* installing *source* package 'SBIOS' ...
** this is package 'SBIOS' version '1.0'
** using staged installation
** libs
using C++ compiler: 'g++.exe (GCC) 14.3.0'
using C++17
g++  -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/BH/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.6/bigmemory/include' -I'D:/RCompile/CRANpkg/lib/4.6/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.6/RSpectra/include'   -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c RcppExports.cpp -o RcppExports.o
In file included from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo:26,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo.h:32,
                 from RcppExports.cpp:4:
D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |                                                                        ^
g++  -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/BH/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.6/bigmemory/include' -I'D:/RCompile/CRANpkg/lib/4.6/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.6/RSpectra/include'   -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c SBIOS0.cpp -o SBIOS0.o
In file included from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo:26,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo.h:32,
                 from SBIOS0.cpp:2:
D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |                                                                        ^
In file included from D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/shared_ptr.hpp:17,
                 from D:/RCompile/CRANpkg/lib/4.6/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from SBIOS0.cpp:10:
D:/RCompile/CRANpkg/lib/4.6/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 D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/memory:78,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo:38:
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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()
      |                               ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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()
      |                      ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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 )
      |                                  ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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 )
      |                                  ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
D:/RCompile/CRANpkg/lib/4.6/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 );
      |                                      ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
SBIOS0.cpp: In function 'Rcpp::List SBIOS0(Rcpp::List&, Rcpp::List&, Rcpp::List&, Rcpp::List&, Rcpp::List&, Rcpp::List&, Rcpp::List&, Rcpp::List&, double, double, int, int, int, double, int, int, double, double, int, int, int, int, bool, int, double, double, double, bool, bool, bool)':
SBIOS0.cpp:155:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  155 |   for(arma::uword iter=0; iter<n_mcmc; iter++){
      |                           ~~~~^~~~~~~
SBIOS0.cpp:162:41: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  162 |     if(update_individual_effect && iter > start_eta ){
      |                                    ~~~~~^~~~~~~~~~~
SBIOS0.cpp:169:27: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  169 |     for(arma::uword r=0; r<num_region; r++){
      |                          ~^~~~~~~~~~~
SBIOS0.cpp:173:11: warning: unused variable 'pr' [-Wunused-variable]
  173 |       int pr = Q.n_rows;
      |           ^~
SBIOS0.cpp:304:13: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  304 |     if(iter >= start_delta){
      |        ~~~~~^~~~~~~~~~~~~~
SBIOS0.cpp:312:28: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  312 |       for(arma::uword j=0;j<p;j++){
      |                           ~^~
SBIOS0.cpp:336:53: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  336 |       for(arma::uword batch_counter=0; batch_counter<total_batch;batch_counter++){
      |                                        ~~~~~~~~~~~~~^~~~~~~~~~~~
SBIOS0.cpp:418:13: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  418 |     if(iter > burnin){
      |        ~~~~~^~~~~~~~
SBIOS0.cpp:436:13: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  436 |     if(iter < stop_tuning_stepsize){
      |        ~~~~~^~~~~~~~~~~~~~~~~~~~~~
SBIOS0.cpp:152:10: warning: unused variable 'save_eta_count' [-Wunused-variable]
  152 |   double save_eta_count = 0;
      |          ^~~~~~~~~~~~~~
g++  -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/BH/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.6/bigmemory/include' -I'D:/RCompile/CRANpkg/lib/4.6/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.6/RSpectra/include'   -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c SBIOS_help_fun.cpp -o SBIOS_help_fun.o
In file included from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo:26,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo.h:32,
                 from SBIOS_help_fun.cpp:2:
D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |                                                                        ^
In file included from D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/shared_ptr.hpp:17,
                 from D:/RCompile/CRANpkg/lib/4.6/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from SBIOS_help_fun.cpp:4:
D:/RCompile/CRANpkg/lib/4.6/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 D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/memory:78,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo:38:
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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()
      |                               ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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()
      |                      ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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 )
      |                                  ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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 )
      |                                  ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
D:/RCompile/CRANpkg/lib/4.6/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 );
      |                                      ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
SBIOS_help_fun.cpp: In function 'arma::mat Low_to_high(arma::mat&, int, Rcpp::List&, Rcpp::List&, Rcpp::List&)':
SBIOS_help_fun.cpp:37:25: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   37 |   for(arma::uword r=0; r<num_region; r++){
      |                        ~^~~~~~~~~~~
SBIOS_help_fun.cpp: In function 'arma::colvec Low_to_high_vec(const arma::colvec&, int, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&)':
SBIOS_help_fun.cpp:51:25: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   51 |   for(arma::uword r=0; r<num_region; r++){
      |                        ~^~~~~~~~~~~
g++  -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/BH/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.6/bigmemory/include' -I'D:/RCompile/CRANpkg/lib/4.6/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.6/RSpectra/include'   -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c SBIOSimp.cpp -o SBIOSimp.o
In file included from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo:26,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo.h:32,
                 from SBIOSimp.cpp:3:
D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |                                                                        ^
In file included from D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/shared_ptr.hpp:17,
                 from D:/RCompile/CRANpkg/lib/4.6/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from SBIOSimp.cpp:11:
D:/RCompile/CRANpkg/lib/4.6/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 D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/memory:78,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo:38:
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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()
      |                               ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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()
      |                      ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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 )
      |                                  ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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 )
      |                                  ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
D:/RCompile/CRANpkg/lib/4.6/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 );
      |                                      ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
SBIOSimp.cpp: In function 'arma::vec High_to_low_vec(arma::vec&, int, Rcpp::List&, Rcpp::List&, Rcpp::List&)':
SBIOSimp.cpp:36:25: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   36 |   for(arma::uword r=0; r<num_region; r++){
      |                        ~^~~~~~~~~~~
SBIOSimp.cpp: In function 'arma::mat High_to_low(const arma::mat&, int, Rcpp::List&, Rcpp::List&, Rcpp::List&)':
SBIOSimp.cpp:51:25: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   51 |   for(arma::uword r=0; r<num_region; r++){
      |                        ~^~~~~~~~~~~
SBIOSimp.cpp: In function 'void update_Y_star(arma::mat&, arma::vec&, arma::uword, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const int&)':
SBIOSimp.cpp:94:17: warning: comparison of integer expressions of different signedness: 'int' and 'arma::uword' {aka 'unsigned int'} [-Wsign-compare]
   94 |   for(int r=0; r<num_region; r++){
      |                ~^~~~~~~~~~~
SBIOSimp.cpp:101:18: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
  101 |     for(int i=0;i<batch_size;i++){
      |                 ~^~~~~~~~~~~
SBIOSimp.cpp: In function 'void update_Y_imp(const arma::mat&, arma::vec&, arma::vec, arma::rowvec, double, arma::mat, arma::mat, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&)':
SBIOSimp.cpp:130:17: warning: comparison of integer expressions of different signedness: 'int' and 'arma::uword' {aka 'unsigned int'} [-Wsign-compare]
  130 |   for(int r=0; r<num_region; r++){
      |                ~^~~~~~~~~~~
SBIOSimp.cpp:138:18: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
  138 |     for(int i=0;i<X_b.n_elem;i++){
      |                 ~^~~~~~~~~~~
SBIOSimp.cpp: In function 'void update_Y_mat(arma::mat&, arma::vec&, arma::rowvec, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&)':
SBIOSimp.cpp:167:17: warning: comparison of integer expressions of different signedness: 'int' and 'arma::uword' {aka 'unsigned int'} [-Wsign-compare]
  167 |   for(int r=0; r<num_region; r++){
      |                ~^~~~~~~~~~~
SBIOSimp.cpp:172:18: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
  172 |     for(int i=0;i<X_b.n_elem;i++){
      |                 ~^~~~~~~~~~~
SBIOSimp.cpp: In function 'Rcpp::List SBIOSimp(Rcpp::List&, Rcpp::List&, Rcpp::List&, Rcpp::List&, arma::uvec, Rcpp::List&, Rcpp::List&, Rcpp::List&, Rcpp::List&, double, double, int, int, int, int, double, int, int, int, int, double, double, int, bool, double, double, double, bool, bool, bool)':
SBIOSimp.cpp:363:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  363 |   for(arma::uword iter=0; iter<n_mcmc; iter++){
      |                           ~~~~^~~~~~~
SBIOSimp.cpp:371:27: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  371 |     for(arma::uword r=0; r<num_region; r++){
      |                          ~^~~~~~~~~~~
SBIOSimp.cpp:483:13: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  483 |     if(iter >= start_delta){
      |        ~~~~~^~~~~~~~~~~~~~
SBIOSimp.cpp:491:28: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  491 |       for(arma::uword j=0;j<p;j++){
      |                           ~^~
SBIOSimp.cpp:521:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  521 |       for(arma::uword b=0; b<total_batch;b++){
      |                            ~^~~~~~~~~~~~
SBIOSimp.cpp:545:45: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  545 |         if(update_individual_effect && iter > begin_eta){
      |                                        ~~~~~^~~~~~~~~~~
SBIOSimp.cpp:575:17: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  575 |         if(iter > start_saving_imp){
      |            ~~~~~^~~~~~~~~~~~~~~~~~
SBIOSimp.cpp:609:43: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  609 |       if(update_individual_effect && iter > begin_eta){
      |                                      ~~~~~^~~~~~~~~~~
SBIOSimp.cpp:661:13: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  661 |     if(iter > burnin){
      |        ~~~~~^~~~~~~~
SBIOSimp.cpp:694:25: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  694 |   for(arma::uword b=0; b<total_batch;b++){
      |                        ~^~~~~~~~~~~~
SBIOSimp.cpp:355:10: warning: variable 'sigma_Y2_diff' set but not used [-Wunused-but-set-variable]
  355 |   double sigma_Y2_diff=0;
      |          ^~~~~~~~~~~~~
SBIOSimp.cpp:610:67: warning: 'sigma_eta2' may be used uninitialized [-Wmaybe-uninitialized]
  610 |         arma::colvec eta_sigma_pos = 1/(1/sigma_Y2 + 1/sigma_eta2/D_vec);
      |                                                                   ^~~~~
SBIOSimp.cpp:248:21: note: 'sigma_eta2' was declared here
  248 |   double sigma_eta, sigma_eta2;
      |                     ^~~~~~~~~~
g++  -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/BH/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.6/bigmemory/include' -I'D:/RCompile/CRANpkg/lib/4.6/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.6/RSpectra/include'   -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c method2_final_zero_imp_allSGLD.cpp -o method2_final_zero_imp_allSGLD.o
In file included from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo:26,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo.h:32,
                 from method2_final_zero_imp_allSGLD.cpp:2:
D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |                                                                        ^
In file included from D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/shared_ptr.hpp:17,
                 from D:/RCompile/CRANpkg/lib/4.6/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from method2_final_zero_imp_allSGLD.cpp:10:
D:/RCompile/CRANpkg/lib/4.6/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 D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/memory:78,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo:38:
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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()
      |                               ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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()
      |                      ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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 )
      |                                  ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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 )
      |                                  ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
D:/RCompile/CRANpkg/lib/4.6/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 );
      |                                      ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
method2_final_zero_imp_allSGLD.cpp: In function 'Rcpp::List method2_SGLD_multiGP_w_eta(Rcpp::List&, Rcpp::List&, Rcpp::List&, Rcpp::List&, Rcpp::List&, Rcpp::List&, Rcpp::List&, double, double, int, int, int, double, int, int, double, double, int, int, int, bool, double, double, double, bool, bool, bool)':
method2_final_zero_imp_allSGLD.cpp:171:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  171 |   for(arma::uword iter=0; iter<n_mcmc; iter++){
      |                           ~~~~^~~~~~~
method2_final_zero_imp_allSGLD.cpp:177:41: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  177 |     if(update_individual_effect && iter > start_eta ){
      |                                    ~~~~~^~~~~~~~~~~
method2_final_zero_imp_allSGLD.cpp:184:27: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  184 |     for(arma::uword r=0; r<num_region; r++){
      |                          ~^~~~~~~~~~~
method2_final_zero_imp_allSGLD.cpp:188:11: warning: unused variable 'pr' [-Wunused-variable]
  188 |       int pr = Q.n_rows;
      |           ^~
method2_final_zero_imp_allSGLD.cpp:288:13: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  288 |     if(iter >= start_delta){
      |        ~~~~~^~~~~~~~~~~~~~
method2_final_zero_imp_allSGLD.cpp:296:28: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  296 |       for(arma::uword j=0;j<p;j++){
      |                           ~^~
method2_final_zero_imp_allSGLD.cpp:322:53: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  322 |       for(arma::uword batch_counter=0; batch_counter<total_batch;batch_counter++){
      |                                        ~~~~~~~~~~~~~^~~~~~~~~~~~
method2_final_zero_imp_allSGLD.cpp:429:12: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  429 |     if(iter>start_saving_eta){
      |        ~~~~^~~~~~~~~~~~~~~~~
method2_final_zero_imp_allSGLD.cpp:435:13: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  435 |     if(iter > burnin){
      |        ~~~~~^~~~~~~~
g++  -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/BH/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.6/bigmemory/include' -I'D:/RCompile/CRANpkg/lib/4.6/bigstatsr/include' -I'D:/RCompile/CRANpkg/lib/4.6/RSpectra/include'   -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c method2_gs_noMem.cpp -o method2_gs_noMem.o
In file included from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo:26,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo.h:32,
                 from method2_gs_noMem.cpp:2:
D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |                                                                        ^
method2_gs_noMem.cpp: In function 'Rcpp::List method2_gs_no_mem(Rcpp::List&, Rcpp::List&, Rcpp::List&, Rcpp::List&, Rcpp::List&, Rcpp::List&, Rcpp::List&, double, double, int, int, int, double, int, int, double, double, int, int, int, bool, int, bool, bool)':
method2_gs_noMem.cpp:171:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  171 |   for(arma::uword iter=0; iter<n_mcmc; iter++){
      |                           ~~~~^~~~~~~
method2_gs_noMem.cpp:175:41: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  175 |     if(update_individual_effect && iter > start_eta ){
      |                                    ~~~~~^~~~~~~~~~~
method2_gs_noMem.cpp:181:27: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  181 |     for(arma::uword r=0; r<num_region; r++){
      |                          ~^~~~~~~~~~~
method2_gs_noMem.cpp:184:11: warning: unused variable 'Lr' [-Wunused-variable]
  184 |       int Lr = D.n_elem;
      |           ^~
method2_gs_noMem.cpp:185:11: warning: unused variable 'pr' [-Wunused-variable]
  185 |       int pr = Q.n_rows;
      |           ^~
method2_gs_noMem.cpp:293:13: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  293 |     if(iter >= start_delta){
      |        ~~~~~^~~~~~~~~~~~~~
method2_gs_noMem.cpp:301:28: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  301 |       for(arma::uword j=0;j<p;j++){
      |                           ~^~
method2_gs_noMem.cpp:378:12: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  378 |     if(iter>start_saving_eta){
      |        ~~~~^~~~~~~~~~~~~~~~~
method2_gs_noMem.cpp:384:13: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  384 |     if(iter > burnin){
      |        ~~~~~^~~~~~~~
method2_gs_noMem.cpp:323:12: warning: unused variable 'b_Y' [-Wunused-variable]
  323 |     double b_Y=0; // for sigma_Y2 update
      |            ^~~
method2_gs_noMem.cpp:357:38: warning: 'log_prior_theta_eta' may be used uninitialized [-Wmaybe-uninitialized]
  357 |     log_prior = log_prior_theta_beta + log_prior_theta_eta + arma::accu(log_prior_theta_gamma);
      |                 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
method2_gs_noMem.cpp:169:10: note: 'log_prior_theta_eta' was declared here
  169 |   double log_prior_theta_eta;
      |          ^~~~~~~~~~~~~~~~~~~
g++ -shared -s -static-libgcc -o SBIOS.dll tmp.def RcppExports.o SBIOS0.o SBIOS_help_fun.o SBIOSimp.o method2_final_zero_imp_allSGLD.o method2_gs_noMem.o -LD:/RCompile/recent/R/bin/x64 -lRlapack -LD:/RCompile/recent/R/bin/x64 -lRblas -lgfortran -lquadmath -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR
installing to d:/RCompile/CRANincoming/R-devel/lib/00LOCK-SBIOS/00new/SBIOS/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (SBIOS)