dosp.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c dpreglist.cpp -o dpreglist.o
dpreglist.cpp: In function 'void DiagListToDPRegionList(const DiagList&, DPRegionList&, unsigned int, unsigned int)':
dpreglist.cpp:82:19: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c drawtree.cpp -o drawtree.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c edgelist.cpp -o edgelist.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c enumopts.cpp -o enumopts.o
In file included from enumopts.cpp:8:0:
enums.h:15:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:15:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:15:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:15:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:28:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:28:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:28:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:28:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:41:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:41:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:41:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:94:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:94:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:94:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:94:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c enumtostr.cpp -o enumtostr.o
In file included from enumtostr.cpp:16:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c estring.cpp -o estring.o
estring.cpp: In function 'void EstringsToPath(const short int*, const short int*, PWPath&)':
estring.cpp:409:3: warning: 'cType' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
estring.cpp:464:13: warning: 'bool CanMultiplyEstrings(const short int*, const short int*)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fasta.cpp -o fasta.o
fasta.cpp: In member function 'void MSA::FromFASTAFile(TextFile&)':
fasta.cpp:15:11: warning: unused variable 'uSeqCount' [-Wunused-variable]
fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fasta2.cpp -o fasta2.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastclust.cpp -o fastclust.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdist.cpp -o fastdist.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistjones.cpp -o fastdistjones.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistkbit.cpp -o fastdistkbit.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistkmer.cpp -o fastdistkmer.o
fastdistkmer.cpp: In function 'void FastDistKmer(const SeqVect&, DistFunc&)':
fastdistkmer.cpp:235:11: warning: unused variable 'KD' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistmafft.cpp -o fastdistmafft.o
fastdistmafft.cpp: In function 'void DistKmer6_6(const SeqVect&, DistFunc&)':
fastdistmafft.cpp:239:15: warning: unused variable 'pName1' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
fastdistmafft.cpp:104:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistnuc.cpp -o fastdistnuc.o
fastdistnuc.cpp: In function 'void DistKmer4_6(const SeqVect&, DistFunc&)':
fastdistnuc.cpp:223:15: warning: unused variable 'pName1' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
fastdistnuc.cpp:33:17: warning: 'uResidueGroupCount' defined but not used [-Wunused-variable]
fastdistnuc.cpp:85:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastscorepath2.cpp -o fastscorepath2.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c finddiags.cpp -o finddiags.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
finddiags.cpp:11:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c finddiagsn.cpp -o finddiagsn.o
finddiagsn.cpp: In function 'char* TupleToStr(int)':
finddiagsn.cpp:16:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
finddiagsn.cpp:12:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
In file included from glbalign352.cpp:6:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignle.cpp -o glbalignle.o
glbalignle.cpp: In function 'SCORE GlobalAlignLE(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
glbalignle.cpp:431:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignsimple.cpp -o glbalignsimple.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
glbalignsimple.cpp:28:13: warning: 'void ListTB(const char*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
glbalignsimple.cpp:52:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignsp.cpp -o glbalignsp.o
glbalignsp.cpp: In function 'SCORE GlobalAlignSP(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
glbalignsp.cpp:366:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
glbalignsp.cpp:305:50: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignspn.cpp -o glbalignspn.o
glbalignspn.cpp: In function 'SCORE GlobalAlignSPN(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
glbalignspn.cpp:401:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
glbalignspn.cpp:340:50: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignss.cpp -o glbalignss.o
glbalignss.cpp: In function 'SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)':
glbalignss.cpp:177:16: warning: unused variable 'ptrRowA' [-Wunused-variable]
glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable]
glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
glbalignss.cpp:310:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
glbalignss.cpp:252:50: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
glbalignss.cpp:11:14: warning: 'SCORE Subst(const Seq&, const Seq&, unsigned int, unsigned int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalndimer.cpp -o glbalndimer.o
glbalndimer.cpp: In function 'SCORE ScoreProfPosDimer(const ProfPos&, const ProfPos&)':
glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_SPN' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
glbalndimer.cpp:14:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c globals.cpp -o globals.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c globalslinux.cpp -o globalslinux.o
In file included from globalslinux.cpp:1:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c globalsosx.cpp -o globalsosx.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c globalsother.cpp -o globalsother.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c globalswin32.cpp -o globalswin32.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c gonnet.cpp -o gonnet.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
gonnet.cpp:137:14: warning: 'Gonnet160' defined but not used [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c henikoffweight.cpp -o henikoffweight.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c henikoffweightpb.cpp -o henikoffweightpb.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c html.cpp -o html.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c hydro.cpp -o hydro.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c intmath.cpp -o intmath.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c local.cpp -o local.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c main.cpp -o main.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c makerootmsa.cpp -o makerootmsa.o
makerootmsa.cpp: In function 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)':
makerootmsa.cpp:18:17: warning: unused variable 'uSeqLength' [-Wunused-variable]
makerootmsa.cpp: In function 'short int* MakeRootSeqE(const Seq&, const Tree&, unsigned int, const ProgNode*, Seq&, short int*, short int*)':
makerootmsa.cpp:94:17: warning: unused variable 'Path' [-Wunused-variable]
makerootmsa.cpp: In function 'void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)':
makerootmsa.cpp:168:17: warning: unused variable 'uTreeNodeCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
makerootmsa.cpp:12:13: warning: 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c makerootmsab.cpp -o makerootmsab.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c maketree.cpp -o maketree.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c mhack.cpp -o mhack.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c mpam200.cpp -o mpam200.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c msa.cpp -o msa.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
msa.cpp:385:13: warning: 'void FmtChar(char, unsigned int)' defined but not used [-Wunused-function]
msa.cpp:392:13: warning: 'void FmtInt(unsigned int, unsigned int)' defined but not used [-Wunused-function]
msa.cpp:407:13: warning: 'void FmtInt0(unsigned int, unsigned int)' defined but not used [-Wunused-function]
msa.cpp:419:13: warning: 'void FmtPad(unsigned int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c msa2.cpp -o msa2.o
msa2.cpp: In function 'void SetMSAWeightsMuscle(MSA&)':
msa2.cpp:357:9: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch]
msa2.cpp: In function 'void MSAAppend(MSA&, const MSA&)':
msa2.cpp:476:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c msadistkimura.cpp -o msadistkimura.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c msf.cpp -o msf.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
msf.cpp:24:20: warning: 'const char* strfind(const char*, const char*)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c muscle.cpp -o muscle.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c muscleout.cpp -o muscleout.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nucmx.cpp -o nucmx.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nwdasimple.cpp -o nwdasimple.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nwdasimple2.cpp -o nwdasimple2.o
In file included from nwdasimple2.cpp:3:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nwdasmall.cpp -o nwdasmall.o
In file included from nwdasmall.cpp:4:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nwrec.cpp -o nwrec.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nwsmall.cpp -o nwsmall.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
objscore.cpp: In function 'SCORE ObjScore(const MSA&, const unsigned int*, unsigned int, const unsigned int*, unsigned int)':
objscore.cpp:31:9: warning: enumeration value 'OBJSCORE_Undefined' not handled in switch [-Wswitch]
objscore.cpp:31:9: warning: enumeration value 'OBJSCORE_SPM' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c objscore2.cpp -o objscore2.o
objscore2.cpp: In function 'SCORE TermGapScore(bool)':
objscore2.cpp:22:9: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch]
objscore2.cpp: In function 'SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)':
objscore2.cpp:62:8: warning: unused variable 'scoreGaps' [-Wunused-variable]
objscore2.cpp:63:7: warning: unused variable 'bGapping1' [-Wunused-variable]
objscore2.cpp:64:7: warning: unused variable 'bGapping2' [-Wunused-variable]
objscore2.cpp:67:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
objscore2.cpp:82:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
objscore2.cpp: In function 'SCORE ScoreSeqPairGaps(const MSA&, unsigned int, const MSA&, unsigned int)':
objscore2.cpp:140:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
objscore2.cpp:155:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
objscore2.cpp: In function 'SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)':
objscore2.cpp:314:17: warning: unused variable 'uColCount2' [-Wunused-variable]
objscore2.cpp: In function 'SCORE ObjScoreXP(const MSA&, const MSA&)':
objscore2.cpp:493:17: warning: unused variable 'w' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c objscoreda.cpp -o objscoreda.o
In file included from objscoreda.cpp:4:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c onexception.cpp -o onexception.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c options.cpp -o options.o
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c outweights.cpp -o outweights.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c pam200mafft.cpp -o pam200mafft.o
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
pam200mafft.cpp:6:14: warning: 'PAM200' defined but not used [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c params.cpp -o params.o
params.cpp: In function 'void SetPPScore(bool)':
params.cpp:441:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phy.cpp -o phy.o
phy.cpp: In member function 'void Tree::RootUnrootedTree(ROOT)':
phy.cpp:665:9: warning: unused variable 'dEdgeLength' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phy2.cpp -o phy2.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phy3.cpp -o phy3.o
phy3.cpp: In function 'void CalcInfo(const Tree&, unsigned int, unsigned int, EdgeInfo**)':
phy3.cpp:125:15: warning: unused variable 'dThisDist' [-Wunused-variable]
phy3.cpp: In function 'void FindRoot(const Tree&, unsigned int*, unsigned int*, double*, double*, ROOT)':
phy3.cpp:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable]
phy3.cpp:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable]
phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable]
phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable]
phy3.cpp: In function 'void RootByMidLongestSpan(const Tree&, EdgeInfo**, unsigned int*, unsigned int*, double*, double*)':
phy3.cpp:263:11: warning: variable 'uMostDistantLeaf' set but not used [-Wunused-but-set-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
phy3.cpp:45:13: warning: 'void ListEIs(EdgeInfo**, unsigned int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phy4.cpp -o phy4.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phyfromclust.cpp -o phyfromclust.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phyfromfile.cpp -o phyfromfile.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c physeq.cpp -o physeq.o
physeq.cpp: In member function 'void MSA::ToPhySequentialFile(TextFile&) const':
physeq.cpp:60:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
physeq.cpp:71:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
physeq.cpp: In member function 'void MSA::ToPhyInterleavedFile(TextFile&) const':
physeq.cpp:112:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
physeq.cpp:124:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phytofile.cpp -o phytofile.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c posgap.cpp -o posgap.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c ppscore.cpp -o ppscore.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c profdb.cpp -o profdb.o
In file included from clustsetmsa.h:8:0,
                 from profdb.cpp:9:
msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c profile.cpp -o profile.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c profilefrommsa.cpp -o profilefrommsa.o
profilefrommsa.cpp: In function 'void ListProfile(const ProfPos*, unsigned int, const MSA*)':
profilefrommsa.cpp:131:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
profilefrommsa.cpp: In function 'unsigned int ResidueGroupFromFCounts(const FCOUNT*)':
profilefrommsa.cpp:230:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
profilefrommsa.cpp: In function 'ProfPos* ProfileFromMSA(const MSA&)':
profilefrommsa.cpp:245:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
profilefrommsa.cpp:253:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
profilefrommsa.cpp:15:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c progalign.cpp -o progalign.o
progalign.cpp: In function 'ProgNode* ProgressiveAlignE(const SeqVect&, const Tree&, MSA&)':
progalign.cpp:41:17: warning: unused variable 'uIterCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c progress.cpp -o progress.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c progressivealign.cpp -o progressivealign.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c pwpath.cpp -o pwpath.o
pwpath.cpp: In member function 'void PWPath::Validate() const':
pwpath.cpp:80:16: warning: unused variable 'LastEdge' [-Wunused-variable]
pwpath.cpp: In member function 'void PWPath::FromFile(TextFile&)':
pwpath.cpp:213:11: warning: unused variable 'uEdgeIndex' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c readmx.cpp -o readmx.o
readmx.cpp: In function 'float (* ReadMx(TextFile&))[32][32]':
readmx.cpp:83:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readmx.cpp:84:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readmx.cpp: In function 'float (* ReadMxFromR(std::vector<std::basic_string<char> >, float (*)[32]))[32][32]':
readmx.cpp:184:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readmx.cpp:185:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
readmx.cpp:30:17: warning: 'unsigned int MxCharToLetter(char)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c realigndiffs.cpp -o realigndiffs.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c realigndiffse.cpp -o realigndiffse.o
realigndiffse.cpp: In function 'void RealignDiffsE(const MSA&, const SeqVect&, const Tree&, const Tree&, const unsigned int*, MSA&, ProgNode*)':
realigndiffse.cpp:77:13: warning: unused variable 'uNewRight' [-Wunused-variable]
realigndiffse.cpp:80:13: warning: unused variable 'uOldRight' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refine.cpp -o refine.o
In file included from clustsetmsa.h:8:0,
                 from refine.cpp:9:
msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinehoriz.cpp -o refinehoriz.o
refinehoriz.cpp: In function 'bool RefineHoriz(MSA&, const Tree&, unsigned int, bool, bool)':
refinehoriz.cpp:187:59: warning: 'scoreAfter' may be used uninitialized in this function [-Wuninitialized]
refinehoriz.cpp:174:9: note: 'scoreAfter' was declared here
refinehoriz.cpp:187:59: warning: 'scoreBefore' may be used uninitialized in this function [-Wuninitialized]
refinehoriz.cpp:173:9: note: 'scoreBefore' was declared here
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinesubfams.cpp -o refinesubfams.o
refinesubfams.cpp: In function 'bool RefineSubfams(MSA&, const Tree&, unsigned int)':
refinesubfams.cpp:63:17: warning: unused variable 'uNodeCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinetree.cpp -o refinetree.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinetreee.cpp -o refinetreee.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinevert.cpp -o refinevert.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinew.cpp -o refinew.o
refinew.cpp: In function 'void AppendMSA(MSA&, const MSA&)':
refinew.cpp:22:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
refinew.cpp: In function 'void RefineW(const MSA&, MSA&)':
refinew.cpp:125:13: warning: unused variable 'uOutCols' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c savebest.cpp -o savebest.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c scoredist.cpp -o scoredist.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c scoregaps.cpp -o scoregaps.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
scoregaps.cpp:37:13: warning: 'void FreeGapInfo(GAPINFO*)' defined but not used [-Wunused-function]
scoregaps.cpp:80:14: warning: 'SCORE Penalty(unsigned int, bool)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c scorehistory.cpp -o scorehistory.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c scorepp.cpp -o scorepp.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c seq.cpp -o seq.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c seqvect.cpp -o seqvect.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c setblosumweights.cpp -o setblosumweights.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c setgscweights.cpp -o setgscweights.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c setnewhandler.cpp -o setnewhandler.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c spfast.cpp -o spfast.o
spfast.cpp: In function 'SCORE ObjScoreSPDimer(const MSA&)':
spfast.cpp:252:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
spfast.cpp:14:20: warning: 'const char* GapTypeToStr(int)' defined but not used [-Wunused-function]
spfast.cpp:59:14: warning: 'SCORE SPColBrute(const MSA&, unsigned int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c sptest.cpp -o sptest.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c stabilize.cpp -o stabilize.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c subfam.cpp -o subfam.o
subfam.cpp: In function 'void AlignSubFam(SeqVect&, const Tree&, unsigned int, MSA&)':
subfam.cpp:173:6: warning: unused variable 'NotUsed' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c subfams.cpp -o subfams.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
subfams.cpp:10:13: warning: 'void GetMostDistantPair(DistFunc&, unsigned int*, unsigned int*)' defined but not used [-Wunused-function]
subfams.cpp:40:13: warning: 'void InitializeSingleSource(DistFunc&, unsigned int)' defined but not used [-Wunused-function]
subfams.cpp:52:13: warning: 'void Relax(DistFunc&, unsigned int, unsigned int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c sw.cpp -o sw.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
sw.cpp:20:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c termgaps.cpp -o termgaps.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c textfile.cpp -o textfile.o
textfile.cpp: In member function 'void TextFile::PutChar(char)':
textfile.cpp:111:6: warning: unused variable 'i' [-Wunused-variable]
textfile.cpp: In member function 'void TextFile::PutString(const char*)':
textfile.cpp:124:6: warning: unused variable 'iError' [-Wunused-variable]
textfile.cpp: In member function 'TEXTFILEPOS TextFile::GetPos()':
textfile.cpp:224:6: warning: unused variable 'i' [-Wunused-variable]
textfile.cpp: In member function 'void TextFile::SetPos(TEXTFILEPOS)':
textfile.cpp:237:6: warning: unused variable 'i' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c threewaywt.cpp -o threewaywt.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c tomhydro.cpp -o tomhydro.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c traceback.cpp -o traceback.o
traceback.cpp: In function 'SCORE TraceBack(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, PWPath&)':
traceback.cpp:21:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
traceback.cpp:59:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c tracebackopt.cpp -o tracebackopt.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c tracebacksw.cpp -o tracebacksw.o
tracebacksw.cpp: In function 'void TraceBackSW(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, unsigned int, unsigned int, PWPath&)':
tracebacksw.cpp:22:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
tracebacksw.cpp:29:8: warning: unused variable 'scoreMax' [-Wunused-variable]
tracebacksw.cpp:34:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wuninitialized]
tracebacksw.cpp:47:3: warning: 'cEdgeType' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c treefrommsa.cpp -o treefrommsa.o
In file included from clustsetmsa.h:8:0,
                 from treefrommsa.cpp:5:
msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c typetostr.cpp -o typetostr.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c upgma2.cpp -o upgma2.o
upgma2.cpp: In member function 'virtual void DistCalcTest::CalcDistRange(unsigned int, dist_t*) const':
upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces]
upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces]
upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces]
upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces]
upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces]
upgma2.cpp: In function 'void UPGMA2(const DistCalc&, Tree&, LINKAGE)':
upgma2.cpp:293:4: warning: 'dtNewDist' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
upgma2.cpp:68:13: warning: 'void ListState()' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c usage.cpp -o usage.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c validateids.cpp -o validateids.o
In file included from validateids.cpp:4:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c vtml2.cpp -o vtml2.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c writescorefile.cpp -o writescorefile.o
writescorefile.cpp: In function 'void WriteScoreFile(const MSA&)':
writescorefile.cpp:40:17: warning: 'Score' may be used uninitialized in this function [-Wuninitialized]
writescorefile.cpp:27:11: note: 'Score' was declared here
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c RMuscle.cpp -o RMuscle.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m32 -shared -s -static-libgcc -o Muscle.dll tmp.def aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o 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 -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
make[2]: Leaving directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/RtmpCUgzyL/R.INSTALLab0513b4995/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/d/biocbld/bbs-3.2-bioc/tmpdir/RtmpCUgzyL/R.INSTALLab0513b4995/msa/src/Muscle'
----------------------------------------
---------------- MUSCLE ----------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile.win --directory=ClustalW
make[1]: Entering directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/RtmpCUgzyL/R.INSTALLab0513b4995/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. "; \
D:/biocbld/BBS-3˜1.2-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/d/biocbld/bbs-3.2-bioc/tmpdir/RtmpCUgzyL/R.INSTALLab0513b4995/msa/src/ClustalW/src'
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c pairwise/FullPairwiseAlign.cpp -o pairwise/FullPairwiseAlign.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c pairwise/FastPairwiseAlign.cpp -o pairwise/FastPairwiseAlign.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/MSFFileParser.cpp -o fileInput/MSFFileParser.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/FileReader.cpp -o fileInput/FileReader.o
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]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/PIRFileParser.cpp -o fileInput/PIRFileParser.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/RSFFileParser.cpp -o fileInput/RSFFileParser.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/GDEFileParser.cpp -o fileInput/GDEFileParser.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/InFileStream.cpp -o fileInput/InFileStream.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/ClustalFileParser.cpp -o fileInput/ClustalFileParser.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/PearsonFileParser.cpp -o fileInput/PearsonFileParser.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/EMBLFileParser.cpp -o fileInput/EMBLFileParser.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UPGMA/RootedClusterTree.cpp -o tree/UPGMA/RootedClusterTree.o
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]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UPGMA/UPGMAAlgorithm.cpp -o tree/UPGMA/UPGMAAlgorithm.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UPGMA/Node.cpp -o tree/UPGMA/Node.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UPGMA/RootedGuideTree.cpp -o tree/UPGMA/RootedGuideTree.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UPGMA/RootedTreeOutput.cpp -o tree/UPGMA/RootedTreeOutput.o
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]
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]
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]
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]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/Tree.cpp -o tree/Tree.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/ClusterTree.cpp -o tree/ClusterTree.o
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]
tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/TreeInterface.cpp -o tree/TreeInterface.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UnRootedClusterTree.cpp -o tree/UnRootedClusterTree.o
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]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/ClusterTreeOutput.cpp -o tree/ClusterTreeOutput.o
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]
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]
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]
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]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/RandomGenerator.cpp -o tree/RandomGenerator.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/NJTree.cpp -o tree/NJTree.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/AlignmentSteps.cpp -o tree/AlignmentSteps.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c interface/CommandLineParser.cpp -o interface/CommandLineParser.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c substitutionMatrix/SubMatrix.cpp -o substitutionMatrix/SubMatrix.o
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]
substitutionMatrix/SubMatrix.cpp:1307:9: warning: unused variable 'nmat' [-Wunused-variable]
substitutionMatrix/SubMatrix.cpp:1308:9: warning: unused variable 'n' [-Wunused-variable]
substitutionMatrix/SubMatrix.cpp:1308:12: warning: unused variable 'llimit' [-Wunused-variable]
substitutionMatrix/SubMatrix.cpp:1308:20: warning: unused variable 'ulimit' [-Wunused-variable]
substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readUserMatrixFromR(Rcpp::NumericMatrix, clustalw::Matrix&, clustalw::Xref&)':
substitutionMatrix/SubMatrix.cpp:1361:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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]
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 [-Wuninitialized]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/Iteration.cpp -o multipleAlign/Iteration.o
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]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/MSA.cpp -o multipleAlign/MSA.o
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]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/MyersMillerProfileAlign.cpp -o multipleAlign/MyersMillerProfileAlign.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/ProfileStandard.cpp -o multipleAlign/ProfileStandard.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/ProfileWithSub.cpp -o multipleAlign/ProfileWithSub.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/ProfileBase.cpp -o multipleAlign/ProfileBase.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/LowScoreSegProfile.cpp -o multipleAlign/LowScoreSegProfile.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/OutputFile.cpp -o general/OutputFile.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/UserParameters.cpp -o general/UserParameters.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/InvalidCombination.cpp -o general/InvalidCombination.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/DebugLog.cpp -o general/DebugLog.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/VectorOutOfRange.cpp -o general/VectorOutOfRange.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/SymMatrix.cpp -o general/SymMatrix.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/Stats.cpp -o general/Stats.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c Help.cpp -o Help.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c alignment/Alignment.cpp -o alignment/Alignment.o
alignment/Alignment.cpp: In member function 'bool clustalw::Alignment::keepPortionOfSeqArray(int, int)':
alignment/Alignment.cpp:1715:24: warning: variable 'posToAddTo' set but not used [-Wunused-but-set-variable]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c alignment/AlignmentOutput.cpp -o alignment/AlignmentOutput.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c alignment/ObjectiveScore.cpp -o alignment/ObjectiveScore.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c alignment/Sequence.cpp -o alignment/Sequence.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c Clustal.cpp -o Clustal.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c RClustalWMain.cpp -o RClustalWMain.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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:513:56: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
g++ -m32 -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 -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
make[2]: Leaving directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/RtmpCUgzyL/R.INSTALLab0513b4995/msa/src/ClustalW/src'
make[1]: Leaving directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/RtmpCUgzyL/R.INSTALLab0513b4995/msa/src/ClustalW'
----------------------------------------
--------------- ClustalW ---------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile.win --directory=ClustalOmega
make[1]: Entering directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/RtmpCUgzyL/R.INSTALLab0513b4995/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=" -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; \
D:/biocbld/BBS-3˜1.2-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/d/biocbld/bbs-3.2-bioc/tmpdir/RtmpCUgzyL/R.INSTALLab0513b4995/msa/src/ClustalOmega/src'
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
exceptions4c/e4c_lite.c:16:8: warning: (near initialization for 'e4c.jump') [-Wmissing-braces]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
argtable2/arg_int.c:89:4: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"   -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
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"   -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
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"   -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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<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]
clustal/hhalign_wrapper.c:84:9: warning: unused variable 'iR' [-Wunused-variable]
clustal/hhalign_wrapper.c: In function 'ReAttachLeadingGaps':
clustal/hhalign_wrapper.c:239:9: warning: variable 'iSize2' set but not used [-Wunused-but-set-variable]
clustal/hhalign_wrapper.c:238:9: warning: variable 'iSize1' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<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]
clustal/ktuple_pair.c:801:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
clustal/ktuple_pair.c:822:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
clustal/list.c: In function 'IntListRemoveNext':
clustal/list.c:248:20: warning: 'piData' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<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]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<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]
clustal/pair_dist.c:218:0: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
clustal/pair_dist.c:228:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
clustal/pair_dist.c:177:10: warning: unused variable 'bPrintCR' [-Wunused-variable]
clustal/pair_dist.c: In function 'PairDistances':
clustal/pair_dist.c:336:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
clustal/pair_dist.c:359:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
clustal/pair_dist.c:376:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<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]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<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]
squid/clustal.c: In function 'WriteClustalForR':
squid/clustal.c:438:6: warning: unused variable 'cons' [-Wunused-variable]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<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 [-Wuninitialized]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<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]
squid/msf.c:85:11: warning: variable 'alleged_alen' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<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]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"   -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:56:0:
hhalign/util-C.h: In function 'float fast_log2(float)':
hhalign/util-C.h:92:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
hhalign/util-C.h:93:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
hhalign/util-C.h:94:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
hhalign/util-C.h: In function 'float fpow2(float)':
hhalign/util-C.h:109:23: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
hhalign/util-C.h: In function 'float fast_pow2(float)':
hhalign/util-C.h:156:35: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
hhalign/util-C.h:200:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
In file included from hhalign/hhalign.cpp:70:0:
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]
In file included from hhalign/hhalign.cpp:71:0:
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]
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]
hhalign/hhalignment-C.h:1430:19: warning: variable 'score_prev' set but not used [-Wunused-but-set-variable]
In file included from hhalign/hhalign.cpp:75:0:
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]
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]
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]
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]
In file included from hhalign/hhalign.cpp:76:0:
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]
hhalign/hhfunc-C.h:80:11: warning: unused variable 'fGThgiew' [-Wunused-variable]
hhalign/hhfunc-C.h:85:11: warning: unused variable 'zf1SeqTrans' [-Wunused-variable]
hhalign/hhfunc-C.h:86:11: warning: unused variable 'zf1SeqInit' [-Wunused-variable]
hhalign/hhfunc-C.h:87:11: warning: unused variable 'zf1SeqDel' [-Wunused-variable]
hhalign/hhfunc-C.h:88:11: warning: unused variable 'zf1SeqRevrt' [-Wunused-variable]
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]
hhalign/hhfunc-C.h:511:17: warning: unused variable 'NEFF_SCORE' [-Wunused-variable]
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:715:9: warning: variable 'Nali' set but not used [-Wunused-but-set-variable]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"   -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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
g++ -m32 -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 -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
make[2]: Leaving directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/RtmpCUgzyL/R.INSTALLab0513b4995/msa/src/ClustalOmega/src'
make[1]: Leaving directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/RtmpCUgzyL/R.INSTALLab0513b4995/msa/src/ClustalOmega'
----------------------------------------
------------- ClustalOmega -------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
g++ -m32 -shared -s -static-libgcc -o msa.dll tmp.def R_init_msa.o -Wl,--whole-archive ./libGC.a ./libMuscle.a ./libClustalW.a ./libClustalOmega.a -Wl,--no-whole-archive -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/msa.buildbin-libdir/msa/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'print' from package 'base' in package 'msa'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'msa' ...
** libs
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
./Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
make --file=msaMakefile.win --directory=gc-7.2
make[1]: Entering directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/Rtmpawe44h/R.INSTALL1cc411d1305b/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"; \
D:/biocbld/BBS-3˜1.2-B/R/bin/x64/R.exe CMD SHLIB -o gc72.dll *.c; \
D:/biocbld/BBS-3˜1.2-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/d/biocbld/bbs-3.2-bioc/tmpdir/Rtmpawe44h/R.INSTALL1cc411d1305b/msa/src/gc-7.2'
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
g++ -m64 -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 -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
make[2]: Leaving directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/Rtmpawe44h/R.INSTALL1cc411d1305b/msa/src/gc-7.2'
make[2]: Entering directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/Rtmpawe44h/R.INSTALL1cc411d1305b/msa/src/gc-7.2'
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
g++ -m64 -shared -s -static-libgcc -o gccpp72.dll tmp.def gc_cpp.o -L. -lgc72 -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
make[2]: Leaving directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/Rtmpawe44h/R.INSTALL1cc411d1305b/msa/src/gc-7.2'
make[1]: Leaving directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/Rtmpawe44h/R.INSTALL1cc411d1305b/msa/src/gc-7.2'
----------------------------------------
------------------ GC  -----------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile.win --directory=Muscle
make[1]: Entering directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/Rtmpawe44h/R.INSTALL1cc411d1305b/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/"
D:/biocbld/BBS-3˜1.2-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/d/biocbld/bbs-3.2-bioc/tmpdir/Rtmpawe44h/R.INSTALL1cc411d1305b/msa/src/Muscle'
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c aligngivenpath.cpp -o aligngivenpath.o
aligngivenpath.cpp: In function 'void AppendTplInserts(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)':
aligngivenpath.cpp:186:17: warning: unused variable 'uLengthA' [-Wunused-variable]
aligngivenpath.cpp:187:17: warning: unused variable 'uLengthB' [-Wunused-variable]
aligngivenpath.cpp: In function 'void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)':
aligngivenpath.cpp:335:19: warning: unused variable 'uColA' [-Wunused-variable]
aligngivenpath.cpp:336:19: warning: unused variable 'uColB' [-Wunused-variable]
aligngivenpath.cpp:346:19: warning: unused variable 'uColA' [-Wunused-variable]
aligngivenpath.cpp:354:19: warning: unused variable 'uColB' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c aligngivenpathsw.cpp -o aligngivenpathsw.o
aligngivenpathsw.cpp: In function 'void AppendUnalignedTerminals(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)':
aligngivenpathsw.cpp:58:17: warning: unused variable 'uLengthA' [-Wunused-variable]
aligngivenpathsw.cpp:59:17: warning: unused variable 'uLengthB' [-Wunused-variable]
aligngivenpathsw.cpp: In function 'void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)':
aligngivenpathsw.cpp:204:19: warning: unused variable 'uColA' [-Wunused-variable]
aligngivenpathsw.cpp:205:19: warning: unused variable 'uColB' [-Wunused-variable]
aligngivenpathsw.cpp:215:19: warning: unused variable 'uColA' [-Wunused-variable]
aligngivenpathsw.cpp:223:19: warning: unused variable 'uColB' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c aligntwoprofs.cpp -o aligntwoprofs.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c aln.cpp -o aln.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c alpha.cpp -o alpha.o
alpha.cpp: In function 'unsigned int GetAlphaSize(ALPHA)':
alpha.cpp:84:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c anchors.cpp -o anchors.o
anchors.cpp: In function 'void MergeBestCols(const SCORE*, const unsigned int*, unsigned int, unsigned int, unsigned int*, unsigned int*)':
anchors.cpp:162:13: warning: unused variable 'uWindowCenter' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
anchors.cpp:53:13: warning: 'void FindBestColsGrade(const SCORE*, unsigned int, double, unsigned int*, unsigned int*)' defined but not used [-Wunused-function]
anchors.cpp:105:13: warning: 'void ListBestCols(const MSA&, const SCORE*, const SCORE*, unsigned int*, unsigned int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c bittraceback.cpp -o bittraceback.o
bittraceback.cpp: In function 'void BitTraceBack(char**, unsigned int, unsigned int, char, PWPath&)':
bittraceback.cpp:146:7: warning: unused variable 'Bits' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
bittraceback.cpp:15:20: warning: 'const char* BitsToStr(char)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c blosum62.cpp -o blosum62.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c blosumla.cpp -o blosumla.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
blosumla.cpp:7:14: warning: 'Blosum62LA' defined but not used [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c clust.cpp -o clust.o
clust.cpp: In member function 'void Clust::ChooseJoin(unsigned int*, unsigned int*, float*, float*)':
clust.cpp:167:9: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
clust.cpp: In member function 'void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)':
clust.cpp:184:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
clust.cpp: In member function 'void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)':
clust.cpp:204:17: warning: unused variable 'uClusterCount' [-Wunused-variable]
clust.cpp: In member function 'float Clust::ComputeDist(unsigned int, unsigned int)':
clust.cpp:295:9: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch]
clust.cpp: In member function 'float Clust::ComputeDistMAFFT(unsigned int, unsigned int)':
clust.cpp:360:14: warning: unused variable 'dDistLR' [-Wunused-variable]
clust.cpp: In member function 'float Clust::ComputeMetric(unsigned int, unsigned int) const':
clust.cpp:611:9: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c cluster.cpp -o cluster.o
cluster.cpp: In member function 'void ClusterTree::Create(const DistFunc&)':
cluster.cpp:284:8: warning: variable 'bFound' set but not used [-Wunused-but-set-variable]
cluster.cpp:267:9: warning: unused variable 'dMaxDist' [-Wunused-variable]
cluster.cpp:308:47: warning: 'uIndexClosest2' may be used uninitialized in this function [-Wuninitialized]
cluster.cpp:307:47: warning: 'uIndexClosest1' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c clwwt.cpp -o clwwt.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c color.cpp -o color.o
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
color.cpp:72:12: warning: 'int BlosumScore(char, char)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c cons.cpp -o cons.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c diaglist.cpp -o diaglist.o
diaglist.cpp: In member function 'void DiagList::FromPath(const PWPath&)':
diaglist.cpp:77:39: warning: 'uStartPosB' may be used uninitialized in this function [-Wuninitialized]
diaglist.cpp:77:39: warning: 'uStartPosA' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c diffobjscore.cpp -o diffobjscore.o
diffobjscore.cpp: In function 'SCORE ScoreLetters(const MSA&, const unsigned int*, unsigned int)':
diffobjscore.cpp:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c diffpaths.cpp -o diffpaths.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c difftrees.cpp -o difftrees.o
difftrees.cpp: In function 'void DiffTrees(const Tree&, const Tree&, Tree&, unsigned int*)':
difftrees.cpp:161:17: warning: unused variable 'uLeafCount2' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c difftreese.cpp -o difftreese.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c distcalc.cpp -o distcalc.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c distfunc.cpp -o distfunc.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c distpwkimura.cpp -o distpwkimura.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
domuscle.cpp: In function 'void DoMuscle(MuscleInput*, MuscleOutput*)':
domuscle.cpp:180:6: warning: unused variable 'PNlength' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c dosp.cpp -o dosp.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c dpreglist.cpp -o dpreglist.o
dpreglist.cpp: In function 'void DiagListToDPRegionList(const DiagList&, DPRegionList&, unsigned int, unsigned int)':
dpreglist.cpp:82:19: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c drawtree.cpp -o drawtree.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c edgelist.cpp -o edgelist.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c enumopts.cpp -o enumopts.o
In file included from enumopts.cpp:8:0:
enums.h:15:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:15:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:15:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:15:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:28:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:28:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:28:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:28:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:41:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:41:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:41:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:94:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:94:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:94:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
enums.h:94:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c enumtostr.cpp -o enumtostr.o
In file included from enumtostr.cpp:16:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c estring.cpp -o estring.o
estring.cpp: In function 'void EstringsToPath(const short int*, const short int*, PWPath&)':
estring.cpp:409:3: warning: 'cType' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
estring.cpp:464:13: warning: 'bool CanMultiplyEstrings(const short int*, const short int*)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fasta.cpp -o fasta.o
fasta.cpp: In member function 'void MSA::FromFASTAFile(TextFile&)':
fasta.cpp:15:11: warning: unused variable 'uSeqCount' [-Wunused-variable]
fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fasta2.cpp -o fasta2.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastclust.cpp -o fastclust.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdist.cpp -o fastdist.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistjones.cpp -o fastdistjones.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistkbit.cpp -o fastdistkbit.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistkmer.cpp -o fastdistkmer.o
fastdistkmer.cpp: In function 'void FastDistKmer(const SeqVect&, DistFunc&)':
fastdistkmer.cpp:235:11: warning: unused variable 'KD' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistmafft.cpp -o fastdistmafft.o
fastdistmafft.cpp: In function 'void DistKmer6_6(const SeqVect&, DistFunc&)':
fastdistmafft.cpp:239:15: warning: unused variable 'pName1' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
fastdistmafft.cpp:104:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastdistnuc.cpp -o fastdistnuc.o
fastdistnuc.cpp: In function 'void DistKmer4_6(const SeqVect&, DistFunc&)':
fastdistnuc.cpp:223:15: warning: unused variable 'pName1' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
fastdistnuc.cpp:33:17: warning: 'uResidueGroupCount' defined but not used [-Wunused-variable]
fastdistnuc.cpp:85:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fastscorepath2.cpp -o fastscorepath2.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c finddiags.cpp -o finddiags.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
finddiags.cpp:11:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c finddiagsn.cpp -o finddiagsn.o
finddiagsn.cpp: In function 'char* TupleToStr(int)':
finddiagsn.cpp:16:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
finddiagsn.cpp:12:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
In file included from glbalign352.cpp:6:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignle.cpp -o glbalignle.o
glbalignle.cpp: In function 'SCORE GlobalAlignLE(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
glbalignle.cpp:431:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignsimple.cpp -o glbalignsimple.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
glbalignsimple.cpp:28:13: warning: 'void ListTB(const char*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
glbalignsimple.cpp:52:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignsp.cpp -o glbalignsp.o
glbalignsp.cpp: In function 'SCORE GlobalAlignSP(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
glbalignsp.cpp:366:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
glbalignsp.cpp:305:50: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignspn.cpp -o glbalignspn.o
glbalignspn.cpp: In function 'SCORE GlobalAlignSPN(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
glbalignspn.cpp:401:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
glbalignspn.cpp:340:50: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalignss.cpp -o glbalignss.o
glbalignss.cpp: In function 'SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)':
glbalignss.cpp:177:16: warning: unused variable 'ptrRowA' [-Wunused-variable]
glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable]
glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
glbalignss.cpp:310:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
glbalignss.cpp:252:50: warning: 'uInsertPos' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
glbalignss.cpp:11:14: warning: 'SCORE Subst(const Seq&, const Seq&, unsigned int, unsigned int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c glbalndimer.cpp -o glbalndimer.o
glbalndimer.cpp: In function 'SCORE ScoreProfPosDimer(const ProfPos&, const ProfPos&)':
glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_SPN' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
glbalndimer.cpp:14:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c globals.cpp -o globals.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c globalslinux.cpp -o globalslinux.o
In file included from globalslinux.cpp:1:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c globalsosx.cpp -o globalsosx.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c globalsother.cpp -o globalsother.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c globalswin32.cpp -o globalswin32.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c gonnet.cpp -o gonnet.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
gonnet.cpp:137:14: warning: 'Gonnet160' defined but not used [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c henikoffweight.cpp -o henikoffweight.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c henikoffweightpb.cpp -o henikoffweightpb.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c html.cpp -o html.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c hydro.cpp -o hydro.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c intmath.cpp -o intmath.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c local.cpp -o local.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c main.cpp -o main.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c makerootmsa.cpp -o makerootmsa.o
makerootmsa.cpp: In function 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)':
makerootmsa.cpp:18:17: warning: unused variable 'uSeqLength' [-Wunused-variable]
makerootmsa.cpp: In function 'short int* MakeRootSeqE(const Seq&, const Tree&, unsigned int, const ProgNode*, Seq&, short int*, short int*)':
makerootmsa.cpp:94:17: warning: unused variable 'Path' [-Wunused-variable]
makerootmsa.cpp: In function 'void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)':
makerootmsa.cpp:168:17: warning: unused variable 'uTreeNodeCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
makerootmsa.cpp:12:13: warning: 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c makerootmsab.cpp -o makerootmsab.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c maketree.cpp -o maketree.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c mhack.cpp -o mhack.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c mpam200.cpp -o mpam200.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c msa.cpp -o msa.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
msa.cpp:385:13: warning: 'void FmtChar(char, unsigned int)' defined but not used [-Wunused-function]
msa.cpp:392:13: warning: 'void FmtInt(unsigned int, unsigned int)' defined but not used [-Wunused-function]
msa.cpp:407:13: warning: 'void FmtInt0(unsigned int, unsigned int)' defined but not used [-Wunused-function]
msa.cpp:419:13: warning: 'void FmtPad(unsigned int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c msa2.cpp -o msa2.o
msa2.cpp: In function 'void SetMSAWeightsMuscle(MSA&)':
msa2.cpp:357:9: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch]
msa2.cpp: In function 'void MSAAppend(MSA&, const MSA&)':
msa2.cpp:476:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c msadistkimura.cpp -o msadistkimura.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c msf.cpp -o msf.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
msf.cpp:24:20: warning: 'const char* strfind(const char*, const char*)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c muscle.cpp -o muscle.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c muscleout.cpp -o muscleout.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nucmx.cpp -o nucmx.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nwdasimple.cpp -o nwdasimple.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nwdasimple2.cpp -o nwdasimple2.o
In file included from nwdasimple2.cpp:3:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nwdasmall.cpp -o nwdasmall.o
In file included from nwdasmall.cpp:4:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nwrec.cpp -o nwrec.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c nwsmall.cpp -o nwsmall.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
objscore.cpp: In function 'SCORE ObjScore(const MSA&, const unsigned int*, unsigned int, const unsigned int*, unsigned int)':
objscore.cpp:31:9: warning: enumeration value 'OBJSCORE_Undefined' not handled in switch [-Wswitch]
objscore.cpp:31:9: warning: enumeration value 'OBJSCORE_SPM' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c objscore2.cpp -o objscore2.o
objscore2.cpp: In function 'SCORE TermGapScore(bool)':
objscore2.cpp:22:9: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch]
objscore2.cpp: In function 'SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)':
objscore2.cpp:62:8: warning: unused variable 'scoreGaps' [-Wunused-variable]
objscore2.cpp:63:7: warning: unused variable 'bGapping1' [-Wunused-variable]
objscore2.cpp:64:7: warning: unused variable 'bGapping2' [-Wunused-variable]
objscore2.cpp:67:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
objscore2.cpp:82:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
objscore2.cpp: In function 'SCORE ScoreSeqPairGaps(const MSA&, unsigned int, const MSA&, unsigned int)':
objscore2.cpp:140:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
objscore2.cpp:155:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
objscore2.cpp: In function 'SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)':
objscore2.cpp:314:17: warning: unused variable 'uColCount2' [-Wunused-variable]
objscore2.cpp: In function 'SCORE ObjScoreXP(const MSA&, const MSA&)':
objscore2.cpp:493:17: warning: unused variable 'w' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c objscoreda.cpp -o objscoreda.o
In file included from objscoreda.cpp:4:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c onexception.cpp -o onexception.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c options.cpp -o options.o
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c outweights.cpp -o outweights.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c pam200mafft.cpp -o pam200mafft.o
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces]
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
pam200mafft.cpp:6:14: warning: 'PAM200' defined but not used [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c params.cpp -o params.o
params.cpp: In function 'void SetPPScore(bool)':
params.cpp:441:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phy.cpp -o phy.o
phy.cpp: In member function 'void Tree::RootUnrootedTree(ROOT)':
phy.cpp:665:9: warning: unused variable 'dEdgeLength' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phy2.cpp -o phy2.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phy3.cpp -o phy3.o
phy3.cpp: In function 'void CalcInfo(const Tree&, unsigned int, unsigned int, EdgeInfo**)':
phy3.cpp:125:15: warning: unused variable 'dThisDist' [-Wunused-variable]
phy3.cpp: In function 'void FindRoot(const Tree&, unsigned int*, unsigned int*, double*, double*, ROOT)':
phy3.cpp:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable]
phy3.cpp:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable]
phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable]
phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable]
phy3.cpp: In function 'void RootByMidLongestSpan(const Tree&, EdgeInfo**, unsigned int*, unsigned int*, double*, double*)':
phy3.cpp:263:11: warning: variable 'uMostDistantLeaf' set but not used [-Wunused-but-set-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
phy3.cpp:45:13: warning: 'void ListEIs(EdgeInfo**, unsigned int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phy4.cpp -o phy4.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phyfromclust.cpp -o phyfromclust.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phyfromfile.cpp -o phyfromfile.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c physeq.cpp -o physeq.o
physeq.cpp: In member function 'void MSA::ToPhySequentialFile(TextFile&) const':
physeq.cpp:60:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
physeq.cpp:71:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
physeq.cpp: In member function 'void MSA::ToPhyInterleavedFile(TextFile&) const':
physeq.cpp:112:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
physeq.cpp:124:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c phytofile.cpp -o phytofile.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c posgap.cpp -o posgap.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c ppscore.cpp -o ppscore.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c profdb.cpp -o profdb.o
In file included from clustsetmsa.h:8:0,
                 from profdb.cpp:9:
msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c profile.cpp -o profile.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c profilefrommsa.cpp -o profilefrommsa.o
profilefrommsa.cpp: In function 'void ListProfile(const ProfPos*, unsigned int, const MSA*)':
profilefrommsa.cpp:131:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
profilefrommsa.cpp: In function 'unsigned int ResidueGroupFromFCounts(const FCOUNT*)':
profilefrommsa.cpp:230:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
profilefrommsa.cpp: In function 'ProfPos* ProfileFromMSA(const MSA&)':
profilefrommsa.cpp:245:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
profilefrommsa.cpp:253:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
profilefrommsa.cpp:15:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c progalign.cpp -o progalign.o
progalign.cpp: In function 'ProgNode* ProgressiveAlignE(const SeqVect&, const Tree&, MSA&)':
progalign.cpp:41:17: warning: unused variable 'uIterCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c progress.cpp -o progress.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c progressivealign.cpp -o progressivealign.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c pwpath.cpp -o pwpath.o
pwpath.cpp: In member function 'void PWPath::Validate() const':
pwpath.cpp:80:16: warning: unused variable 'LastEdge' [-Wunused-variable]
pwpath.cpp: In member function 'void PWPath::FromFile(TextFile&)':
pwpath.cpp:213:11: warning: unused variable 'uEdgeIndex' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c readmx.cpp -o readmx.o
readmx.cpp: In function 'float (* ReadMx(TextFile&))[32][32]':
readmx.cpp:83:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readmx.cpp:84:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readmx.cpp: In function 'float (* ReadMxFromR(std::vector<std::basic_string<char> >, float (*)[32]))[32][32]':
readmx.cpp:184:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readmx.cpp:185:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
readmx.cpp:30:17: warning: 'unsigned int MxCharToLetter(char)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c realigndiffs.cpp -o realigndiffs.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c realigndiffse.cpp -o realigndiffse.o
realigndiffse.cpp: In function 'void RealignDiffsE(const MSA&, const SeqVect&, const Tree&, const Tree&, const unsigned int*, MSA&, ProgNode*)':
realigndiffse.cpp:77:13: warning: unused variable 'uNewRight' [-Wunused-variable]
realigndiffse.cpp:80:13: warning: unused variable 'uOldRight' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refine.cpp -o refine.o
In file included from clustsetmsa.h:8:0,
                 from refine.cpp:9:
msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinehoriz.cpp -o refinehoriz.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinesubfams.cpp -o refinesubfams.o
refinesubfams.cpp: In function 'bool RefineSubfams(MSA&, const Tree&, unsigned int)':
refinesubfams.cpp:63:17: warning: unused variable 'uNodeCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinetree.cpp -o refinetree.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinetreee.cpp -o refinetreee.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinevert.cpp -o refinevert.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c refinew.cpp -o refinew.o
refinew.cpp: In function 'void AppendMSA(MSA&, const MSA&)':
refinew.cpp:22:17: warning: unused variable 'uColCountCat' [-Wunused-variable]
refinew.cpp: In function 'void RefineW(const MSA&, MSA&)':
refinew.cpp:125:13: warning: unused variable 'uOutCols' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c savebest.cpp -o savebest.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c scoredist.cpp -o scoredist.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c scoregaps.cpp -o scoregaps.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
scoregaps.cpp:37:13: warning: 'void FreeGapInfo(GAPINFO*)' defined but not used [-Wunused-function]
scoregaps.cpp:80:14: warning: 'SCORE Penalty(unsigned int, bool)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c scorehistory.cpp -o scorehistory.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c scorepp.cpp -o scorepp.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c seq.cpp -o seq.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c seqvect.cpp -o seqvect.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c setblosumweights.cpp -o setblosumweights.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c setgscweights.cpp -o setgscweights.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c setnewhandler.cpp -o setnewhandler.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c spfast.cpp -o spfast.o
spfast.cpp: In function 'SCORE ObjScoreSPDimer(const MSA&)':
spfast.cpp:252:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
spfast.cpp:14:20: warning: 'const char* GapTypeToStr(int)' defined but not used [-Wunused-function]
spfast.cpp:59:14: warning: 'SCORE SPColBrute(const MSA&, unsigned int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c sptest.cpp -o sptest.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c stabilize.cpp -o stabilize.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c subfam.cpp -o subfam.o
subfam.cpp: In function 'void AlignSubFam(SeqVect&, const Tree&, unsigned int, MSA&)':
subfam.cpp:173:6: warning: unused variable 'NotUsed' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c subfams.cpp -o subfams.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
subfams.cpp:10:13: warning: 'void GetMostDistantPair(DistFunc&, unsigned int*, unsigned int*)' defined but not used [-Wunused-function]
subfams.cpp:40:13: warning: 'void InitializeSingleSource(DistFunc&, unsigned int)' defined but not used [-Wunused-function]
subfams.cpp:52:13: warning: 'void Relax(DistFunc&, unsigned int, unsigned int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c sw.cpp -o sw.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
sw.cpp:20:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c termgaps.cpp -o termgaps.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c textfile.cpp -o textfile.o
textfile.cpp: In member function 'void TextFile::PutChar(char)':
textfile.cpp:111:6: warning: unused variable 'i' [-Wunused-variable]
textfile.cpp: In member function 'void TextFile::PutString(const char*)':
textfile.cpp:124:6: warning: unused variable 'iError' [-Wunused-variable]
textfile.cpp: In member function 'TEXTFILEPOS TextFile::GetPos()':
textfile.cpp:224:6: warning: unused variable 'i' [-Wunused-variable]
textfile.cpp: In member function 'void TextFile::SetPos(TEXTFILEPOS)':
textfile.cpp:237:6: warning: unused variable 'i' [-Wunused-variable]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c threewaywt.cpp -o threewaywt.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c tomhydro.cpp -o tomhydro.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c traceback.cpp -o traceback.o
traceback.cpp: In function 'SCORE TraceBack(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, PWPath&)':
traceback.cpp:21:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
traceback.cpp:59:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wuninitialized]
traceback.cpp:72:3: warning: 'cEdgeType' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c tracebackopt.cpp -o tracebackopt.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c tracebacksw.cpp -o tracebacksw.o
tracebacksw.cpp: In function 'void TraceBackSW(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, unsigned int, unsigned int, PWPath&)':
tracebacksw.cpp:22:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
tracebacksw.cpp:29:8: warning: unused variable 'scoreMax' [-Wunused-variable]
tracebacksw.cpp:34:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wuninitialized]
tracebacksw.cpp:47:3: warning: 'cEdgeType' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c treefrommsa.cpp -o treefrommsa.o
In file included from clustsetmsa.h:8:0,
                 from treefrommsa.cpp:5:
msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch]
msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c typetostr.cpp -o typetostr.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c upgma2.cpp -o upgma2.o
upgma2.cpp: In member function 'virtual void DistCalcTest::CalcDistRange(unsigned int, dist_t*) const':
upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces]
upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces]
upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces]
upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces]
upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces]
upgma2.cpp: In function 'void UPGMA2(const DistCalc&, Tree&, LINKAGE)':
upgma2.cpp:293:4: warning: 'dtNewDist' may be used uninitialized in this function [-Wuninitialized]
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
upgma2.cpp:68:13: warning: 'void ListState()' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c usage.cpp -o usage.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c validateids.cpp -o validateids.o
In file included from validateids.cpp:4:0:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c vtml2.cpp -o vtml2.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c writescorefile.cpp -o writescorefile.o
writescorefile.cpp: In function 'void WriteScoreFile(const MSA&)':
writescorefile.cpp:40:17: warning: 'Score' may be used uninitialized in this function [-Wuninitialized]
writescorefile.cpp:27:11: note: 'Score' was declared here
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c RMuscle.cpp -o RMuscle.o
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
g++ -m64 -shared -s -static-libgcc -o Muscle.dll tmp.def aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o 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 -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
make[2]: Leaving directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/Rtmpawe44h/R.INSTALL1cc411d1305b/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/d/biocbld/bbs-3.2-bioc/tmpdir/Rtmpawe44h/R.INSTALL1cc411d1305b/msa/src/Muscle'
----------------------------------------
---------------- MUSCLE ----------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile.win --directory=ClustalW
make[1]: Entering directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/Rtmpawe44h/R.INSTALL1cc411d1305b/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. "; \
D:/biocbld/BBS-3˜1.2-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/d/biocbld/bbs-3.2-bioc/tmpdir/Rtmpawe44h/R.INSTALL1cc411d1305b/msa/src/ClustalW/src'
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c pairwise/FullPairwiseAlign.cpp -o pairwise/FullPairwiseAlign.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c pairwise/FastPairwiseAlign.cpp -o pairwise/FastPairwiseAlign.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/MSFFileParser.cpp -o fileInput/MSFFileParser.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/FileReader.cpp -o fileInput/FileReader.o
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]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/PIRFileParser.cpp -o fileInput/PIRFileParser.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/RSFFileParser.cpp -o fileInput/RSFFileParser.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/GDEFileParser.cpp -o fileInput/GDEFileParser.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/InFileStream.cpp -o fileInput/InFileStream.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/ClustalFileParser.cpp -o fileInput/ClustalFileParser.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/PearsonFileParser.cpp -o fileInput/PearsonFileParser.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c fileInput/EMBLFileParser.cpp -o fileInput/EMBLFileParser.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UPGMA/RootedClusterTree.cpp -o tree/UPGMA/RootedClusterTree.o
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]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UPGMA/UPGMAAlgorithm.cpp -o tree/UPGMA/UPGMAAlgorithm.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UPGMA/Node.cpp -o tree/UPGMA/Node.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UPGMA/RootedGuideTree.cpp -o tree/UPGMA/RootedGuideTree.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UPGMA/RootedTreeOutput.cpp -o tree/UPGMA/RootedTreeOutput.o
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]
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]
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]
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]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/Tree.cpp -o tree/Tree.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/ClusterTree.cpp -o tree/ClusterTree.o
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]
tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/TreeInterface.cpp -o tree/TreeInterface.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/UnRootedClusterTree.cpp -o tree/UnRootedClusterTree.o
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]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/ClusterTreeOutput.cpp -o tree/ClusterTreeOutput.o
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]
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]
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]
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]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/RandomGenerator.cpp -o tree/RandomGenerator.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/NJTree.cpp -o tree/NJTree.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c tree/AlignmentSteps.cpp -o tree/AlignmentSteps.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c interface/CommandLineParser.cpp -o interface/CommandLineParser.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c substitutionMatrix/SubMatrix.cpp -o substitutionMatrix/SubMatrix.o
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]
substitutionMatrix/SubMatrix.cpp:1307:9: warning: unused variable 'nmat' [-Wunused-variable]
substitutionMatrix/SubMatrix.cpp:1308:9: warning: unused variable 'n' [-Wunused-variable]
substitutionMatrix/SubMatrix.cpp:1308:12: warning: unused variable 'llimit' [-Wunused-variable]
substitutionMatrix/SubMatrix.cpp:1308:20: warning: unused variable 'ulimit' [-Wunused-variable]
substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readUserMatrixFromR(Rcpp::NumericMatrix, clustalw::Matrix&, clustalw::Xref&)':
substitutionMatrix/SubMatrix.cpp:1361:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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]
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 [-Wuninitialized]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/Iteration.cpp -o multipleAlign/Iteration.o
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]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/MSA.cpp -o multipleAlign/MSA.o
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]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/MyersMillerProfileAlign.cpp -o multipleAlign/MyersMillerProfileAlign.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/ProfileStandard.cpp -o multipleAlign/ProfileStandard.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/ProfileWithSub.cpp -o multipleAlign/ProfileWithSub.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/ProfileBase.cpp -o multipleAlign/ProfileBase.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c multipleAlign/LowScoreSegProfile.cpp -o multipleAlign/LowScoreSegProfile.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/OutputFile.cpp -o general/OutputFile.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/UserParameters.cpp -o general/UserParameters.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/InvalidCombination.cpp -o general/InvalidCombination.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/DebugLog.cpp -o general/DebugLog.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/VectorOutOfRange.cpp -o general/VectorOutOfRange.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/SymMatrix.cpp -o general/SymMatrix.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c general/Stats.cpp -o general/Stats.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c Help.cpp -o Help.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c alignment/Alignment.cpp -o alignment/Alignment.o
alignment/Alignment.cpp: In member function 'bool clustalw::Alignment::keepPortionOfSeqArray(int, int)':
alignment/Alignment.cpp:1715:24: warning: variable 'posToAddTo' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c alignment/AlignmentOutput.cpp -o alignment/AlignmentOutput.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c alignment/ObjectiveScore.cpp -o alignment/ObjectiveScore.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c alignment/Sequence.cpp -o alignment/Sequence.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c Clustal.cpp -o Clustal.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"  -DHAVE_CONFIG_H -I.    -O2 -Wall  -mtune=core2 -c RClustalWMain.cpp -o RClustalWMain.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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:513:56: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
g++ -m64 -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 -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
make[2]: Leaving directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/Rtmpawe44h/R.INSTALL1cc411d1305b/msa/src/ClustalW/src'
make[1]: Leaving directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/Rtmpawe44h/R.INSTALL1cc411d1305b/msa/src/ClustalW'
----------------------------------------
--------------- ClustalW ---------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile.win --directory=ClustalOmega
make[1]: Entering directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/Rtmpawe44h/R.INSTALL1cc411d1305b/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=" -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; \
D:/biocbld/BBS-3˜1.2-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/d/biocbld/bbs-3.2-bioc/tmpdir/Rtmpawe44h/R.INSTALL1cc411d1305b/msa/src/ClustalOmega/src'
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
exceptions4c/e4c_lite.c:16:8: warning: (near initialization for 'e4c.jump') [-Wmissing-braces]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
argtable2/arg_int.c:89:4: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"   -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
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"   -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
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"   -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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<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]
clustal/hhalign_wrapper.c:84:9: warning: unused variable 'iR' [-Wunused-variable]
clustal/hhalign_wrapper.c: In function 'ReAttachLeadingGaps':
clustal/hhalign_wrapper.c:239:9: warning: variable 'iSize2' set but not used [-Wunused-but-set-variable]
clustal/hhalign_wrapper.c:238:9: warning: variable 'iSize1' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<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]
clustal/ktuple_pair.c:801:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
clustal/ktuple_pair.c:822:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<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]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<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]
clustal/pair_dist.c:218:0: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
clustal/pair_dist.c:228:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
clustal/pair_dist.c:177:10: warning: unused variable 'bPrintCR' [-Wunused-variable]
clustal/pair_dist.c: In function 'PairDistances':
clustal/pair_dist.c:336:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
clustal/pair_dist.c:359:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
clustal/pair_dist.c:376:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<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]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<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]
squid/clustal.c: In function 'WriteClustalForR':
squid/clustal.c:438:6: warning: unused variable 'cons' [-Wunused-variable]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
squid/hsregex.c: In function 'regbranch':
squid/hsregex.c:510:18: warning: 'flags' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<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]
squid/msf.c:85:11: warning: variable 'alleged_alen' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<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]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"   -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:56:0:
hhalign/util-C.h: In function 'float fast_log2(float)':
hhalign/util-C.h:92:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
hhalign/util-C.h:93:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
hhalign/util-C.h:94:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
hhalign/util-C.h: In function 'float fpow2(float)':
hhalign/util-C.h:109:23: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
hhalign/util-C.h: In function 'float fast_pow2(float)':
hhalign/util-C.h:156:35: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
hhalign/util-C.h:200:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
In file included from hhalign/hhalign.cpp:70:0:
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]
In file included from hhalign/hhalign.cpp:71:0:
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]
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]
hhalign/hhalignment-C.h:1430:19: warning: variable 'score_prev' set but not used [-Wunused-but-set-variable]
In file included from hhalign/hhalign.cpp:75:0:
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]
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]
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]
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]
In file included from hhalign/hhalign.cpp:76:0:
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]
hhalign/hhfunc-C.h:80:11: warning: unused variable 'fGThgiew' [-Wunused-variable]
hhalign/hhfunc-C.h:85:11: warning: unused variable 'zf1SeqTrans' [-Wunused-variable]
hhalign/hhfunc-C.h:86:11: warning: unused variable 'zf1SeqInit' [-Wunused-variable]
hhalign/hhfunc-C.h:87:11: warning: unused variable 'zf1SeqDel' [-Wunused-variable]
hhalign/hhfunc-C.h:88:11: warning: unused variable 'zf1SeqRevrt' [-Wunused-variable]
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]
hhalign/hhfunc-C.h:511:17: warning: unused variable 'NEFF_SCORE' [-Wunused-variable]
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:715:9: warning: variable 'Nali' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"   -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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/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 [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
g++ -m64 -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 -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
make[2]: Leaving directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/Rtmpawe44h/R.INSTALL1cc411d1305b/msa/src/ClustalOmega/src'
make[1]: Leaving directory `/cygdrive/d/biocbld/bbs-3.2-bioc/tmpdir/Rtmpawe44h/R.INSTALL1cc411d1305b/msa/src/ClustalOmega'
----------------------------------------
------------- ClustalOmega -------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
g++ -m64 -shared -s -static-libgcc -o msa.dll tmp.def R_init_msa.o -Wl,--whole-archive ./libGC.a ./libMuscle.a ./libClustalW.a ./libClustalOmega.a -Wl,--no-whole-archive -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/msa.buildbin-libdir/msa/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'msa' as msa_1.2.1.zip
* DONE (msa)

msa.Rcheck/examples_i386/msa-Ex.timings:

nameusersystemelapsed
MsaMetaData-class0.500.003.71
MsaMultipleAlignmentClasses0.320.000.31
msa-package0.320.000.89
msa0.800.010.81
msaClustalOmega0.540.000.55
msaClustalW0.610.002.51
msaMuscle0.880.021.22
msaPrettyPrint0.420.007.24

msa.Rcheck/examples_x64/msa-Ex.timings:

nameusersystemelapsed
MsaMetaData-class0.520.011.78
MsaMultipleAlignmentClasses0.430.020.45
msa-package0.390.001.78
msa0.830.030.86
msaClustalOmega0.450.000.45
msaClustalW0.50.00.5
msaMuscle0.700.020.71
msaPrettyPrint0.330.005.17