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BioC 3.3: CHECK report for CoGAPS on moscato2

This page was generated on 2016-10-13 12:49:27 -0700 (Thu, 13 Oct 2016).

Package 225/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoGAPS 2.6.0
Elana J. Fertig
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/CoGAPS
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (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: CoGAPS
Version: 2.6.0
Command: rm -rf CoGAPS.buildbin-libdir CoGAPS.Rcheck && mkdir CoGAPS.buildbin-libdir CoGAPS.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CoGAPS.buildbin-libdir CoGAPS_2.6.0.tar.gz >CoGAPS.Rcheck\00install.out 2>&1 && cp CoGAPS.Rcheck\00install.out CoGAPS-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=CoGAPS.buildbin-libdir --install="check:CoGAPS-install.out" --force-multiarch --no-vignettes --timings CoGAPS_2.6.0.tar.gz
StartedAt: 2016-10-13 02:24:20 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 02:29:13 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 292.9 seconds
RetCode: 0
Status:  OK  
CheckDir: CoGAPS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CoGAPS.buildbin-libdir CoGAPS.Rcheck && mkdir CoGAPS.buildbin-libdir CoGAPS.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CoGAPS.buildbin-libdir CoGAPS_2.6.0.tar.gz >CoGAPS.Rcheck\00install.out 2>&1 && cp CoGAPS.Rcheck\00install.out CoGAPS-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=CoGAPS.buildbin-libdir --install="check:CoGAPS-install.out" --force-multiarch --no-vignettes --timings CoGAPS_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/CoGAPS.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CoGAPS/DESCRIPTION' ... OK
* this is package 'CoGAPS' version '2.6.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'CoGAPS' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
binaryA: no visible global function definition for 'mtext'
gapsIntraPattern: no visible global function definition for 'cor'
plotAtoms: no visible global function definition for 'plot'
plotDiag: no visible global function definition for 'par'
plotDiag: no visible global function definition for 'hist'
plotDiag: no visible global function definition for 'plot'
plotGAPS: no visible global function definition for 'rainbow'
plotGAPS: no visible global function definition for 'legend'
plotP: no visible global function definition for 'rainbow'
plotP: no visible global function definition for 'plotCI'
plotP: no visible global function definition for 'points'
plotP: no visible global function definition for 'legend'
plotSmoothPatterns: no visible global function definition for
  'split.screen'
plotSmoothPatterns: no visible global function definition for 'screen'
plotSmoothPatterns: no visible global function definition for 'plot'
plotSmoothPatterns: no visible global function definition for 'loess'
plotSmoothPatterns: no visible global function definition for 'abline'
plotSmoothPatterns: no visible global function definition for 'lines'
plotSmoothPatterns: no visible global function definition for 'points'
plotSmoothPatterns: no visible global function definition for
  'close.screen'
reorderByPatternMatch: no visible global function definition for 'cor'
residuals: no visible global function definition for 'colorRampPalette'
Undefined global functions or variables:
  abline close.screen colorRampPalette cor hist legend lines loess
  mtext par plot plotCI points rainbow screen split.screen
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "abline", "close.screen", "hist", "legend",
             "lines", "mtext", "par", "plot", "points", "screen",
             "split.screen")
  importFrom("stats", "cor", "loess")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... NOTE
Found the following Makefile(s) without a final LF:
  src/Makevars
Some 'make' programs ignore lines not ending in LF.
* 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 'E:/biocbld/bbs-3.3-bioc/meat/CoGAPS.buildbin-libdir/CoGAPS/libs/i386/CoGAPS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'E:/biocbld/bbs-3.3-bioc/meat/CoGAPS.Rcheck/00check.log'
for details.

CoGAPS.Rcheck/00install.out:


install for i386

* installing *source* package 'CoGAPS' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c AtomicSupport.cc -o AtomicSupport.o
AtomicSupport.cc: In member function 'void gaps::AtomicSupport::FixedBins_initializeAtomic(unsigned int, long long unsigned int, double, double, char, const char*)':
AtomicSupport.cc:143:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (length != nBin)
                ^
AtomicSupport.cc: In member function 'void gaps::AtomicSupport::FixedBins_initializeAtomic(unsigned int, long long unsigned int, double, double, char, std::vector<std::vector<double> >)':
AtomicSupport.cc:218:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (length != nBin)
                ^
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c GAPSNorm.cpp -o GAPSNorm.o
GAPSNorm.cpp: In static member function 'static double gaps::GAPSNorm::calChi2(const double* const*, const double* const*, const double* const*, const double* const*, unsigned int, unsigned int, unsigned int)':
GAPSNorm.cpp:72:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m=0; m < nRow; ++m){
                         ^
GAPSNorm.cpp:86:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m=0; m < nRow; ++m)
                         ^
GAPSNorm.cpp: In static member function 'static std::pair<double, double> gaps::GAPSNorm::calcAlphaParameters(char, unsigned int, unsigned int, unsigned int, const double* const*, const double* const*, double**, double**, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int)':
GAPSNorm.cpp:623:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int jSample = 0; jSample < nCol; jSample++) {
                                  ^
GAPSNorm.cpp:626:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int jPattern = 0; jPattern < nFactor; jPattern++) {
                                      ^
GAPSNorm.cpp:639:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int jSample = 0; jSample < nCol; jSample++) {
                                  ^
GAPSNorm.cpp:643:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int jPattern = 0; jPattern < nFactor; jPattern++) {
                                      ^
GAPSNorm.cpp:665:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int jGene = 0; jGene < nRow; jGene++) {
                              ^
GAPSNorm.cpp:668:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int jPattern = 0; jPattern < nFactor; jPattern++) {
                                      ^
GAPSNorm.cpp:680:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int jGene = 0; jGene < nRow; jGene++) {
                              ^
GAPSNorm.cpp:684:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int jPattern = 0; jPattern < nFactor; jPattern++) {
                                      ^
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c GibbsSampler.cpp -o GibbsSampler.o
GibbsSampler.cpp: In member function 'std::vector<std::vector<std::vector<double> > > GibbsSampler::getNormedMatrices()':
GibbsSampler.cpp:511:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m< _nFactor; ++m){
                  ^
GibbsSampler.cpp:513:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n< _nCol; ++n){
                    ^
GibbsSampler.cpp:521:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow; ++m){
                     ^
GibbsSampler.cpp:522:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nFactor; ++n){
                       ^
GibbsSampler.cpp:527:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor; ++m){
                     ^
GibbsSampler.cpp:528:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nCol; ++n){
                       ^
GibbsSampler.cpp: In member function 'std::vector<std::vector<double> > GibbsSampler::createSampleAMat(std::map<long long unsigned int, double>)':
GibbsSampler.cpp:560:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i < _nRow; i++){
                    ^
GibbsSampler.cpp: In member function 'std::vector<std::vector<double> > GibbsSampler::createSamplePMat(std::map<long long unsigned int, double>)':
GibbsSampler.cpp:580:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i < _nFactor; i++){
                    ^
GibbsSampler.cpp: In member function 'bool GibbsSampler::move(char, const double* const*, const double* const*, double**, double**)':
GibbsSampler.cpp:1489:10: warning: variable 'lambda' set but not used [-Wunused-but-set-variable]
   double lambda;
          ^
GibbsSampler.cpp: In member function 'void GibbsSampler::compute_statistics_prepare_matrices(long unsigned int)':
GibbsSampler.cpp:2036:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m< _nFactor; ++m){
                  ^
GibbsSampler.cpp:2038:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n< _nCol; ++n){
                    ^
GibbsSampler.cpp:2051:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow ; ++m)
                     ^
GibbsSampler.cpp:2053:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow; ++m){
                     ^
GibbsSampler.cpp:2054:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nFactor; ++n){
                       ^
GibbsSampler.cpp:2060:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow ; ++m)
                     ^
GibbsSampler.cpp:2062:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow; ++m){
                     ^
GibbsSampler.cpp:2063:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nFactor; ++n){
                       ^
GibbsSampler.cpp:2069:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor ; ++m)
                     ^
GibbsSampler.cpp:2071:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor; ++m){
                     ^
GibbsSampler.cpp:2072:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nCol; ++n){
                       ^
GibbsSampler.cpp:2078:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor ; ++m)
                     ^
GibbsSampler.cpp:2080:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor; ++m){
                     ^
GibbsSampler.cpp:2081:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nCol; ++n){
                       ^
GibbsSampler.cpp:2091:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow; ++m){
                     ^
GibbsSampler.cpp:2092:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nFactor; ++n){
                       ^
GibbsSampler.cpp:2097:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow; ++m){
                     ^
GibbsSampler.cpp:2098:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nFactor; ++n){
                       ^
GibbsSampler.cpp:2103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor; ++m){
                     ^
GibbsSampler.cpp:2104:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nCol; ++n){
                       ^
GibbsSampler.cpp:2109:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor; ++m){
                     ^
GibbsSampler.cpp:2110:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nCol; ++n){
                       ^
GibbsSampler.cpp: In member function 'void GibbsSampler::compute_statistics(char*, char*, char*, char*, char*, char*, unsigned int)':
GibbsSampler.cpp:2127:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nRow ; ++m){
                   ^
GibbsSampler.cpp:2128:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nFactor; ++n){
                    ^
GibbsSampler.cpp:2133:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nRow ; ++m){
                   ^
GibbsSampler.cpp:2134:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nFactor; ++n){
                    ^
GibbsSampler.cpp:2140:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nFactor ; ++m){
                   ^
GibbsSampler.cpp:2141:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nCol; ++n){
                    ^
GibbsSampler.cpp:2146:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nFactor ; ++m){
                   ^
GibbsSampler.cpp:2147:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nCol; ++n){
                    ^
GibbsSampler.cpp:2155:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nRow ; ++m)
                   ^
GibbsSampler.cpp: In member function 'void GibbsSampler::compute_statistics(unsigned int, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&)':
GibbsSampler.cpp:2234:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < _nRow; i++)
                    ^
GibbsSampler.cpp:2239:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < _nRow; i++)
                    ^
GibbsSampler.cpp:2244:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < _nFactor; i++)
                    ^
GibbsSampler.cpp:2249:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < _nFactor; i++)
                    ^
GibbsSampler.cpp:2260:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nRow ; ++m){
                   ^
GibbsSampler.cpp:2261:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nFactor; ++n){
                    ^
GibbsSampler.cpp:2267:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nRow ; ++m){
                   ^
GibbsSampler.cpp:2268:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nFactor; ++n){
                    ^
GibbsSampler.cpp:2276:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nFactor ; ++m){
                   ^
GibbsSampler.cpp:2277:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nCol; ++n){
                    ^
GibbsSampler.cpp:2284:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nFactor ; ++m){
                   ^
GibbsSampler.cpp:2285:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nCol; ++n){
                    ^
GibbsSampler.cpp: In member function 'double GibbsSampler::getMass(char, double, unsigned int, unsigned int, const double* const*, const double* const*, const double* const*, const double* const*, double)':
GibbsSampler.cpp:2406:24: warning: 'lambda' may be used uninitialized in this function [-Wmaybe-uninitialized]
   double mean  = (2*su - lambda)/(2*s);
                        ^
GibbsSampler.cpp: In member function 'bool GibbsSampler::move(char, const double* const*, const double* const*, double**, double**)':
GibbsSampler.cpp:1472:3: warning: 'bin1' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (bin1 == bin2){
   ^
GibbsSampler.cpp:1472:3: warning: 'bin2' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1520:76: warning: 'newMass1' may be used uninitialized in this function [-Wmaybe-uninitialized]
   _new_atomicProposal.insert(pair<unsigned long long, double>(loc1,newMass1-mass1));
                                                                            ^
GibbsSampler.cpp:1520:76: warning: 'mass1' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1521:76: warning: 'newMass2' may be used uninitialized in this function [-Wmaybe-uninitialized]
   _new_atomicProposal.insert(pair<unsigned long long, double>(loc2,newMass2-mass2));
                                                                            ^
GibbsSampler.cpp:1521:76: warning: 'mass2' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1538:29: warning: 'delLLnew' may be used uninitialized in this function [-Wmaybe-uninitialized]
     tmp = priorLL + delLLnew*_annealingTemperature;
                             ^
GibbsSampler.cpp: In member function 'bool GibbsSampler::exchange(char, const double* const*, const double* const*, double**, double**)':
GibbsSampler.cpp:1658:3: warning: 'bin1' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (bin1 == bin2){
   ^
GibbsSampler.cpp:1658:3: warning: 'bin2' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1925:29: warning: 'delLLnew' may be used uninitialized in this function [-Wmaybe-uninitialized]
     tmp = priorLL + delLLnew*_annealingTemperature;
                             ^
GibbsSampler.cpp:1877:61: warning: 'lambda' may be used uninitialized in this function [-Wmaybe-uninitialized]
       pnew = sub_func::dgamma(newMass2, 2., 1./lambda, false);
                                                             ^
GibbsSampler.cpp:1795:70: warning: 'sd' may be used uninitialized in this function [-Wmaybe-uninitialized]
     double pupper = sub_func::pnorm(mass2, mean, sd, DOUBLE_NEGINF, 0);
                                                                      ^
GibbsSampler.cpp:1795:70: warning: 'mean' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1784:21: warning: 'su' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (s == 0. && su == 0.){
                     ^
GibbsSampler.cpp:1764:97: warning: 'iSample2' may be used uninitialized in this function [-Wmaybe-uninitialized]
                                                iPattern1, iGene2, iPattern2, iSample1, iSample2);
                                                                                                 ^
GibbsSampler.cpp:1764:97: warning: 'iSample1' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1764:97: warning: 'iPattern2' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1764:97: warning: 'iGene2' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1764:97: warning: 'iPattern1' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1764:97: warning: 'iGene1' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1909:76: warning: 'newMass2' may be used uninitialized in this function [-Wmaybe-uninitialized]
   _new_atomicProposal.insert(pair<unsigned long long, double>(loc2,newMass2-mass2));
                                                                            ^
GibbsSampler.cpp:1801:14: warning: 'newMass1' may be used uninitialized in this function [-Wmaybe-uninitialized]
  s < epsilon || 
              ^
GibbsSampler.cpp:1795:70: warning: 'mass2' may be used uninitialized in this function [-Wmaybe-uninitialized]
     double pupper = sub_func::pnorm(mass2, mean, sd, DOUBLE_NEGINF, 0);
                                                                      ^
GibbsSampler.cpp:1794:71: warning: 'mass1' may be used uninitialized in this function [-Wmaybe-uninitialized]
     double plower = sub_func::pnorm(-mass1, mean, sd, DOUBLE_NEGINF, 0);
                                                                       ^
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c GibbsSamplerMap.cpp -o GibbsSamplerMap.o
GibbsSamplerMap.cpp: In constructor 'GibbsSamplerMap::GibbsSamplerMap(long unsigned int, long unsigned int, unsigned int, double, double, double, double, long unsigned int, long unsigned int, double, double, long long unsigned int, char, char, char, char, const string&, const string&, const string&, std::vector<std::vector<double> >&, char)':
GibbsSamplerMap.cpp:48:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i < parameters.size(); i++){
                     ^
GibbsSamplerMap.cpp:52:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int j=0; j < parameters[0].size();j++){
                      ^
GibbsSamplerMap.cpp:55:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int j=0; j < parameters[0].size();j++){
                      ^
GibbsSamplerMap.cpp: In constructor 'GibbsSamplerMap::GibbsSamplerMap(long unsigned int, long unsigned int, unsigned int, double, double, double, double, long unsigned int, long unsigned int, double, double, long long unsigned int, char, char, char, char, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, const string&, std::vector<std::vector<double> >&, char)':
GibbsSamplerMap.cpp:79:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i < parameters.size(); i++){
                     ^
GibbsSamplerMap.cpp:83:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int j=0; j < parameters[0].size();j++){
                      ^
GibbsSamplerMap.cpp:86:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int j=0; j < parameters[0].size();j++){
                      ^
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::init_Mapped_Matrix()':
GibbsSamplerMap.cpp:111:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int iCol = 0; iCol < _nFixedMaps; iCol++){
                          ^
GibbsSamplerMap.cpp:117:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int iRow = 0; iRow < _nFixedMaps; iRow++){
                          ^
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::initialize_atomic_domain_map()':
GibbsSamplerMap.cpp:140:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int iCol = 0; iCol < _nFixedMaps; iCol++){
                          ^
GibbsSamplerMap.cpp:144:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int iAtom = 0; iAtom < _nRow; iAtom++){
                             ^
GibbsSamplerMap.cpp:161:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int iRow = 0; iRow < _nFixedMaps; iRow++){
                          ^
GibbsSamplerMap.cpp:167:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int iAtom = 0; iAtom < _nCol; iAtom++){
                              ^
GibbsSamplerMap.cpp: In member function 'std::vector<std::vector<double> > GibbsSamplerMap::createSampleAMatMap(std::map<long long unsigned int, double>)':
GibbsSamplerMap.cpp:520:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i < _nRow; i++){
                    ^
GibbsSamplerMap.cpp:540:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int iRow=0; iRow < _nRow; iRow++){
                          ^
GibbsSamplerMap.cpp: In member function 'std::vector<std::vector<double> > GibbsSamplerMap::createSamplePMatMap(std::map<long long unsigned int, double>)':
GibbsSamplerMap.cpp:556:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i < _nFactor; i++){
                    ^
GibbsSamplerMap.cpp:577:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int iCol=0; iCol < _nCol; iCol++){
                          ^
GibbsSamplerMap.cpp: In member function 'double GibbsSamplerMap::computeDeltaLLBDMap(char, const double* const*, const double* const*, const double* const*, const double* const*, std::vector<double>&, unsigned int)':
GibbsSamplerMap.cpp:219:10: warning: 'DelLL' may be used uninitialized in this function [-Wmaybe-uninitialized]
   return DelLL;
          ^
GibbsSamplerMap.cpp: In member function 'double GibbsSamplerMap::computeDeltaLLMEMap(char, const double* const*, const double* const*, const double* const*, const double* const*, std::vector<double>&, unsigned int, std::vector<double>&, unsigned int)':
GibbsSamplerMap.cpp:254:10: warning: 'DelLL' may be used uninitialized in this function [-Wmaybe-uninitialized]
   return DelLL;
          ^
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c Matrix.cpp -o Matrix.o
Matrix.cpp: In constructor 'Matrix::Matrix(unsigned int, unsigned int, char, double)':
Matrix.cpp:44:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _n_row ; ++m){
                   ^
Matrix.cpp: In constructor 'Matrix::Matrix(std::vector<std::vector<double> >&, char)':
Matrix.cpp:59:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _n_row ; ++m) {
                     ^
Matrix.cpp:62:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _n_row ; ++m) {
                     ^
Matrix.cpp:63:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n < _n_col; ++n) {
                         ^
Matrix.cpp: In constructor 'Matrix::Matrix(const char*, char)':
Matrix.cpp:90:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _n_row ; ++m) {
                     ^
Matrix.cpp:94:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _n_row ; ++m) {
                     ^
Matrix.cpp:95:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n < _n_col; ++n) {
                         ^
Matrix.cpp: In destructor 'Matrix::˜Matrix()':
Matrix.cpp:103:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0 ; m < _n_row ; ++m)
                      ^
Matrix.cpp: In member function 'void Matrix::born_matrix(unsigned int, unsigned int, char, double)':
Matrix.cpp:122:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _n_row ; ++m) {
                     ^
Matrix.cpp: In member function 'void Matrix::matrix_init()':
Matrix.cpp:134:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int m=0;m<_n_row;++m) {
                  ^
Matrix.cpp:135:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n<_n_col;++n) {        
                        ^
Matrix.cpp: In member function 'void Matrix::setRow(std::vector<double>, int)':
Matrix.cpp:160:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n<_n_col;++n) {        
                        ^
Matrix.cpp: In member function 'void Matrix::setCol(std::vector<double>, int)':
Matrix.cpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n<_n_row;++n) {        
                        ^
Matrix.cpp: In member function 'std::vector<double> Matrix::get_Row(int)':
Matrix.cpp:182:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int iCol = 0; iCol < _n_col; iCol++){
                           ^
Matrix.cpp: In member function 'std::vector<double> Matrix::get_Col(int)':
Matrix.cpp:190:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int iRow=0; iRow < _n_row; iRow++){
                         ^
Matrix.cpp: In member function 'double Matrix::cal_mean() const':
Matrix.cpp:238:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int m=0;m < _n_row;++m) {
                   ^
Matrix.cpp:239:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n < _n_col;++n) {
                         ^
Matrix.cpp: In member function 'double Matrix::cal_totalsum() const':
Matrix.cpp:249:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int m=0;m < _n_row;++m) {
                   ^
Matrix.cpp:250:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n < _n_col;++n) {
                         ^
Matrix.cpp: In member function 'void Matrix::display_matrixF(std::ofstream&)':
Matrix.cpp:313:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int m=0;m<_n_row;++m) {
                  ^
Matrix.cpp:314:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n<_n_col;++n) {
                        ^
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c cogapsR.cpp -o cogapsR.o
cogapsR.cpp: In function 'Rcpp::List cogaps(Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::NumericVector)':
cogapsR.cpp:442:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (unsigned long ext_iter=1; ext_iter <= nEquilCool; ++ext_iter){
                                          ^
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c cogapsmapR.cpp -o cogapsmapR.o
cogapsmapR.cpp: In function 'Rcpp::List cogapsMap(Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::NumericVector)':
cogapsmapR.cpp:401:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (unsigned long ext_iter=1; ext_iter <= nEquilCool; ++ext_iter){
                                          ^
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c cogapsmaptestR.cpp -o cogapsmaptestR.o
cogapsmaptestR.cpp: In function 'Rcpp::List cogapsMapTest(Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::NumericVector)':
cogapsmaptestR.cpp:481:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (unsigned long ext_iter=1; ext_iter <= nEquilCool; ++ext_iter){
                                          ^
cogapsmaptestR.cpp:598:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int iEquil=0; iEquil < nEquil; iEquil++){
                             ^
cogapsmaptestR.cpp:607:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int iSample=0; iSample < nSample; iSample++){
                               ^
cogapsmaptestR.cpp:699:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                   ^
cogapsmaptestR.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                   ^
cogapsmaptestR.cpp:731:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                   ^
cogapsmaptestR.cpp:747:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                   ^
cogapsmaptestR.cpp:776:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                   ^
cogapsmaptestR.cpp:791:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                   ^
cogapsmaptestR.cpp:806:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                   ^
cogapsmaptestR.cpp:821:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                   ^
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c cogapstestR.cpp -o cogapstestR.o
cogapstestR.cpp: In function 'Rcpp::List cogapsTest(Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::NumericVector)':
cogapstestR.cpp:509:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (unsigned long ext_iter=1; ext_iter <= nEquilCool; ++ext_iter){
                                          ^
cogapstestR.cpp:634:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int iEquil=0; iEquil < nEquil; iEquil++){
                            ^
cogapstestR.cpp:643:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int iSample=0; iSample < nSample; iSample++){
                              ^
cogapstestR.cpp:733:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                   ^
cogapstestR.cpp:749:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                   ^
cogapstestR.cpp:765:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                   ^
cogapstestR.cpp:781:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                   ^
cogapstestR.cpp:809:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                   ^
cogapstestR.cpp:824:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                   ^
cogapstestR.cpp:839:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                   ^
cogapstestR.cpp:854:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                   ^
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c randgen.cpp -o randgen.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c sub_func.cpp -o sub_func.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o CoGAPS.dll tmp.def AtomicSupport.o GAPSNorm.o GibbsSampler.o GibbsSamplerMap.o Matrix.o RcppExports.o cogapsR.o cogapsmapR.o cogapsmaptestR.o cogapstestR.o randgen.o sub_func.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/CoGAPS.buildbin-libdir/CoGAPS/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'CoGAPS' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c AtomicSupport.cc -o AtomicSupport.o
AtomicSupport.cc: In member function 'void gaps::AtomicSupport::FixedBins_initializeAtomic(unsigned int, long long unsigned int, double, double, char, const char*)':
AtomicSupport.cc:143:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (length != nBin)
                ^
AtomicSupport.cc: In member function 'void gaps::AtomicSupport::FixedBins_initializeAtomic(unsigned int, long long unsigned int, double, double, char, std::vector<std::vector<double> >)':
AtomicSupport.cc:218:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (length != nBin)
                ^
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c GAPSNorm.cpp -o GAPSNorm.o
GAPSNorm.cpp: In static member function 'static double gaps::GAPSNorm::calChi2(const double* const*, const double* const*, const double* const*, const double* const*, unsigned int, unsigned int, unsigned int)':
GAPSNorm.cpp:72:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m=0; m < nRow; ++m){
                         ^
GAPSNorm.cpp:86:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m=0; m < nRow; ++m)
                         ^
GAPSNorm.cpp: In static member function 'static std::pair<double, double> gaps::GAPSNorm::calcAlphaParameters(char, unsigned int, unsigned int, unsigned int, const double* const*, const double* const*, double**, double**, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int)':
GAPSNorm.cpp:623:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int jSample = 0; jSample < nCol; jSample++) {
                                  ^
GAPSNorm.cpp:626:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int jPattern = 0; jPattern < nFactor; jPattern++) {
                                      ^
GAPSNorm.cpp:639:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int jSample = 0; jSample < nCol; jSample++) {
                                  ^
GAPSNorm.cpp:643:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int jPattern = 0; jPattern < nFactor; jPattern++) {
                                      ^
GAPSNorm.cpp:665:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int jGene = 0; jGene < nRow; jGene++) {
                              ^
GAPSNorm.cpp:668:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int jPattern = 0; jPattern < nFactor; jPattern++) {
                                      ^
GAPSNorm.cpp:680:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int jGene = 0; jGene < nRow; jGene++) {
                              ^
GAPSNorm.cpp:684:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int jPattern = 0; jPattern < nFactor; jPattern++) {
                                      ^
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c GibbsSampler.cpp -o GibbsSampler.o
GibbsSampler.cpp: In member function 'std::vector<std::vector<std::vector<double> > > GibbsSampler::getNormedMatrices()':
GibbsSampler.cpp:511:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m< _nFactor; ++m){
                  ^
GibbsSampler.cpp:513:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n< _nCol; ++n){
                    ^
GibbsSampler.cpp:521:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow; ++m){
                     ^
GibbsSampler.cpp:522:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nFactor; ++n){
                       ^
GibbsSampler.cpp:527:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor; ++m){
                     ^
GibbsSampler.cpp:528:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nCol; ++n){
                       ^
GibbsSampler.cpp: In member function 'std::vector<std::vector<double> > GibbsSampler::createSampleAMat(std::map<long long unsigned int, double>)':
GibbsSampler.cpp:560:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i < _nRow; i++){
                    ^
GibbsSampler.cpp: In member function 'std::vector<std::vector<double> > GibbsSampler::createSamplePMat(std::map<long long unsigned int, double>)':
GibbsSampler.cpp:580:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i < _nFactor; i++){
                    ^
GibbsSampler.cpp: In member function 'bool GibbsSampler::move(char, const double* const*, const double* const*, double**, double**)':
GibbsSampler.cpp:1489:10: warning: variable 'lambda' set but not used [-Wunused-but-set-variable]
   double lambda;
          ^
GibbsSampler.cpp: In member function 'void GibbsSampler::compute_statistics_prepare_matrices(long unsigned int)':
GibbsSampler.cpp:2036:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m< _nFactor; ++m){
                  ^
GibbsSampler.cpp:2038:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n< _nCol; ++n){
                    ^
GibbsSampler.cpp:2051:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow ; ++m)
                     ^
GibbsSampler.cpp:2053:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow; ++m){
                     ^
GibbsSampler.cpp:2054:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nFactor; ++n){
                       ^
GibbsSampler.cpp:2060:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow ; ++m)
                     ^
GibbsSampler.cpp:2062:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow; ++m){
                     ^
GibbsSampler.cpp:2063:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nFactor; ++n){
                       ^
GibbsSampler.cpp:2069:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor ; ++m)
                     ^
GibbsSampler.cpp:2071:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor; ++m){
                     ^
GibbsSampler.cpp:2072:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nCol; ++n){
                       ^
GibbsSampler.cpp:2078:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor ; ++m)
                     ^
GibbsSampler.cpp:2080:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor; ++m){
                     ^
GibbsSampler.cpp:2081:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nCol; ++n){
                       ^
GibbsSampler.cpp:2091:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow; ++m){
                     ^
GibbsSampler.cpp:2092:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nFactor; ++n){
                       ^
GibbsSampler.cpp:2097:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nRow; ++m){
                     ^
GibbsSampler.cpp:2098:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nFactor; ++n){
                       ^
GibbsSampler.cpp:2103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor; ++m){
                     ^
GibbsSampler.cpp:2104:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nCol; ++n){
                       ^
GibbsSampler.cpp:2109:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _nFactor; ++m){
                     ^
GibbsSampler.cpp:2110:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int n=0; n < _nCol; ++n){
                       ^
GibbsSampler.cpp: In member function 'void GibbsSampler::compute_statistics(char*, char*, char*, char*, char*, char*, unsigned int)':
GibbsSampler.cpp:2127:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nRow ; ++m){
                   ^
GibbsSampler.cpp:2128:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nFactor; ++n){
                    ^
GibbsSampler.cpp:2133:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nRow ; ++m){
                   ^
GibbsSampler.cpp:2134:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nFactor; ++n){
                    ^
GibbsSampler.cpp:2140:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nFactor ; ++m){
                   ^
GibbsSampler.cpp:2141:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nCol; ++n){
                    ^
GibbsSampler.cpp:2146:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nFactor ; ++m){
                   ^
GibbsSampler.cpp:2147:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nCol; ++n){
                    ^
GibbsSampler.cpp:2155:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nRow ; ++m)
                   ^
GibbsSampler.cpp: In member function 'void GibbsSampler::compute_statistics(unsigned int, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&)':
GibbsSampler.cpp:2234:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < _nRow; i++)
                    ^
GibbsSampler.cpp:2239:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < _nRow; i++)
                    ^
GibbsSampler.cpp:2244:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < _nFactor; i++)
                    ^
GibbsSampler.cpp:2249:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < _nFactor; i++)
                    ^
GibbsSampler.cpp:2260:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nRow ; ++m){
                   ^
GibbsSampler.cpp:2261:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nFactor; ++n){
                    ^
GibbsSampler.cpp:2267:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nRow ; ++m){
                   ^
GibbsSampler.cpp:2268:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nFactor; ++n){
                    ^
GibbsSampler.cpp:2276:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nFactor ; ++m){
                   ^
GibbsSampler.cpp:2277:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nCol; ++n){
                    ^
GibbsSampler.cpp:2284:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _nFactor ; ++m){
                   ^
GibbsSampler.cpp:2285:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n=0; n<_nCol; ++n){
                    ^
GibbsSampler.cpp: In member function 'double GibbsSampler::getMass(char, double, unsigned int, unsigned int, const double* const*, const double* const*, const double* const*, const double* const*, double)':
GibbsSampler.cpp:2406:24: warning: 'lambda' may be used uninitialized in this function [-Wmaybe-uninitialized]
   double mean  = (2*su - lambda)/(2*s);
                        ^
GibbsSampler.cpp: In member function 'bool GibbsSampler::move(char, const double* const*, const double* const*, double**, double**)':
GibbsSampler.cpp:1472:3: warning: 'bin1' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (bin1 == bin2){
   ^
GibbsSampler.cpp:1472:3: warning: 'bin2' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1521:76: warning: 'newMass2' may be used uninitialized in this function [-Wmaybe-uninitialized]
   _new_atomicProposal.insert(pair<unsigned long long, double>(loc2,newMass2-mass2));
                                                                            ^
GibbsSampler.cpp:1520:76: warning: 'newMass1' may be used uninitialized in this function [-Wmaybe-uninitialized]
   _new_atomicProposal.insert(pair<unsigned long long, double>(loc1,newMass1-mass1));
                                                                            ^
GibbsSampler.cpp:1521:76: warning: 'mass2' may be used uninitialized in this function [-Wmaybe-uninitialized]
   _new_atomicProposal.insert(pair<unsigned long long, double>(loc2,newMass2-mass2));
                                                                            ^
GibbsSampler.cpp:1520:76: warning: 'mass1' may be used uninitialized in this function [-Wmaybe-uninitialized]
   _new_atomicProposal.insert(pair<unsigned long long, double>(loc1,newMass1-mass1));
                                                                            ^
GibbsSampler.cpp:1139:17: warning: 'delLLnew' may be used uninitialized in this function [-Wmaybe-uninitialized]
   _sysChi2 -= 2.*delsysChi2;
                 ^
GibbsSampler.cpp:1507:10: note: 'delLLnew' was declared here
   double delLLnew;
          ^
GibbsSampler.cpp: In member function 'bool GibbsSampler::exchange(char, const double* const*, const double* const*, double**, double**)':
GibbsSampler.cpp:1658:3: warning: 'bin1' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (bin1 == bin2){
   ^
GibbsSampler.cpp:1658:3: warning: 'bin2' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1925:29: warning: 'delLLnew' may be used uninitialized in this function [-Wmaybe-uninitialized]
     tmp = priorLL + delLLnew*_annealingTemperature;
                             ^
GibbsSampler.cpp:1877:61: warning: 'lambda' may be used uninitialized in this function [-Wmaybe-uninitialized]
       pnew = sub_func::dgamma(newMass2, 2., 1./lambda, false);
                                                             ^
GibbsSampler.cpp:1795:70: warning: 'sd' may be used uninitialized in this function [-Wmaybe-uninitialized]
     double pupper = sub_func::pnorm(mass2, mean, sd, DOUBLE_NEGINF, 0);
                                                                      ^
GibbsSampler.cpp:1795:70: warning: 'mean' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1784:21: warning: 'su' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (s == 0. && su == 0.){
                     ^
GibbsSampler.cpp:1764:97: warning: 'iSample2' may be used uninitialized in this function [-Wmaybe-uninitialized]
                                                iPattern1, iGene2, iPattern2, iSample1, iSample2);
                                                                                                 ^
GibbsSampler.cpp:1764:97: warning: 'iSample1' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1764:97: warning: 'iPattern2' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1764:97: warning: 'iGene2' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1764:97: warning: 'iPattern1' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1764:97: warning: 'iGene1' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler.cpp:1909:76: warning: 'newMass2' may be used uninitialized in this function [-Wmaybe-uninitialized]
   _new_atomicProposal.insert(pair<unsigned long long, double>(loc2,newMass2-mass2));
                                                                            ^
GibbsSampler.cpp:1801:14: warning: 'newMass1' may be used uninitialized in this function [-Wmaybe-uninitialized]
  s < epsilon || 
              ^
GibbsSampler.cpp:1795:70: warning: 'mass2' may be used uninitialized in this function [-Wmaybe-uninitialized]
     double pupper = sub_func::pnorm(mass2, mean, sd, DOUBLE_NEGINF, 0);
                                                                      ^
GibbsSampler.cpp:1794:71: warning: 'mass1' may be used uninitialized in this function [-Wmaybe-uninitialized]
     double plower = sub_func::pnorm(-mass1, mean, sd, DOUBLE_NEGINF, 0);
                                                                       ^
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c GibbsSamplerMap.cpp -o GibbsSamplerMap.o
GibbsSamplerMap.cpp: In constructor 'GibbsSamplerMap::GibbsSamplerMap(long unsigned int, long unsigned int, unsigned int, double, double, double, double, long unsigned int, long unsigned int, double, double, long long unsigned int, char, char, char, char, const string&, const string&, const string&, std::vector<std::vector<double> >&, char)':
GibbsSamplerMap.cpp:48:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i < parameters.size(); i++){
                     ^
GibbsSamplerMap.cpp:52:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int j=0; j < parameters[0].size();j++){
                      ^
GibbsSamplerMap.cpp:55:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int j=0; j < parameters[0].size();j++){
                      ^
GibbsSamplerMap.cpp: In constructor 'GibbsSamplerMap::GibbsSamplerMap(long unsigned int, long unsigned int, unsigned int, double, double, double, double, long unsigned int, long unsigned int, double, double, long long unsigned int, char, char, char, char, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, const string&, std::vector<std::vector<double> >&, char)':
GibbsSamplerMap.cpp:79:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i < parameters.size(); i++){
                     ^
GibbsSamplerMap.cpp:83:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int j=0; j < parameters[0].size();j++){
                      ^
GibbsSamplerMap.cpp:86:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int j=0; j < parameters[0].size();j++){
                      ^
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::init_Mapped_Matrix()':
GibbsSamplerMap.cpp:111:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int iCol = 0; iCol < _nFixedMaps; iCol++){
                          ^
GibbsSamplerMap.cpp:117:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int iRow = 0; iRow < _nFixedMaps; iRow++){
                          ^
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::initialize_atomic_domain_map()':
GibbsSamplerMap.cpp:140:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int iCol = 0; iCol < _nFixedMaps; iCol++){
                          ^
GibbsSamplerMap.cpp:144:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int iAtom = 0; iAtom < _nRow; iAtom++){
                             ^
GibbsSamplerMap.cpp:161:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int iRow = 0; iRow < _nFixedMaps; iRow++){
                          ^
GibbsSamplerMap.cpp:167:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int iAtom = 0; iAtom < _nCol; iAtom++){
                              ^
GibbsSamplerMap.cpp: In member function 'std::vector<std::vector<double> > GibbsSamplerMap::createSampleAMatMap(std::map<long long unsigned int, double>)':
GibbsSamplerMap.cpp:520:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i < _nRow; i++){
                    ^
GibbsSamplerMap.cpp:540:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int iRow=0; iRow < _nRow; iRow++){
                          ^
GibbsSamplerMap.cpp: In member function 'std::vector<std::vector<double> > GibbsSamplerMap::createSamplePMatMap(std::map<long long unsigned int, double>)':
GibbsSamplerMap.cpp:556:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i < _nFactor; i++){
                    ^
GibbsSamplerMap.cpp:577:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int iCol=0; iCol < _nCol; iCol++){
                          ^
GibbsSamplerMap.cpp: In member function 'double GibbsSamplerMap::computeDeltaLLBDMap(char, const double* const*, const double* const*, const double* const*, const double* const*, std::vector<double>&, unsigned int)':
GibbsSamplerMap.cpp:219:10: warning: 'DelLL' may be used uninitialized in this function [-Wmaybe-uninitialized]
   return DelLL;
          ^
GibbsSamplerMap.cpp: In member function 'double GibbsSamplerMap::computeDeltaLLMEMap(char, const double* const*, const double* const*, const double* const*, const double* const*, std::vector<double>&, unsigned int, std::vector<double>&, unsigned int)':
GibbsSamplerMap.cpp:254:10: warning: 'DelLL' may be used uninitialized in this function [-Wmaybe-uninitialized]
   return DelLL;
          ^
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c Matrix.cpp -o Matrix.o
Matrix.cpp: In constructor 'Matrix::Matrix(unsigned int, unsigned int, char, double)':
Matrix.cpp:44:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int m=0; m < _n_row ; ++m){
                   ^
Matrix.cpp: In constructor 'Matrix::Matrix(std::vector<std::vector<double> >&, char)':
Matrix.cpp:59:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _n_row ; ++m) {
                     ^
Matrix.cpp:62:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _n_row ; ++m) {
                     ^
Matrix.cpp:63:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n < _n_col; ++n) {
                         ^
Matrix.cpp: In constructor 'Matrix::Matrix(const char*, char)':
Matrix.cpp:90:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _n_row ; ++m) {
                     ^
Matrix.cpp:94:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _n_row ; ++m) {
                     ^
Matrix.cpp:95:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n < _n_col; ++n) {
                         ^
Matrix.cpp: In destructor 'Matrix::˜Matrix()':
Matrix.cpp:103:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0 ; m < _n_row ; ++m)
                      ^
Matrix.cpp: In member function 'void Matrix::born_matrix(unsigned int, unsigned int, char, double)':
Matrix.cpp:122:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m=0; m < _n_row ; ++m) {
                     ^
Matrix.cpp: In member function 'void Matrix::matrix_init()':
Matrix.cpp:134:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int m=0;m<_n_row;++m) {
                  ^
Matrix.cpp:135:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n<_n_col;++n) {        
                        ^
Matrix.cpp: In member function 'void Matrix::setRow(std::vector<double>, int)':
Matrix.cpp:160:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n<_n_col;++n) {        
                        ^
Matrix.cpp: In member function 'void Matrix::setCol(std::vector<double>, int)':
Matrix.cpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n<_n_row;++n) {        
                        ^
Matrix.cpp: In member function 'std::vector<double> Matrix::get_Row(int)':
Matrix.cpp:182:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int iCol = 0; iCol < _n_col; iCol++){
                           ^
Matrix.cpp: In member function 'std::vector<double> Matrix::get_Col(int)':
Matrix.cpp:190:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int iRow=0; iRow < _n_row; iRow++){
                         ^
Matrix.cpp: In member function 'double Matrix::cal_mean() const':
Matrix.cpp:238:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int m=0;m < _n_row;++m) {
                   ^
Matrix.cpp:239:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n < _n_col;++n) {
                         ^
Matrix.cpp: In member function 'double Matrix::cal_totalsum() const':
Matrix.cpp:249:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int m=0;m < _n_row;++m) {
                   ^
Matrix.cpp:250:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n < _n_col;++n) {
                         ^
Matrix.cpp: In member function 'void Matrix::display_matrixF(std::ofstream&)':
Matrix.cpp:313:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int m=0;m<_n_row;++m) {
                  ^
Matrix.cpp:314:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n=0; n<_n_col;++n) {
                        ^
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c cogapsR.cpp -o cogapsR.o
cogapsR.cpp: In function 'Rcpp::List cogaps(Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::NumericVector)':
cogapsR.cpp:442:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (unsigned long ext_iter=1; ext_iter <= nEquilCool; ++ext_iter){
                                          ^
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c cogapsmapR.cpp -o cogapsmapR.o
cogapsmapR.cpp: In function 'Rcpp::List cogapsMap(Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::NumericVector)':
cogapsmapR.cpp:401:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (unsigned long ext_iter=1; ext_iter <= nEquilCool; ++ext_iter){
                                          ^
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c cogapsmaptestR.cpp -o cogapsmaptestR.o
cogapsmaptestR.cpp: In function 'Rcpp::List cogapsMapTest(Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::NumericVector)':
cogapsmaptestR.cpp:481:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (unsigned long ext_iter=1; ext_iter <= nEquilCool; ++ext_iter){
                                          ^
cogapsmaptestR.cpp:598:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int iEquil=0; iEquil < nEquil; iEquil++){
                             ^
cogapsmaptestR.cpp:607:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int iSample=0; iSample < nSample; iSample++){
                               ^
cogapsmaptestR.cpp:699:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                   ^
cogapsmaptestR.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                   ^
cogapsmaptestR.cpp:731:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                   ^
cogapsmaptestR.cpp:747:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                   ^
cogapsmaptestR.cpp:776:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                   ^
cogapsmaptestR.cpp:791:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                   ^
cogapsmaptestR.cpp:806:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                   ^
cogapsmaptestR.cpp:821:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                   ^
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c cogapstestR.cpp -o cogapstestR.o
cogapstestR.cpp: In function 'Rcpp::List cogapsTest(Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::NumericVector)':
cogapstestR.cpp:509:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (unsigned long ext_iter=1; ext_iter <= nEquilCool; ++ext_iter){
                                          ^
cogapstestR.cpp:634:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int iEquil=0; iEquil < nEquil; iEquil++){
                            ^
cogapstestR.cpp:643:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int iSample=0; iSample < nSample; iSample++){
                              ^
cogapstestR.cpp:733:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                   ^
cogapstestR.cpp:749:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                   ^
cogapstestR.cpp:765:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                   ^
cogapstestR.cpp:781:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                   ^
cogapstestR.cpp:809:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                   ^
cogapstestR.cpp:824:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                   ^
cogapstestR.cpp:839:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nEquil; k++)
                   ^
cogapstestR.cpp:854:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int k = 0; k < nSample; k++)
                   ^
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c randgen.cpp -o randgen.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c sub_func.cpp -o sub_func.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o CoGAPS.dll tmp.def AtomicSupport.o GAPSNorm.o GibbsSampler.o GibbsSamplerMap.o Matrix.o RcppExports.o cogapsR.o cogapsmapR.o cogapsmaptestR.o cogapstestR.o randgen.o sub_func.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/CoGAPS.buildbin-libdir/CoGAPS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CoGAPS' as CoGAPS_2.6.0.zip
* DONE (CoGAPS)

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

nameusersystemelapsed
CoGAPS000
computeGeneGSProb000
gapsInterPattern0.020.000.01
gapsIntraPattern000
gapsMapRun000
gapsMapTestRun000
gapsRun000
gapsTestRun000
plotSmoothPatterns000

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

nameusersystemelapsed
CoGAPS000
computeGeneGSProb000
gapsInterPattern000
gapsIntraPattern000
gapsMapRun000
gapsMapTestRun000
gapsRun000
gapsTestRun000
plotSmoothPatterns000