Rgin 1.2.0
Hector Climente
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/Rgin |
| Branch: RELEASE_3_8 |
| Last Commit: 91b6885 |
| Last Changed Date: 2018-10-30 11:42:08 -0400 (Tue, 30 Oct 2018) |
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | [ OK ] | |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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###
### Running command:
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### rm -rf Rgin.buildbin-libdir && mkdir Rgin.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rgin.buildbin-libdir Rgin_1.2.0.tar.gz
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install for i386
* installing *source* package 'Rgin' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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:35:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 e = 0; e < __etas.rows(); e++) {
^
src/model_selection/grid.cc:36:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 l = 0; l < __lambdas.rows(); l++) {
^
src/model_selection/grid.cc: In member function 'void Grid::search()':
src/model_selection/grid.cc:46:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 e = 0; e < __etas.rows(); e++) {
^
src/model_selection/grid.cc:47:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 l = 0; l < __lambdas.rows(); l++) {
^
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:68:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 e = 0; e < etas.rows(); e++) {
^
src/model_selection/grid.cc:69:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 l = 0; l < lambdas.rows(); l++) {
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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:117:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint e = 0; e < __etas.rows(); e++ ) {
^
src/model_selection/grid_cv.cc:118:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint l = 0; l < __lambdas.rows(); l++ ) {
^
src/model_selection/grid_cv.cc:128:43: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
if (aggregatedFolds(e,l).array().sum() > (__X->cols() * 0.05) | aggregatedFolds(e,l).array().sum() == 0) {
^
src/model_selection/grid_cv.cc: In member function 'double GridCV::__computeInformation(VectorXd, uint)':
src/model_selection/grid_cv.cc:170:22: 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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/meat/Rgin.buildbin-libdir/Rgin"
cp -r lib/Cephes "C:/Users/biocbuild/bbs-3.8-bioc/meat/Rgin.buildbin-libdir/Rgin/include"
cp -r lib/maxflow "C:/Users/biocbuild/bbs-3.8-bioc/meat/Rgin.buildbin-libdir/Rgin/include"
mkdir -p "C:/Users/biocbuild/bbs-3.8-bioc/meat/Rgin.buildbin-libdir/Rgin/usrlib/i386"
cp libgin.a libmaxflow.a libcephes.a "C:/Users/biocbuild/bbs-3.8-bioc/meat/Rgin.buildbin-libdir/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-3.8-bioc/meat/Rgin.buildbin-libdir/Rgin/usrlib/i386/libgin.a C:/Users/biocbuild/bbs-3.8-bioc/meat/Rgin.buildbin-libdir/Rgin/usrlib/i386/libmaxflow.a C:/Users/biocbuild/bbs-3.8-bioc/meat/Rgin.buildbin-libdir/Rgin/usrlib/i386/libcephes.a -lws2_32 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/Rgin.buildbin-libdir/Rgin/libs/i386
** R
** inst
** 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
In R CMD INSTALL
install for x64
* installing *source* package 'Rgin' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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:35:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 e = 0; e < __etas.rows(); e++) {
^
src/model_selection/grid.cc:36:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 l = 0; l < __lambdas.rows(); l++) {
^
src/model_selection/grid.cc: In member function 'void Grid::search()':
src/model_selection/grid.cc:46:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 e = 0; e < __etas.rows(); e++) {
^
src/model_selection/grid.cc:47:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 l = 0; l < __lambdas.rows(); l++) {
^
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:68:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 e = 0; e < etas.rows(); e++) {
^
src/model_selection/grid.cc:69:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 l = 0; l < lambdas.rows(); l++) {
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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:128:43: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
if (aggregatedFolds(e,l).array().sum() > (__X->cols() * 0.05) | aggregatedFolds(e,l).array().sum() == 0) {
^
src/model_selection/grid_cv.cc: In member function 'double GridCV::__computeInformation(VectorXd, uint)':
src/model_selection/grid_cv.cc:170:22: 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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -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˜1.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/meat/Rgin.buildbin-libdir/Rgin"
cp -r lib/Cephes "C:/Users/biocbuild/bbs-3.8-bioc/meat/Rgin.buildbin-libdir/Rgin/include"
cp -r lib/maxflow "C:/Users/biocbuild/bbs-3.8-bioc/meat/Rgin.buildbin-libdir/Rgin/include"
mkdir -p "C:/Users/biocbuild/bbs-3.8-bioc/meat/Rgin.buildbin-libdir/Rgin/usrlib/x64"
cp libgin.a libmaxflow.a libcephes.a "C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/meat/Rgin.buildbin-libdir/Rgin/usrlib/x64/libgin.a C:/Users/biocbuild/bbs-3.8-bioc/meat/Rgin.buildbin-libdir/Rgin/usrlib/x64/libmaxflow.a C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/Rgin.buildbin-libdir/Rgin/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rgin' as Rgin_1.2.0.zip
* DONE (Rgin)
In R CMD INSTALL
In R CMD INSTALL