Package: Rgin

Version: 1.3.1

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rgin.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Rgin_1.3.1.tar.gz

StartedAt: 2019-04-09 05:21:57 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:22:16 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 19.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Rgin.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rgin.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Rgin_1.3.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rgin/DESCRIPTION' ... OK
* this is package 'Rgin' version '1.3.1'
* package encoding: UTF-8
* 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 'Rgin' can be installed ... WARNING
Found the following significant warnings:
  src/model_selection/grid_cv.cc:132:21: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  6.6Mb
  sub-directories of 1Mb or more:
    include   1.8Mb
    usrlib    4.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... 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 include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rgin/libs/i386/Rgin.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rgin/libs/x64/Rgin.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Rgin_1.3.1.tar.gz && rm -rf Rgin.buildbin-libdir && mkdir Rgin.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rgin.buildbin-libdir Rgin_1.3.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Rgin_1.3.1.zip && rm Rgin_1.3.1.tar.gz Rgin_1.3.1.zip
###
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100  753k  100  753k    0     0  10.1M      0 --:--:-- --:--:-- --:--:-- 11.1M

install for i386

* installing *source* package 'Rgin' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c Rgin-init.c -o Rgin-init.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/feature_selection/feature_selector.cc -o src/feature_selection/feature_selector.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/feature_selection/scones.cc -o src/feature_selection/scones.o
src/feature_selection/scones.cc: In member function 'double Scones::computeScore()':
src/feature_selection/scones.cc:91:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(uint i = 0; i < __c.rows(); i++) {
                    ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/feature_selection/shake.cc -o src/feature_selection/shake.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/gwas/CGWASData.cc -o src/gwas/CGWASData.o
src/gwas/CGWASData.cc: In static member function 'static void CGWASDataHelper::filterNonInformativeSNPs(GWASData*)':
src/gwas/CGWASData.cc:518:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(uint i=0; i<snp_sum.rows(); i++) {
                    ^
src/gwas/CGWASData.cc: In static member function 'static void CGWASDataHelper::filterSNPsByMAF(GWASData*, const float64&)':
src/gwas/CGWASData.cc:562:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(uint i=0; i<data->MAF.rows(); i++) {
                    ^
src/gwas/CGWASData.cc: In static member function 'static GWASData CGWASDataHelper::removeSamples4MissingData(const GWASData&, const uint&, bool)':
src/gwas/CGWASData.cc:733:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(uint i=0; i<data.X.rows(); i++) {
                    ^
src/gwas/CGWASData.cc:757:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(uint64 j=0; j<sindices.size(); j++) {
                          ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/gwas/CScones.cc -o src/gwas/CScones.o
src/gwas/CScones.cc: In member function 'VectorXd CScones::__computeChisqScore(const MatrixXd&, const VectorXd&)':
src/gwas/CScones.cc:203:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (uint64 i = 0; i < X.cols(); i++) {
                          ^
src/gwas/CScones.cc: In member function 'VectorXd CScones::__computeCochranArmitageT(const MatrixXd&, const VectorXd&, const string&)':
src/gwas/CScones.cc:225:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (uint64 i = 0; i < X.cols(); i++) {
                          ^
src/gwas/CScones.cc: In member function 'void CScones::__optimize_objective(const VectorXd&, const float64&, VectorXd*, float64*)':
src/gwas/CScones.cc:335:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(uint i=0; i<c.rows(); i++) {
                  ^
src/gwas/CScones.cc: In member function 'void CScones::__gridsearch(const VectorXd&, const MatrixXd&, const MatrixXd&)':
src/gwas/CScones.cc:371:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(uint i=0; i<__settings.lambdas.rows(); i++) {
                 ^
src/gwas/CScones.cc:373:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(uint j=0;j<__settings.etas.rows(); j++) {
                 ^
src/gwas/CScones.cc: In member function 'void CScones::test_associations()':
src/gwas/CScones.cc:404:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (uint64 i=1; i <= __settings.gridsearch_depth; i++){
                        ^
src/gwas/CScones.cc:436:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (i < __settings.gridsearch_depth){
               ^
src/gwas/CScones.cc:464:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(uint64 i=0; i<__indicator_vector.rows();i++) {
                          ^
src/gwas/CScones.cc: In member function 'MatrixXd CScones::__evaluateInformation()':
src/gwas/CScones.cc:529:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for(uint64 i=0; i<indicator_vector.rows();i++) {
                              ^
src/gwas/CScones.cc: In member function 'VectorXd CScones::getObjectiveFunctionTerms(const float64&, const float64&)':
src/gwas/CScones.cc:596:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(uint i=0; i<__indicator_vector.size(); i++) {
                 ^
src/gwas/CScones.cc: In member function 'SparseMatrixXd CScones::__computeLaplacianMatrix()':
src/gwas/CScones.cc:634:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (uint64 k = 0; k < W.outerSize(); ++k)
                       ^
src/gwas/CScones.cc: In member function 'void CScones::test_associations()':
src/gwas/CScones.cc:400:21: warning: 'best_eta_index' may be used uninitialized in this function [-Wmaybe-uninitialized]
     MatrixXd::Index best_eta_index, best_lambda_index;
                     ^
src/gwas/CScones.cc:400:37: warning: 'best_lambda_index' may be used uninitialized in this function [-Wmaybe-uninitialized]
     MatrixXd::Index best_eta_index, best_lambda_index;
                                     ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/io/CGWASDataIO.cc -o src/io/CGWASDataIO.o
src/io/CGWASDataIO.cc: In static member function 'static void CGWASDataIO::writeSummaryOutput(const string&, const GWASData&, const GWASResults&)':
src/io/CGWASDataIO.cc:17:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(uint i=0; i<results.p_values.rows();i++) {
                 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/io/CIOProgress.cc -o src/io/CIOProgress.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/io/CLogging.cc -o src/io/CLogging.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/io/CPlinkParser.cc -o src/io/CPlinkParser.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/io/CSconesIO.cc -o src/io/CSconesIO.o
src/io/CSconesIO.cc: In static member function 'static void CSconesIO::writeOutput(const string&, const GWASData&, const VectorXd&, const float64&, const float64&)':
src/io/CSconesIO.cc:84:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(uint i=0; i<indicator.rows();i++) {
                    ^
src/io/CSconesIO.cc: In static member function 'static void CSconesIO::writeOutput(const string&, const GWASData&, const VectorXd&, const float64&, const float64&, const VectorXd&, const VectorXd&)':
src/io/CSconesIO.cc:107:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(uint i=0; i<indicator.rows();i++) {
                    ^
src/io/CSconesIO.cc: In static member function 'static void CSconesIO::writeOutput(const string&, GWASData* const&, const VectorXd&, const float64&, const float64&, const VectorXd&)':
src/io/CSconesIO.cc:127:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(uint i=0; i<indicator.rows();i++) {
                 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/io/grid_views.cc -o src/io/grid_views.o
src/io/grid_views.cc: In member function 'MatrixXd GridViews::viewSelectionCriterion()':
src/io/grid_views.cc:21:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (uint e = 0; e < __grid_cv->etas().rows(); e++ ) {
                     ^
src/io/grid_views.cc:22:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (uint l = 0; l < __grid_cv->lambdas().rows(); l++ ) {
                      ^
src/io/grid_views.cc: In member function 'MatrixXd GridViews::viewSelectedAvg()':
src/io/grid_views.cc:35:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (uint e = 0; e < __grid_cv->etas().rows(); e++ ) {
                     ^
src/io/grid_views.cc:36:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (uint l = 0; l < __grid_cv->lambdas().rows(); l++ ) {
                      ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/model_selection/CCrossValidation.cc -o src/model_selection/CCrossValidation.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/model_selection/grid.cc -o src/model_selection/grid.o
src/model_selection/grid.cc: In member function 'void Grid::__initGrid()':
src/model_selection/grid.cc:40:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (uint64 l = 0; l < __lambdas.rows(); l++) {
                       ^
src/model_selection/grid.cc:41:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (uint64 e = 0; e < __etas.rows(); e++) {
                        ^
src/model_selection/grid.cc: In member function 'bool Grid::__trivial(const double&)':
src/model_selection/grid.cc:73:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (uint64 e = 1; e < __etas.rows() - 1; e++) {
                       ^
src/model_selection/grid.cc: In member function 'void Grid::search()':
src/model_selection/grid.cc:84:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (uint64 l = 0; l < __lambdas.rows(); l++) {
                       ^
src/model_selection/grid.cc:92:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (uint64 e = 1; e < __etas.rows() - 1; e++) {
                        ^
src/model_selection/grid.cc: In member function 'std::vector<Eigen::Matrix<double, -1, 1> > Grid::selected(const VectorXd&, const VectorXd&)':
src/model_selection/grid.cc:111:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (uint64 l = 0; l < lambdas.rows(); l++) {
                       ^
src/model_selection/grid.cc:112:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (uint64 e = 0; e < etas.rows(); e++) {
                        ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/model_selection/grid_cv.cc -o src/model_selection/grid_cv.o
src/model_selection/grid_cv.cc: In destructor 'virtual GridCV::˜GridCV()':
src/model_selection/grid_cv.cc:42:9: warning: deleting object of polymorphic class type 'CRegression' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
  delete __classifier;
         ^
src/model_selection/grid_cv.cc: In member function 'virtual void GridCV::scoreModels(uint)':
src/model_selection/grid_cv.cc:120:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (uint l = 0; l < __lambdas.rows(); l++ ) {
                     ^
src/model_selection/grid_cv.cc:121:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (uint e = 0; e < __etas.rows(); e++ ) {
                      ^
src/model_selection/grid_cv.cc:132:21: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
    if (solutionSize > (__X->cols() * 0.05) | solutionSize == 0) {
                     ^
src/model_selection/grid_cv.cc: In member function 'double GridCV::__computeInformation(VectorXd, uint)':
src/model_selection/grid_cv.cc:175:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(uint64 i = 0; i < folds.rows(); i++) {
                      ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/regression/CRegression.cc -o src/regression/CRegression.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/stats/CFisherF.cc -o src/stats/CFisherF.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/stats/CStats.cc -o src/stats/CStats.o
src/stats/CStats.cc: In static member function 'static VectorXd CStats::std(const MatrixXd&, const uint&, const bool&)':
src/stats/CStats.cc:75:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(uint i=0; i<m.rows(); i++) {
                  ^
src/stats/CStats.cc:80:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(uint i=0; i<m.cols(); i++) {
                  ^
src/stats/CStats.cc: In static member function 'static VectorXd CStats::mean(const MatrixXd&, const uint&)':
src/stats/CStats.cc:98:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(uint i=0; i<m.rows(); i++) {
                  ^
src/stats/CStats.cc:103:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(uint i=0; i<m.cols(); i++) {
                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/stats/univariate_association.cc -o src/stats/univariate_association.o
src/stats/univariate_association.cc: In member function 'virtual VectorXd UnivariateAssociation::computeTrendTest(const string&)':
src/stats/univariate_association.cc:86:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (uint64 i = 0; i < __X -> cols(); i++) {
                       ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/stats/CChi2.cc -o src/stats/CChi2.o
src/stats/CChi2.cc: In static member function 'static MatrixXd CChi2::get2DContingencyTable(const VectorXd&, const VectorXd&, bool)':
src/stats/CChi2.cc:62:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (uint64 i = 0; i < x.size(); i++)
                       ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/stats/CGamma.cc -o src/stats/CGamma.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/stats/CStudentT.cc -o src/stats/CStudentT.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/utils/CKernels.cc -o src/utils/CKernels.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/utils/CMisc.cc -o src/utils/CMisc.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/utils/CRootFinding.cc -o src/utils/CRootFinding.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/utils/random.cc -o src/utils/random.o
src/utils/random.cc: In function 'VectorXd urand(int)':
src/utils/random.cc:69:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (uint64 i = 0; i < size; i++) {
                       ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/utils/StringHelper.cc -o src/utils/StringHelper.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/utils/utils.cc -o src/utils/utils.o
C:/Rtools/mingw_32/bin/ar crs libgin.a src/feature_selection/feature_selector.o src/feature_selection/scones.o src/feature_selection/shake.o src/gwas/CGWASData.o src/gwas/CScones.o src/io/CGWASDataIO.o src/io/CIOProgress.o src/io/CLogging.o src/io/CPlinkParser.o src/io/CSconesIO.o src/io/grid_views.o src/model_selection/CCrossValidation.o src/model_selection/grid.o src/model_selection/grid_cv.o src/regression/CRegression.o src/stats/CFisherF.o src/stats/CStats.o src/stats/univariate_association.o src/stats/CChi2.o src/stats/CGamma.o src/stats/CStudentT.o src/utils/CKernels.o src/utils/CMisc.o src/utils/CRootFinding.o src/utils/random.o src/utils/StringHelper.o src/utils/utils.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c lib/maxflow/maxflow.cpp -o lib/maxflow/maxflow.o
C:/Rtools/mingw_32/bin/ar crs libmaxflow.a lib/maxflow/maxflow.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/acosh.c -o lib/Cephes/double/acosh.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/airy.c -o lib/Cephes/double/airy.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/asin.c -o lib/Cephes/double/asin.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/asinh.c -o lib/Cephes/double/asinh.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/atan.c -o lib/Cephes/double/atan.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/atanh.c -o lib/Cephes/double/atanh.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/bdtr.c -o lib/Cephes/double/bdtr.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/beta.c -o lib/Cephes/double/beta.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/btdtr.c -o lib/Cephes/double/btdtr.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/cbrt.c -o lib/Cephes/double/cbrt.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/chbevl.c -o lib/Cephes/double/chbevl.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/chdtr.c -o lib/Cephes/double/chdtr.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/clog.c -o lib/Cephes/double/clog.o
lib/Cephes/double/clog.c:61:8: warning: conflicting types for built-in function 'cabs'
 double cabs (cmplx *);
        ^
lib/Cephes/double/clog.c:64:6: warning: conflicting types for built-in function 'csqrt'
 void csqrt ( cmplx *, cmplx * );
      ^
lib/Cephes/double/clog.c:68:6: warning: conflicting types for built-in function 'clog'
 void clog ( cmplx *, cmplx * );
      ^
lib/Cephes/double/clog.c:69:6: warning: conflicting types for built-in function 'casin'
 void casin ( cmplx *, cmplx * );
      ^
lib/Cephes/double/clog.c:70:6: warning: conflicting types for built-in function 'cacos'
 void cacos ( cmplx *, cmplx * );
      ^
lib/Cephes/double/clog.c:71:6: warning: conflicting types for built-in function 'catan'
 void catan ( cmplx *, cmplx * );
      ^
lib/Cephes/double/clog.c:142:6: warning: conflicting types for built-in function 'cexp'
 void cexp( z, w )
      ^
lib/Cephes/double/clog.c:187:6: warning: conflicting types for built-in function 'csin'
 void csin( z, w )
      ^
lib/Cephes/double/clog.c:255:6: warning: conflicting types for built-in function 'ccos'
 void ccos( z, w )
      ^
lib/Cephes/double/clog.c:304:6: warning: conflicting types for built-in function 'ctan'
 void ctan( z, w )
      ^
lib/Cephes/double/clog.c:765:1: warning: conflicting types for built-in function 'csinh'
 csinh (z, w)
 ^
lib/Cephes/double/clog.c:805:1: warning: conflicting types for built-in function 'casinh'
 casinh (z, w)
 ^
lib/Cephes/double/clog.c:847:1: warning: conflicting types for built-in function 'ccosh'
 ccosh (z, w)
 ^
lib/Cephes/double/clog.c:887:1: warning: conflicting types for built-in function 'cacosh'
 cacosh (z, w)
 ^
lib/Cephes/double/clog.c:929:1: warning: conflicting types for built-in function 'ctanh'
 ctanh (z, w)
 ^
lib/Cephes/double/clog.c:971:1: warning: conflicting types for built-in function 'catanh'
 catanh (z, w)
 ^
lib/Cephes/double/clog.c:1018:1: warning: conflicting types for built-in function 'cpow'
 cpow (a, z, w)
 ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/cmplx.c -o lib/Cephes/double/cmplx.o
lib/Cephes/double/cmplx.c:76:15: warning: conflicting types for built-in function 'cabs'
 extern double cabs ( cmplx * );
               ^
lib/Cephes/double/cmplx.c:390:6: warning: conflicting types for built-in function 'csqrt'
 void csqrt( z, w )
      ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/const.c -o lib/Cephes/double/const.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/cosh.c -o lib/Cephes/double/cosh.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/dawsn.c -o lib/Cephes/double/dawsn.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/drand.c -o lib/Cephes/double/drand.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/ei.c -o lib/Cephes/double/ei.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/ellie.c -o lib/Cephes/double/ellie.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/ellik.c -o lib/Cephes/double/ellik.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/ellpe.c -o lib/Cephes/double/ellpe.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/ellpj.c -o lib/Cephes/double/ellpj.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/ellpk.c -o lib/Cephes/double/ellpk.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/exp.c -o lib/Cephes/double/exp.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/exp10.c -o lib/Cephes/double/exp10.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/exp2.c -o lib/Cephes/double/exp2.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/expn.c -o lib/Cephes/double/expn.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/expx2.c -o lib/Cephes/double/expx2.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/fabs.c -o lib/Cephes/double/fabs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/fac.c -o lib/Cephes/double/fac.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/fdtr.c -o lib/Cephes/double/fdtr.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/fresnl.c -o lib/Cephes/double/fresnl.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/gamma.c -o lib/Cephes/double/gamma.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/gdtr.c -o lib/Cephes/double/gdtr.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/hyp2f1.c -o lib/Cephes/double/hyp2f1.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/hyperg.c -o lib/Cephes/double/hyperg.o
lib/Cephes/double/hyperg.c: In function 'hyperg':
lib/Cephes/double/hyperg.c:110:3: warning: 'pcanc' may be used uninitialized in this function [-Wmaybe-uninitialized]
 if( acanc < pcanc )
   ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/i0.c -o lib/Cephes/double/i0.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/i1.c -o lib/Cephes/double/i1.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/igami.c -o lib/Cephes/double/igami.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/incbet.c -o lib/Cephes/double/incbet.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/incbi.c -o lib/Cephes/double/incbi.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/igam.c -o lib/Cephes/double/igam.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/isnan.c -o lib/Cephes/double/isnan.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/iv.c -o lib/Cephes/double/iv.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/j0.c -o lib/Cephes/double/j0.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/j1.c -o lib/Cephes/double/j1.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/jn.c -o lib/Cephes/double/jn.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/jv.c -o lib/Cephes/double/jv.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/k0.c -o lib/Cephes/double/k0.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/k1.c -o lib/Cephes/double/k1.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/kn.c -o lib/Cephes/double/kn.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/kolmogorov.c -o lib/Cephes/double/kolmogorov.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/log.c -o lib/Cephes/double/log.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/log2.c -o lib/Cephes/double/log2.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/log10.c -o lib/Cephes/double/log10.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/lrand.c -o lib/Cephes/double/lrand.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/nbdtr.c -o lib/Cephes/double/nbdtr.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/ndtr.c -o lib/Cephes/double/ndtr.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/ndtri.c -o lib/Cephes/double/ndtri.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/pdtr.c -o lib/Cephes/double/pdtr.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/planck.c -o lib/Cephes/double/planck.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/polevl.c -o lib/Cephes/double/polevl.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/polmisc.c -o lib/Cephes/double/polmisc.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/polylog.c -o lib/Cephes/double/polylog.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/polyn.c -o lib/Cephes/double/polyn.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/pow.c -o lib/Cephes/double/pow.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/powi.c -o lib/Cephes/double/powi.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/psi.c -o lib/Cephes/double/psi.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/rgamma.c -o lib/Cephes/double/rgamma.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/round.c -o lib/Cephes/double/round.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/shichi.c -o lib/Cephes/double/shichi.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/sici.c -o lib/Cephes/double/sici.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/sin.c -o lib/Cephes/double/sin.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/sindg.c -o lib/Cephes/double/sindg.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/sinh.c -o lib/Cephes/double/sinh.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/spence.c -o lib/Cephes/double/spence.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/stdtr.c -o lib/Cephes/double/stdtr.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/struve.c -o lib/Cephes/double/struve.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/tan.c -o lib/Cephes/double/tan.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/tandg.c -o lib/Cephes/double/tandg.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/tanh.c -o lib/Cephes/double/tanh.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/unity.c -o lib/Cephes/double/unity.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/yn.c -o lib/Cephes/double/yn.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/zeta.c -o lib/Cephes/double/zeta.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/zetac.c -o lib/Cephes/double/zetac.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/sqrt.c -o lib/Cephes/double/sqrt.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/floor.c -o lib/Cephes/double/floor.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/setprec.c -o lib/Cephes/double/setprec.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/mtherr.c -o lib/Cephes/double/mtherr.o
lib/Cephes/double/mtherr.c:66:14: warning: 'ermsg' defined but not used [-Wunused-variable]
 static char *ermsg[7] = {
              ^
C:/Rtools/mingw_32/bin/ar crs libcephes.a lib/Cephes/double/acosh.o lib/Cephes/double/airy.o lib/Cephes/double/asin.o lib/Cephes/double/asinh.o lib/Cephes/double/atan.o lib/Cephes/double/atanh.o lib/Cephes/double/bdtr.o lib/Cephes/double/beta.o lib/Cephes/double/btdtr.o lib/Cephes/double/cbrt.o lib/Cephes/double/chbevl.o lib/Cephes/double/chdtr.o lib/Cephes/double/clog.o lib/Cephes/double/cmplx.o lib/Cephes/double/const.o lib/Cephes/double/cosh.o lib/Cephes/double/dawsn.o lib/Cephes/double/drand.o lib/Cephes/double/ei.o lib/Cephes/double/ellie.o lib/Cephes/double/ellik.o lib/Cephes/double/ellpe.o lib/Cephes/double/ellpj.o lib/Cephes/double/ellpk.o lib/Cephes/double/exp.o lib/Cephes/double/exp10.o lib/Cephes/double/exp2.o lib/Cephes/double/expn.o lib/Cephes/double/expx2.o lib/Cephes/double/fabs.o lib/Cephes/double/fac.o lib/Cephes/double/fdtr.o lib/Cephes/double/fresnl.o lib/Cephes/double/gamma.o lib/Cephes/double/gdtr.o lib/Cephes/double/hyp2f1.o lib/Cephes/double/hyperg.o lib/Cephes/double/i0.o lib/Cephes/double/i1.o lib/Cephes/double/igami.o lib/Cephes/double/incbet.o lib/Cephes/double/incbi.o lib/Cephes/double/igam.o lib/Cephes/double/isnan.o lib/Cephes/double/iv.o lib/Cephes/double/j0.o lib/Cephes/double/j1.o lib/Cephes/double/jn.o lib/Cephes/double/jv.o lib/Cephes/double/k0.o lib/Cephes/double/k1.o lib/Cephes/double/kn.o lib/Cephes/double/kolmogorov.o lib/Cephes/double/log.o lib/Cephes/double/log2.o lib/Cephes/double/log10.o lib/Cephes/double/lrand.o lib/Cephes/double/nbdtr.o lib/Cephes/double/ndtr.o lib/Cephes/double/ndtri.o lib/Cephes/double/pdtr.o lib/Cephes/double/planck.o lib/Cephes/double/polevl.o lib/Cephes/double/polmisc.o lib/Cephes/double/polylog.o lib/Cephes/double/polyn.o lib/Cephes/double/pow.o lib/Cephes/double/powi.o lib/Cephes/double/psi.o lib/Cephes/double/rgamma.o lib/Cephes/double/round.o lib/Cephes/double/shichi.o lib/Cephes/double/sici.o lib/Cephes/double/sin.o lib/Cephes/double/sindg.o lib/Cephes/double/sinh.o lib/Cephes/double/spence.o lib/Cephes/double/stdtr.o lib/Cephes/double/struve.o lib/Cephes/double/tan.o lib/Cephes/double/tandg.o lib/Cephes/double/tanh.o lib/Cephes/double/unity.o lib/Cephes/double/yn.o lib/Cephes/double/zeta.o lib/Cephes/double/zetac.o lib/Cephes/double/sqrt.o lib/Cephes/double/floor.o lib/Cephes/double/setprec.o lib/Cephes/double/mtherr.o
cp -r include "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.buildbin-libdir/00LOCK-Rgin/00new/Rgin"
cp -r lib/Cephes "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.buildbin-libdir/00LOCK-Rgin/00new/Rgin/include"
cp -r lib/maxflow "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.buildbin-libdir/00LOCK-Rgin/00new/Rgin/include"
mkdir -p "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.buildbin-libdir/00LOCK-Rgin/00new/Rgin/usrlib/i386"
cp libgin.a libmaxflow.a libcephes.a "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.buildbin-libdir/00LOCK-Rgin/00new/Rgin/usrlib/i386"
C:\Rtools\mingw_32\bin\nm.exe: 'libs': No such file
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o Rgin.dll tmp.def Rgin-init.o -pthread -fopenmp C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.buildbin-libdir/00LOCK-Rgin/00new/Rgin/usrlib/i386/libgin.a C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.buildbin-libdir/00LOCK-Rgin/00new/Rgin/usrlib/i386/libmaxflow.a C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.buildbin-libdir/00LOCK-Rgin/00new/Rgin/usrlib/i386/libcephes.a -lws2_32 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.buildbin-libdir/00LOCK-Rgin/00new/Rgin/libs/i386
** R
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  'Rgin' 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'Rgin' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c Rgin-init.c -o Rgin-init.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/feature_selection/feature_selector.cc -o src/feature_selection/feature_selector.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/feature_selection/scones.cc -o src/feature_selection/scones.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/feature_selection/shake.cc -o src/feature_selection/shake.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/gwas/CGWASData.cc -o src/gwas/CGWASData.o
src/gwas/CGWASData.cc: In static member function 'static GWASData CGWASDataHelper::removeSamples4MissingData(const GWASData&, const uint&, bool)':
src/gwas/CGWASData.cc:757:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(uint64 j=0; j<sindices.size(); j++) {
                          ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/gwas/CScones.cc -o src/gwas/CScones.o
src/gwas/CScones.cc: In member function 'VectorXd CScones::__computeChisqScore(const MatrixXd&, const VectorXd&)':
src/gwas/CScones.cc:203:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (uint64 i = 0; i < X.cols(); i++) {
                          ^
src/gwas/CScones.cc: In member function 'VectorXd CScones::__computeCochranArmitageT(const MatrixXd&, const VectorXd&, const string&)':
src/gwas/CScones.cc:225:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (uint64 i = 0; i < X.cols(); i++) {
                          ^
src/gwas/CScones.cc: In member function 'void CScones::test_associations()':
src/gwas/CScones.cc:404:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (uint64 i=1; i <= __settings.gridsearch_depth; i++){
                        ^
src/gwas/CScones.cc:436:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (i < __settings.gridsearch_depth){
               ^
src/gwas/CScones.cc:464:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(uint64 i=0; i<__indicator_vector.rows();i++) {
                          ^
src/gwas/CScones.cc: In member function 'MatrixXd CScones::__evaluateInformation()':
src/gwas/CScones.cc:529:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for(uint64 i=0; i<indicator_vector.rows();i++) {
                              ^
src/gwas/CScones.cc: In member function 'SparseMatrixXd CScones::__computeLaplacianMatrix()':
src/gwas/CScones.cc:634:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (uint64 k = 0; k < W.outerSize(); ++k)
                       ^
src/gwas/CScones.cc: In member function 'void CScones::test_associations()':
src/gwas/CScones.cc:400:21: warning: 'best_eta_index' may be used uninitialized in this function [-Wmaybe-uninitialized]
     MatrixXd::Index best_eta_index, best_lambda_index;
                     ^
src/gwas/CScones.cc:400:37: warning: 'best_lambda_index' may be used uninitialized in this function [-Wmaybe-uninitialized]
     MatrixXd::Index best_eta_index, best_lambda_index;
                                     ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/io/CGWASDataIO.cc -o src/io/CGWASDataIO.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/io/CIOProgress.cc -o src/io/CIOProgress.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/io/CLogging.cc -o src/io/CLogging.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/io/CPlinkParser.cc -o src/io/CPlinkParser.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/io/CSconesIO.cc -o src/io/CSconesIO.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/io/grid_views.cc -o src/io/grid_views.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/model_selection/CCrossValidation.cc -o src/model_selection/CCrossValidation.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/model_selection/grid.cc -o src/model_selection/grid.o
src/model_selection/grid.cc: In member function 'void Grid::__initGrid()':
src/model_selection/grid.cc:40:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (uint64 l = 0; l < __lambdas.rows(); l++) {
                       ^
src/model_selection/grid.cc:41:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (uint64 e = 0; e < __etas.rows(); e++) {
                        ^
src/model_selection/grid.cc: In member function 'bool Grid::__trivial(const double&)':
src/model_selection/grid.cc:73:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (uint64 e = 1; e < __etas.rows() - 1; e++) {
                       ^
src/model_selection/grid.cc: In member function 'void Grid::search()':
src/model_selection/grid.cc:84:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (uint64 l = 0; l < __lambdas.rows(); l++) {
                       ^
src/model_selection/grid.cc:92:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (uint64 e = 1; e < __etas.rows() - 1; e++) {
                        ^
src/model_selection/grid.cc: In member function 'std::vector<Eigen::Matrix<double, -1, 1> > Grid::selected(const VectorXd&, const VectorXd&)':
src/model_selection/grid.cc:111:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (uint64 l = 0; l < lambdas.rows(); l++) {
                       ^
src/model_selection/grid.cc:112:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (uint64 e = 0; e < etas.rows(); e++) {
                        ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/model_selection/grid_cv.cc -o src/model_selection/grid_cv.o
src/model_selection/grid_cv.cc: In destructor 'virtual GridCV::˜GridCV()':
src/model_selection/grid_cv.cc:42:9: warning: deleting object of polymorphic class type 'CRegression' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
  delete __classifier;
         ^
src/model_selection/grid_cv.cc: In member function 'virtual void GridCV::scoreModels(uint)':
src/model_selection/grid_cv.cc:132:21: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
    if (solutionSize > (__X->cols() * 0.05) | solutionSize == 0) {
                     ^
src/model_selection/grid_cv.cc: In member function 'double GridCV::__computeInformation(VectorXd, uint)':
src/model_selection/grid_cv.cc:175:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(uint64 i = 0; i < folds.rows(); i++) {
                      ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/regression/CRegression.cc -o src/regression/CRegression.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/stats/CFisherF.cc -o src/stats/CFisherF.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/stats/CStats.cc -o src/stats/CStats.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/stats/univariate_association.cc -o src/stats/univariate_association.o
src/stats/univariate_association.cc: In member function 'virtual VectorXd UnivariateAssociation::computeTrendTest(const string&)':
src/stats/univariate_association.cc:86:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (uint64 i = 0; i < __X -> cols(); i++) {
                       ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/stats/CChi2.cc -o src/stats/CChi2.o
src/stats/CChi2.cc: In static member function 'static MatrixXd CChi2::get2DContingencyTable(const VectorXd&, const VectorXd&, bool)':
src/stats/CChi2.cc:62:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (uint64 i = 0; i < x.size(); i++)
                       ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/stats/CGamma.cc -o src/stats/CGamma.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/stats/CStudentT.cc -o src/stats/CStudentT.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/utils/CKernels.cc -o src/utils/CKernels.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/utils/CMisc.cc -o src/utils/CMisc.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/utils/CRootFinding.cc -o src/utils/CRootFinding.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/utils/random.cc -o src/utils/random.o
src/utils/random.cc: In function 'VectorXd urand(int)':
src/utils/random.cc:69:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (uint64 i = 0; i < size; i++) {
                       ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/utils/StringHelper.cc -o src/utils/StringHelper.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c src/utils/utils.cc -o src/utils/utils.o
C:/Rtools/mingw_64/bin/ar crs libgin.a src/feature_selection/feature_selector.o src/feature_selection/scones.o src/feature_selection/shake.o src/gwas/CGWASData.o src/gwas/CScones.o src/io/CGWASDataIO.o src/io/CIOProgress.o src/io/CLogging.o src/io/CPlinkParser.o src/io/CSconesIO.o src/io/grid_views.o src/model_selection/CCrossValidation.o src/model_selection/grid.o src/model_selection/grid_cv.o src/regression/CRegression.o src/stats/CFisherF.o src/stats/CStats.o src/stats/univariate_association.o src/stats/CChi2.o src/stats/CGamma.o src/stats/CStudentT.o src/utils/CKernels.o src/utils/CMisc.o src/utils/CRootFinding.o src/utils/random.o src/utils/StringHelper.o src/utils/utils.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e "Rcpp:::CxxFlags()"`   -O2 -Wall  -mtune=generic -c lib/maxflow/maxflow.cpp -o lib/maxflow/maxflow.o
C:/Rtools/mingw_64/bin/ar crs libmaxflow.a lib/maxflow/maxflow.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/acosh.c -o lib/Cephes/double/acosh.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/airy.c -o lib/Cephes/double/airy.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/asin.c -o lib/Cephes/double/asin.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/asinh.c -o lib/Cephes/double/asinh.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/atan.c -o lib/Cephes/double/atan.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/atanh.c -o lib/Cephes/double/atanh.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/bdtr.c -o lib/Cephes/double/bdtr.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/beta.c -o lib/Cephes/double/beta.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/btdtr.c -o lib/Cephes/double/btdtr.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/cbrt.c -o lib/Cephes/double/cbrt.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/chbevl.c -o lib/Cephes/double/chbevl.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/chdtr.c -o lib/Cephes/double/chdtr.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/clog.c -o lib/Cephes/double/clog.o
lib/Cephes/double/clog.c:61:8: warning: conflicting types for built-in function 'cabs'
 double cabs (cmplx *);
        ^
lib/Cephes/double/clog.c:64:6: warning: conflicting types for built-in function 'csqrt'
 void csqrt ( cmplx *, cmplx * );
      ^
lib/Cephes/double/clog.c:68:6: warning: conflicting types for built-in function 'clog'
 void clog ( cmplx *, cmplx * );
      ^
lib/Cephes/double/clog.c:69:6: warning: conflicting types for built-in function 'casin'
 void casin ( cmplx *, cmplx * );
      ^
lib/Cephes/double/clog.c:70:6: warning: conflicting types for built-in function 'cacos'
 void cacos ( cmplx *, cmplx * );
      ^
lib/Cephes/double/clog.c:71:6: warning: conflicting types for built-in function 'catan'
 void catan ( cmplx *, cmplx * );
      ^
lib/Cephes/double/clog.c:142:6: warning: conflicting types for built-in function 'cexp'
 void cexp( z, w )
      ^
lib/Cephes/double/clog.c:187:6: warning: conflicting types for built-in function 'csin'
 void csin( z, w )
      ^
lib/Cephes/double/clog.c:255:6: warning: conflicting types for built-in function 'ccos'
 void ccos( z, w )
      ^
lib/Cephes/double/clog.c:304:6: warning: conflicting types for built-in function 'ctan'
 void ctan( z, w )
      ^
lib/Cephes/double/clog.c:765:1: warning: conflicting types for built-in function 'csinh'
 csinh (z, w)
 ^
lib/Cephes/double/clog.c:805:1: warning: conflicting types for built-in function 'casinh'
 casinh (z, w)
 ^
lib/Cephes/double/clog.c:847:1: warning: conflicting types for built-in function 'ccosh'
 ccosh (z, w)
 ^
lib/Cephes/double/clog.c:887:1: warning: conflicting types for built-in function 'cacosh'
 cacosh (z, w)
 ^
lib/Cephes/double/clog.c:929:1: warning: conflicting types for built-in function 'ctanh'
 ctanh (z, w)
 ^
lib/Cephes/double/clog.c:971:1: warning: conflicting types for built-in function 'catanh'
 catanh (z, w)
 ^
lib/Cephes/double/clog.c:1018:1: warning: conflicting types for built-in function 'cpow'
 cpow (a, z, w)
 ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/cmplx.c -o lib/Cephes/double/cmplx.o
lib/Cephes/double/cmplx.c:76:15: warning: conflicting types for built-in function 'cabs'
 extern double cabs ( cmplx * );
               ^
lib/Cephes/double/cmplx.c:390:6: warning: conflicting types for built-in function 'csqrt'
 void csqrt( z, w )
      ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/const.c -o lib/Cephes/double/const.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/cosh.c -o lib/Cephes/double/cosh.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/dawsn.c -o lib/Cephes/double/dawsn.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/drand.c -o lib/Cephes/double/drand.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/ei.c -o lib/Cephes/double/ei.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/ellie.c -o lib/Cephes/double/ellie.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/ellik.c -o lib/Cephes/double/ellik.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/ellpe.c -o lib/Cephes/double/ellpe.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/ellpj.c -o lib/Cephes/double/ellpj.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/ellpk.c -o lib/Cephes/double/ellpk.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/exp.c -o lib/Cephes/double/exp.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/exp10.c -o lib/Cephes/double/exp10.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/exp2.c -o lib/Cephes/double/exp2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/expn.c -o lib/Cephes/double/expn.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/expx2.c -o lib/Cephes/double/expx2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/fabs.c -o lib/Cephes/double/fabs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/fac.c -o lib/Cephes/double/fac.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/fdtr.c -o lib/Cephes/double/fdtr.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/fresnl.c -o lib/Cephes/double/fresnl.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/gamma.c -o lib/Cephes/double/gamma.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/gdtr.c -o lib/Cephes/double/gdtr.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/hyp2f1.c -o lib/Cephes/double/hyp2f1.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/hyperg.c -o lib/Cephes/double/hyperg.o
lib/Cephes/double/hyperg.c: In function 'hyperg':
lib/Cephes/double/hyperg.c:110:3: warning: 'pcanc' may be used uninitialized in this function [-Wmaybe-uninitialized]
 if( acanc < pcanc )
   ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/i0.c -o lib/Cephes/double/i0.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/i1.c -o lib/Cephes/double/i1.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/igami.c -o lib/Cephes/double/igami.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/incbet.c -o lib/Cephes/double/incbet.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/incbi.c -o lib/Cephes/double/incbi.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/igam.c -o lib/Cephes/double/igam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/isnan.c -o lib/Cephes/double/isnan.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/iv.c -o lib/Cephes/double/iv.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/j0.c -o lib/Cephes/double/j0.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/j1.c -o lib/Cephes/double/j1.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/jn.c -o lib/Cephes/double/jn.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/jv.c -o lib/Cephes/double/jv.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/k0.c -o lib/Cephes/double/k0.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/k1.c -o lib/Cephes/double/k1.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/kn.c -o lib/Cephes/double/kn.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/kolmogorov.c -o lib/Cephes/double/kolmogorov.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/log.c -o lib/Cephes/double/log.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/log2.c -o lib/Cephes/double/log2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/log10.c -o lib/Cephes/double/log10.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/lrand.c -o lib/Cephes/double/lrand.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/nbdtr.c -o lib/Cephes/double/nbdtr.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/ndtr.c -o lib/Cephes/double/ndtr.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/ndtri.c -o lib/Cephes/double/ndtri.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/pdtr.c -o lib/Cephes/double/pdtr.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/planck.c -o lib/Cephes/double/planck.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/polevl.c -o lib/Cephes/double/polevl.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/polmisc.c -o lib/Cephes/double/polmisc.o
lib/Cephes/double/polmisc.c:21:15: warning: conflicting types for built-in function 'malloc'
 extern void * malloc ( long );
               ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/polylog.c -o lib/Cephes/double/polylog.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/polyn.c -o lib/Cephes/double/polyn.o
lib/Cephes/double/polyn.c:66:15: warning: conflicting types for built-in function 'malloc'
 extern void * malloc ( long );
               ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/pow.c -o lib/Cephes/double/pow.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/powi.c -o lib/Cephes/double/powi.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/psi.c -o lib/Cephes/double/psi.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/rgamma.c -o lib/Cephes/double/rgamma.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/round.c -o lib/Cephes/double/round.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/shichi.c -o lib/Cephes/double/shichi.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/sici.c -o lib/Cephes/double/sici.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/sin.c -o lib/Cephes/double/sin.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/sindg.c -o lib/Cephes/double/sindg.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/sinh.c -o lib/Cephes/double/sinh.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/spence.c -o lib/Cephes/double/spence.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/stdtr.c -o lib/Cephes/double/stdtr.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/struve.c -o lib/Cephes/double/struve.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/tan.c -o lib/Cephes/double/tan.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/tandg.c -o lib/Cephes/double/tandg.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/tanh.c -o lib/Cephes/double/tanh.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/unity.c -o lib/Cephes/double/unity.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/yn.c -o lib/Cephes/double/yn.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/zeta.c -o lib/Cephes/double/zeta.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/zetac.c -o lib/Cephes/double/zetac.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/sqrt.c -o lib/Cephes/double/sqrt.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/floor.c -o lib/Cephes/double/floor.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/setprec.c -o lib/Cephes/double/setprec.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"   -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c lib/Cephes/double/mtherr.c -o lib/Cephes/double/mtherr.o
lib/Cephes/double/mtherr.c:66:14: warning: 'ermsg' defined but not used [-Wunused-variable]
 static char *ermsg[7] = {
              ^
C:/Rtools/mingw_64/bin/ar crs libcephes.a lib/Cephes/double/acosh.o lib/Cephes/double/airy.o lib/Cephes/double/asin.o lib/Cephes/double/asinh.o lib/Cephes/double/atan.o lib/Cephes/double/atanh.o lib/Cephes/double/bdtr.o lib/Cephes/double/beta.o lib/Cephes/double/btdtr.o lib/Cephes/double/cbrt.o lib/Cephes/double/chbevl.o lib/Cephes/double/chdtr.o lib/Cephes/double/clog.o lib/Cephes/double/cmplx.o lib/Cephes/double/const.o lib/Cephes/double/cosh.o lib/Cephes/double/dawsn.o lib/Cephes/double/drand.o lib/Cephes/double/ei.o lib/Cephes/double/ellie.o lib/Cephes/double/ellik.o lib/Cephes/double/ellpe.o lib/Cephes/double/ellpj.o lib/Cephes/double/ellpk.o lib/Cephes/double/exp.o lib/Cephes/double/exp10.o lib/Cephes/double/exp2.o lib/Cephes/double/expn.o lib/Cephes/double/expx2.o lib/Cephes/double/fabs.o lib/Cephes/double/fac.o lib/Cephes/double/fdtr.o lib/Cephes/double/fresnl.o lib/Cephes/double/gamma.o lib/Cephes/double/gdtr.o lib/Cephes/double/hyp2f1.o lib/Cephes/double/hyperg.o lib/Cephes/double/i0.o lib/Cephes/double/i1.o lib/Cephes/double/igami.o lib/Cephes/double/incbet.o lib/Cephes/double/incbi.o lib/Cephes/double/igam.o lib/Cephes/double/isnan.o lib/Cephes/double/iv.o lib/Cephes/double/j0.o lib/Cephes/double/j1.o lib/Cephes/double/jn.o lib/Cephes/double/jv.o lib/Cephes/double/k0.o lib/Cephes/double/k1.o lib/Cephes/double/kn.o lib/Cephes/double/kolmogorov.o lib/Cephes/double/log.o lib/Cephes/double/log2.o lib/Cephes/double/log10.o lib/Cephes/double/lrand.o lib/Cephes/double/nbdtr.o lib/Cephes/double/ndtr.o lib/Cephes/double/ndtri.o lib/Cephes/double/pdtr.o lib/Cephes/double/planck.o lib/Cephes/double/polevl.o lib/Cephes/double/polmisc.o lib/Cephes/double/polylog.o lib/Cephes/double/polyn.o lib/Cephes/double/pow.o lib/Cephes/double/powi.o lib/Cephes/double/psi.o lib/Cephes/double/rgamma.o lib/Cephes/double/round.o lib/Cephes/double/shichi.o lib/Cephes/double/sici.o lib/Cephes/double/sin.o lib/Cephes/double/sindg.o lib/Cephes/double/sinh.o lib/Cephes/double/spence.o lib/Cephes/double/stdtr.o lib/Cephes/double/struve.o lib/Cephes/double/tan.o lib/Cephes/double/tandg.o lib/Cephes/double/tanh.o lib/Cephes/double/unity.o lib/Cephes/double/yn.o lib/Cephes/double/zeta.o lib/Cephes/double/zetac.o lib/Cephes/double/sqrt.o lib/Cephes/double/floor.o lib/Cephes/double/setprec.o lib/Cephes/double/mtherr.o
cp -r include "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.buildbin-libdir/Rgin"
cp -r lib/Cephes "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.buildbin-libdir/Rgin/include"
cp -r lib/maxflow "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.buildbin-libdir/Rgin/include"
mkdir -p "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.buildbin-libdir/Rgin/usrlib/x64"
cp libgin.a libmaxflow.a libcephes.a "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.buildbin-libdir/Rgin/usrlib/x64"
C:\Rtools\mingw_64\bin\nm.exe: 'libs': No such file
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Rgin.dll tmp.def Rgin-init.o -pthread -fopenmp C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.buildbin-libdir/Rgin/usrlib/x64/libgin.a C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.buildbin-libdir/Rgin/usrlib/x64/libmaxflow.a C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.buildbin-libdir/Rgin/usrlib/x64/libcephes.a -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/Rgin.buildbin-libdir/Rgin/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rgin' as Rgin_1.3.1.zip
* DONE (Rgin)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Rgin' successfully unpacked and MD5 sums checked