##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL epistasisGA
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'epistasisGA' ...
** this is package 'epistasisGA' version '1.11.2'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/bigmemory/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/bigmemory/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c epistasisGA.cpp -o epistasisGA.o
In file included from F:/biocbuild/bbs-3.22-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from F:/biocbuild/bbs-3.22-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from F:/biocbuild/bbs-3.22-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from epistasisGA.cpp:7:
F:/biocbuild/bbs-3.22-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
                 from F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include/armadillo:38,
                 from F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
                 from F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from epistasisGA.cpp:1:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.22-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.22-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.22-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.22-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
F:/biocbuild/bbs-3.22-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
F:/biocbuild/bbs-3.22-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
epistasisGA.cpp: In function 'Rcpp::List GxE_fitness_score_mvlm(Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericMatrix, arma::uvec, arma::vec, arma::vec, arma::vec, bool, Rcpp::NumericVector, int, int, bool)':
epistasisGA.cpp:1115:27: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
 1115 |         for (int i = 0; i < exposure_mat.n_rows; i++){
      |                         ~~^~~~~~~~~~~~~~~~~~~~~
epistasisGA.cpp:1212:27: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
 1212 |         for (int i = 1; i < beta_full.n_rows; i++){
      |                         ~~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -s -static-libgcc -o epistasisGA.dll tmp.def RcppExports.o epistasisGA.o -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lRblas -lgfortran -lquadmath -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-epistasisGA/00new/epistasisGA/libs/x64
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (epistasisGA)