* installing *source* package 'simer' ...
** package 'simer' successfully unpacked and MD5 sums checked
** using staged installation
** libs

*** arch - i386
make[1]: Entering directory '/d/temp/RtmpM1ikGn/R.INSTALL16bac76fc795e/simer/src-i386'
d:/Compiler/rtools40/mingw32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R-4.1.3/include" -DNDEBUG  -I'd:/RCompile/CRANpkg/lib/4.1/Rcpp/include' -I'd:/RCompile/CRANpkg/lib/4.1/RcppArmadillo/include' -I'd:/RCompile/CRANpkg/lib/4.1/RcppProgress/include' -I'd:/RCompile/CRANpkg/lib/4.1/BH/include' -I'd:/RCompile/CRANpkg/lib/4.1/bigmemory/include'   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_64BIT_WORD=1 -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
d:/Compiler/rtools40/mingw32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R-4.1.3/include" -DNDEBUG  -I'd:/RCompile/CRANpkg/lib/4.1/Rcpp/include' -I'd:/RCompile/CRANpkg/lib/4.1/RcppArmadillo/include' -I'd:/RCompile/CRANpkg/lib/4.1/RcppProgress/include' -I'd:/RCompile/CRANpkg/lib/4.1/BH/include' -I'd:/RCompile/CRANpkg/lib/4.1/bigmemory/include'   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_64BIT_WORD=1 -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c data_converter.cpp -o data_converter.o
In file included from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/bind/mem_fn.hpp:25,
                 from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/mem_fn.hpp:22,
                 from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/bind/bind.hpp:26,
                 from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/bind.hpp:29,
                 from data_converter.cpp:2:
d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/RcppCommon.h:53,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/Rcpp.h:27,
                 from simer_omp.h:10,
                 from data_converter.cpp:1:
D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from data_converter.cpp:2:
d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/bind.hpp:41:1: note: #pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.
 )
 ^
In file included from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/mpl/arg.hpp:25,
                 from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/mpl/placeholders.hpp:24,
                 from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/range/iterator_range_core.hpp:27,
                 from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/range/iterator_range.hpp:13,
                 from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/range/as_literal.hpp:18,
                 from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/algorithm/string/trim.hpp:19,
                 from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/algorithm/string.hpp:19,
                 from data_converter.cpp:3:
d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/shared_ptr.hpp:17,
                 from d:/RCompile/CRANpkg/lib/4.1/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from data_converter.cpp:4:
d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/RcppCommon.h:53,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/Rcpp.h:27,
                 from simer_omp.h:10,
                 from data_converter.cpp:1:
D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/shared_ptr.hpp:17,
                 from d:/RCompile/CRANpkg/lib/4.1/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from data_converter.cpp:4:
d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/RcppCommon.h:53,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/Rcpp.h:27,
                 from simer_omp.h:10,
                 from data_converter.cpp:1:
D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/shared_ptr.hpp:17,
                 from d:/RCompile/CRANpkg/lib/4.1/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from data_converter.cpp:4:
d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/RcppCommon.h:53,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/Rcpp.h:27,
                 from simer_omp.h:10,
                 from data_converter.cpp:1:
D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/shared_ptr.hpp:17,
                 from d:/RCompile/CRANpkg/lib/4.1/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from data_converter.cpp:4:
d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/RcppCommon.h:53,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/Rcpp.h:27,
                 from simer_omp.h:10,
                 from data_converter.cpp:1:
D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/shared_ptr.hpp:17,
                 from d:/RCompile/CRANpkg/lib/4.1/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from data_converter.cpp:4:
d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/RcppCommon.h:53,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/Rcpp.h:27,
                 from simer_omp.h:10,
                 from data_converter.cpp:1:
D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/shared_ptr.hpp:17,
                 from d:/RCompile/CRANpkg/lib/4.1/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from data_converter.cpp:4:
d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/RcppCommon.h:53,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/Rcpp.h:27,
                 from simer_omp.h:10,
                 from data_converter.cpp:1:
D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/shared_ptr.hpp:17,
                 from d:/RCompile/CRANpkg/lib/4.1/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from data_converter.cpp:4:
d:/RCompile/CRANpkg/lib/4.1/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/4.1/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/RcppCommon.h:53,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/Rcpp.h:27,
                 from simer_omp.h:10,
                 from data_converter.cpp:1:
D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
data_converter.cpp: In instantiation of 'void read_bfile(std::__cxx11::string, Rcpp::XPtr<BigMatrix>, long int, double, int, bool) [with T = char; std::__cxx11::string = std::__cxx11::basic_string<char>]':
data_converter.cpp:166:80:   required from here
data_converter.cpp:131:10: warning: variable 'n_bytes_read' set but not used [-Wunused-but-set-variable]
   size_t n_bytes_read = static_cast<size_t>(fread(buffer, 1, 3, fin));
          ^~~~~~~~~~~~
data_converter.cpp: In instantiation of 'void read_bfile(std::__cxx11::string, Rcpp::XPtr<BigMatrix>, long int, double, int, bool) [with T = short int; std::__cxx11::string = std::__cxx11::basic_string<char>]':
data_converter.cpp:168:82:   required from here
data_converter.cpp:131:10: warning: variable 'n_bytes_read' set but not used [-Wunused-but-set-variable]
data_converter.cpp: In instantiation of 'void read_bfile(std::__cxx11::string, Rcpp::XPtr<BigMatrix>, long int, double, int, bool) [with T = int; std::__cxx11::string = std::__cxx11::basic_string<char>]':
data_converter.cpp:170:82:   required from here
data_converter.cpp:131:10: warning: variable 'n_bytes_read' set but not used [-Wunused-but-set-variable]
data_converter.cpp: In instantiation of 'void read_bfile(std::__cxx11::string, Rcpp::XPtr<BigMatrix>, long int, double, int, bool) [with T = double; std::__cxx11::string = std::__cxx11::basic_string<char>]':
data_converter.cpp:172:82:   required from here
data_converter.cpp:131:10: warning: variable 'n_bytes_read' set but not used [-Wunused-but-set-variable]
d:/Compiler/rtools40/mingw32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R-4.1.3/include" -DNDEBUG  -I'd:/RCompile/CRANpkg/lib/4.1/Rcpp/include' -I'd:/RCompile/CRANpkg/lib/4.1/RcppArmadillo/include' -I'd:/RCompile/CRANpkg/lib/4.1/RcppProgress/include' -I'd:/RCompile/CRANpkg/lib/4.1/BH/include' -I'd:/RCompile/CRANpkg/lib/4.1/bigmemory/include'   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_64BIT_WORD=1 -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c genotype.cpp -o genotype.o
In file included from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/shared_ptr.hpp:17,
                 from d:/RCompile/CRANpkg/lib/4.1/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from genotype.cpp:3:
d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/RcppCommon.h:53,
                 from d:/RCompile/CRANpkg/lib/4.1/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from d:/RCompile/CRANpkg/lib/4.1/RcppArmadillo/include/RcppArmadillo.h:29,
                 from genotype.cpp:1:
D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/shared_ptr.hpp:17,
                 from d:/RCompile/CRANpkg/lib/4.1/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from genotype.cpp:3:
d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/RcppCommon.h:53,
                 from d:/RCompile/CRANpkg/lib/4.1/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from d:/RCompile/CRANpkg/lib/4.1/RcppArmadillo/include/RcppArmadillo.h:29,
                 from genotype.cpp:1:
D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/shared_ptr.hpp:17,
                 from d:/RCompile/CRANpkg/lib/4.1/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from genotype.cpp:3:
d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/RcppCommon.h:53,
                 from d:/RCompile/CRANpkg/lib/4.1/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from d:/RCompile/CRANpkg/lib/4.1/RcppArmadillo/include/RcppArmadillo.h:29,
                 from genotype.cpp:1:
D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/shared_ptr.hpp:17,
                 from d:/RCompile/CRANpkg/lib/4.1/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from genotype.cpp:3:
d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/RcppCommon.h:53,
                 from d:/RCompile/CRANpkg/lib/4.1/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from d:/RCompile/CRANpkg/lib/4.1/RcppArmadillo/include/RcppArmadillo.h:29,
                 from genotype.cpp:1:
D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/shared_ptr.hpp:17,
                 from d:/RCompile/CRANpkg/lib/4.1/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from genotype.cpp:3:
d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/RcppCommon.h:53,
                 from d:/RCompile/CRANpkg/lib/4.1/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from d:/RCompile/CRANpkg/lib/4.1/RcppArmadillo/include/RcppArmadillo.h:29,
                 from genotype.cpp:1:
D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/shared_ptr.hpp:17,
                 from d:/RCompile/CRANpkg/lib/4.1/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from genotype.cpp:3:
d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/RcppCommon.h:53,
                 from d:/RCompile/CRANpkg/lib/4.1/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from d:/RCompile/CRANpkg/lib/4.1/RcppArmadillo/include/RcppArmadillo.h:29,
                 from genotype.cpp:1:
D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/shared_ptr.hpp:17,
                 from d:/RCompile/CRANpkg/lib/4.1/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from genotype.cpp:3:
d:/RCompile/CRANpkg/lib/4.1/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/4.1/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/RcppCommon.h:53,
                 from d:/RCompile/CRANpkg/lib/4.1/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from d:/RCompile/CRANpkg/lib/4.1/RcppArmadillo/include/RcppArmadillo.h:29,
                 from genotype.cpp:1:
D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
genotype.cpp: In instantiation of 'Rcpp::NumericVector FilterGeno(Rcpp::XPtr<BigMatrix>, double, Rcpp::IntegerVector, Rcpp::IntegerVector, int) [with T = char; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
genotype.cpp:75:68:   required from here
genotype.cpp:61:3: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
   for (j = 0; j < colIdx.size(); j++) {
   ^~~
genotype.cpp:62:19: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     for (i = 0; i < rowIdx.size(); i++) {
                 ~~^~~~~~~~~~~~~~~
genotype.cpp: In instantiation of 'Rcpp::NumericVector FilterGeno(Rcpp::XPtr<BigMatrix>, double, Rcpp::IntegerVector, Rcpp::IntegerVector, int) [with T = short int; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
genotype.cpp:77:70:   required from here
genotype.cpp:61:3: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
   for (j = 0; j < colIdx.size(); j++) {
   ^~~
genotype.cpp:62:19: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     for (i = 0; i < rowIdx.size(); i++) {
                 ~~^~~~~~~~~~~~~~~
genotype.cpp: In instantiation of 'Rcpp::NumericVector FilterGeno(Rcpp::XPtr<BigMatrix>, double, Rcpp::IntegerVector, Rcpp::IntegerVector, int) [with T = int; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
genotype.cpp:79:70:   required from here
genotype.cpp:61:3: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
   for (j = 0; j < colIdx.size(); j++) {
   ^~~
genotype.cpp:62:19: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     for (i = 0; i < rowIdx.size(); i++) {
                 ~~^~~~~~~~~~~~~~~
genotype.cpp: In instantiation of 'Rcpp::NumericVector FilterGeno(Rcpp::XPtr<BigMatrix>, double, Rcpp::IntegerVector, Rcpp::IntegerVector, int) [with T = double; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
genotype.cpp:81:70:   required from here
genotype.cpp:61:3: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
   for (j = 0; j < colIdx.size(); j++) {
   ^~~
genotype.cpp:62:19: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     for (i = 0; i < rowIdx.size(); i++) {
                 ~~^~~~~~~~~~~~~~~
genotype.cpp: In instantiation of 'arma::mat CalGenoFreq(Rcpp::XPtr<BigMatrix>, double, Rcpp::IntegerVector, Rcpp::IntegerVector, int) [with T = char; arma::mat = arma::Mat<double>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
genotype.cpp:117:69:   required from here
genotype.cpp:97:3: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
   for (i = 0; i < rowIdx.size(); i++) {
   ^~~
genotype.cpp:98:19: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     for (j = 0; j < colIdx.size(); j++) {
                 ~~^~~~~~~~~~~~~~~
genotype.cpp: In instantiation of 'arma::mat CalGenoFreq(Rcpp::XPtr<BigMatrix>, double, Rcpp::IntegerVector, Rcpp::IntegerVector, int) [with T = short int; arma::mat = arma::Mat<double>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
genotype.cpp:119:71:   required from here
genotype.cpp:97:3: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
   for (i = 0; i < rowIdx.size(); i++) {
   ^~~
genotype.cpp:98:19: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     for (j = 0; j < colIdx.size(); j++) {
                 ~~^~~~~~~~~~~~~~~
genotype.cpp: In instantiation of 'arma::mat CalGenoFreq(Rcpp::XPtr<BigMatrix>, double, Rcpp::IntegerVector, Rcpp::IntegerVector, int) [with T = int; arma::mat = arma::Mat<double>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
genotype.cpp:121:71:   required from here
genotype.cpp:97:3: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
   for (i = 0; i < rowIdx.size(); i++) {
   ^~~
genotype.cpp:98:19: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     for (j = 0; j < colIdx.size(); j++) {
                 ~~^~~~~~~~~~~~~~~
genotype.cpp: In instantiation of 'arma::mat CalGenoFreq(Rcpp::XPtr<BigMatrix>, double, Rcpp::IntegerVector, Rcpp::IntegerVector, int) [with T = double; arma::mat = arma::Mat<double>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
genotype.cpp:123:71:   required from here
genotype.cpp:97:3: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
   for (i = 0; i < rowIdx.size(); i++) {
   ^~~
genotype.cpp:98:19: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     for (j = 0; j < colIdx.size(); j++) {
                 ~~^~~~~~~~~~~~~~~
genotype.cpp: In instantiation of 'void Mat2BigMat(Rcpp::XPtr<BigMatrix>, Rcpp::IntegerMatrix, Rcpp::Nullable<Rcpp::Vector<13> >, int, int) [with T = char; Rcpp::IntegerMatrix = Rcpp::Matrix<13>]':
genotype.cpp:399:60:   required from here
genotype.cpp:374:9: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (m != pMat->nrow()) {
       ~~^~~~~~~~~~~~~~~
genotype.cpp:377:14: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (op + n > pMat->ncol()) {
       ~~~~~~~^~~~~~~~~~~~~~
genotype.cpp: In instantiation of 'void Mat2BigMat(Rcpp::XPtr<BigMatrix>, Rcpp::IntegerMatrix, Rcpp::Nullable<Rcpp::Vector<13> >, int, int) [with T = short int; Rcpp::IntegerMatrix = Rcpp::Matrix<13>]':
genotype.cpp:401:61:   required from here
genotype.cpp:374:9: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (m != pMat->nrow()) {
       ~~^~~~~~~~~~~~~~~
genotype.cpp:377:14: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (op + n > pMat->ncol()) {
       ~~~~~~~^~~~~~~~~~~~~~
genotype.cpp: In instantiation of 'void Mat2BigMat(Rcpp::XPtr<BigMatrix>, Rcpp::IntegerMatrix, Rcpp::Nullable<Rcpp::Vector<13> >, int, int) [with T = int; Rcpp::IntegerMatrix = Rcpp::Matrix<13>]':
genotype.cpp:403:59:   required from here
genotype.cpp:374:9: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (m != pMat->nrow()) {
       ~~^~~~~~~~~~~~~~~
genotype.cpp:377:14: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (op + n > pMat->ncol()) {
       ~~~~~~~^~~~~~~~~~~~~~
genotype.cpp: In instantiation of 'void Mat2BigMat(Rcpp::XPtr<BigMatrix>, Rcpp::IntegerMatrix, Rcpp::Nullable<Rcpp::Vector<13> >, int, int) [with T = double; Rcpp::IntegerMatrix = Rcpp::Matrix<13>]':
genotype.cpp:405:62:   required from here
genotype.cpp:374:9: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (m != pMat->nrow()) {
       ~~^~~~~~~~~~~~~~~
genotype.cpp:377:14: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (op + n > pMat->ncol()) {
       ~~~~~~~^~~~~~~~~~~~~~
genotype.cpp: In instantiation of 'void BigMat2BigMat(Rcpp::XPtr<BigMatrix>, Rcpp::XPtr<BigMatrix>, Rcpp::Nullable<Rcpp::Vector<13> >, int, int) [with T = char]':
genotype.cpp:462:65:   required from here
genotype.cpp:428:9: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (m != pMat->nrow()) {
       ~~^~~~~~~~~~~~~~~
genotype.cpp:431:14: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (op + n > pMat->ncol()) {
       ~~~~~~~^~~~~~~~~~~~~~
genotype.cpp:440:3: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   for (j = 0; j < pmat->ncol(); j++) {
   ^~~
genotype.cpp: In instantiation of 'void BigMat2BigMat(Rcpp::XPtr<BigMatrix>, Rcpp::XPtr<BigMatrix>, Rcpp::Nullable<Rcpp::Vector<13> >, int, int) [with T = short int]':
genotype.cpp:464:66:   required from here
genotype.cpp:428:9: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (m != pMat->nrow()) {
       ~~^~~~~~~~~~~~~~~
genotype.cpp:431:14: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (op + n > pMat->ncol()) {
       ~~~~~~~^~~~~~~~~~~~~~
genotype.cpp:440:3: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   for (j = 0; j < pmat->ncol(); j++) {
   ^~~
genotype.cpp: In instantiation of 'void BigMat2BigMat(Rcpp::XPtr<BigMatrix>, Rcpp::XPtr<BigMatrix>, Rcpp::Nullable<Rcpp::Vector<13> >, int, int) [with T = int]':
genotype.cpp:466:64:   required from here
genotype.cpp:428:9: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (m != pMat->nrow()) {
       ~~^~~~~~~~~~~~~~~
genotype.cpp:431:14: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (op + n > pMat->ncol()) {
       ~~~~~~~^~~~~~~~~~~~~~
genotype.cpp:440:3: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   for (j = 0; j < pmat->ncol(); j++) {
   ^~~
genotype.cpp: In instantiation of 'void BigMat2BigMat(Rcpp::XPtr<BigMatrix>, Rcpp::XPtr<BigMatrix>, Rcpp::Nullable<Rcpp::Vector<13> >, int, int) [with T = double]':
genotype.cpp:468:67:   required from here
genotype.cpp:428:9: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (m != pMat->nrow()) {
       ~~^~~~~~~~~~~~~~~
genotype.cpp:431:14: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (op + n > pMat->ncol()) {
       ~~~~~~~^~~~~~~~~~~~~~
genotype.cpp:440:3: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   for (j = 0; j < pmat->ncol(); j++) {
   ^~~
genotype.cpp: In instantiation of 'void GenoMixer(Rcpp::XPtr<BigMatrix>, Rcpp::XPtr<BigMatrix>, Rcpp::IntegerVector, Rcpp::IntegerVector, int, int, int) [with T = char; Rcpp::IntegerVector = Rcpp::Vector<13>]':
genotype.cpp:546:77:   required from here
genotype.cpp:490:9: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (m != pMat->nrow()) {
       ~~^~~~~~~~~~~~~~~
genotype.cpp:493:14: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (op + n > pMat->ncol()) {
       ~~~~~~~^~~~~~~~~~~~~~
genotype.cpp:507:17: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   for (i = 0; i < nBlock; i++) {
               ~~^~~~~~~~
genotype.cpp:512:17: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   for (i = 1; i < nBlock; i++) {
               ~~^~~~~~~~
genotype.cpp:518:3: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   for (j = 0; j < pmat->ncol(); j++) {
   ^~~
genotype.cpp:525:3: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   for (k = 0; k < nBlock; k++) {
   ^~~
genotype.cpp: In instantiation of 'void GenoMixer(Rcpp::XPtr<BigMatrix>, Rcpp::XPtr<BigMatrix>, Rcpp::IntegerVector, Rcpp::IntegerVector, int, int, int) [with T = short int; Rcpp::IntegerVector = Rcpp::Vector<13>]':
genotype.cpp:548:78:   required from here
genotype.cpp:490:9: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (m != pMat->nrow()) {
       ~~^~~~~~~~~~~~~~~
genotype.cpp:493:14: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (op + n > pMat->ncol()) {
       ~~~~~~~^~~~~~~~~~~~~~
genotype.cpp:507:17: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   for (i = 0; i < nBlock; i++) {
               ~~^~~~~~~~
genotype.cpp:512:17: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   for (i = 1; i < nBlock; i++) {
               ~~^~~~~~~~
genotype.cpp:518:3: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   for (j = 0; j < pmat->ncol(); j++) {
   ^~~
genotype.cpp:525:3: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   for (k = 0; k < nBlock; k++) {
   ^~~
genotype.cpp: In instantiation of 'void GenoMixer(Rcpp::XPtr<BigMatrix>, Rcpp::XPtr<BigMatrix>, Rcpp::IntegerVector, Rcpp::IntegerVector, int, int, int) [with T = int; Rcpp::IntegerVector = Rcpp::Vector<13>]':
genotype.cpp:550:76:   required from here
genotype.cpp:490:9: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (m != pMat->nrow()) {
       ~~^~~~~~~~~~~~~~~
genotype.cpp:493:14: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (op + n > pMat->ncol()) {
       ~~~~~~~^~~~~~~~~~~~~~
genotype.cpp:507:17: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   for (i = 0; i < nBlock; i++) {
               ~~^~~~~~~~
genotype.cpp:512:17: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   for (i = 1; i < nBlock; i++) {
               ~~^~~~~~~~
genotype.cpp:518:3: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   for (j = 0; j < pmat->ncol(); j++) {
   ^~~
genotype.cpp:525:3: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   for (k = 0; k < nBlock; k++) {
   ^~~
genotype.cpp: In instantiation of 'void GenoMixer(Rcpp::XPtr<BigMatrix>, Rcpp::XPtr<BigMatrix>, Rcpp::IntegerVector, Rcpp::IntegerVector, int, int, int) [with T = double; Rcpp::IntegerVector = Rcpp::Vector<13>]':
genotype.cpp:552:79:   required from here
genotype.cpp:490:9: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (m != pMat->nrow()) {
       ~~^~~~~~~~~~~~~~~
genotype.cpp:493:14: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   if (op + n > pMat->ncol()) {
       ~~~~~~~^~~~~~~~~~~~~~
genotype.cpp:507:17: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   for (i = 0; i < nBlock; i++) {
               ~~^~~~~~~~
genotype.cpp:512:17: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   for (i = 1; i < nBlock; i++) {
               ~~^~~~~~~~
genotype.cpp:518:3: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'index_type' {aka 'int'} [-Wsign-compare]
   for (j = 0; j < pmat->ncol(); j++) {
   ^~~
genotype.cpp:525:3: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   for (k = 0; k < nBlock; k++) {
   ^~~
In file included from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/Rcpp/Vector.h:52,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/Rcpp.h:40,
                 from d:/RCompile/CRANpkg/lib/4.1/RcppArmadillo/include/RcppArmadillo.h:32,
                 from genotype.cpp:1:
d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/Rcpp/vector/Vector.h: In instantiation of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(InputIterator, InputIterator) [with InputIterator = int; int RTYPE = 14; StoragePolicy = Rcpp::PreserveStorage]':
genotype.cpp:58:17:   required from 'Rcpp::NumericVector FilterGeno(Rcpp::XPtr<BigMatrix>, double, Rcpp::IntegerVector, Rcpp::IntegerVector, int) [with T = char; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>]'
genotype.cpp:75:68:   required from here
d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/Rcpp/vector/Vector.h:213:60: error: no matching function for call to 'distance(int&, int&)'
         Storage::set__( Rf_allocVector(RTYPE, std::distance(first, last) ) ) ;
                                               ~~~~~~~~~~~~~^~~~~~~~~~~~~
In file included from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/stl_algobase.h:66,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/char_traits.h:39,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/string:40,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/stdexcept:39,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/array:39,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/tuple:39,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/hashtable_policy.h:34,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/hashtable.h:35,
                 from D:/Compiler/rtools40/mingw32/include/c++/8.3.0/unordered_map:46,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/Rcpp/r/headers.h:62,
                 from d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/RcppCommon.h:30,
                 from d:/RCompile/CRANpkg/lib/4.1/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from d:/RCompile/CRANpkg/lib/4.1/RcppArmadillo/include/RcppArmadillo.h:29,
                 from genotype.cpp:1:
D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/stl_iterator_base_funcs.h:138:5: note: candidate: 'template<class _InputIterator> typename std::iterator_traits<_Iterator>::difference_type std::distance(_InputIterator, _InputIterator)'
     distance(_InputIterator __first, _InputIterator __last)
     ^~~~~~~~
D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/stl_iterator_base_funcs.h:138:5: note:   template argument deduction/substitution failed:
D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/stl_iterator_base_funcs.h: In substitution of 'template<class _InputIterator> typename std::iterator_traits<_Iterator>::difference_type std::distance(_InputIterator, _InputIterator) [with _InputIterator = int]':
d:/RCompile/CRANpkg/lib/4.1/Rcpp/include/Rcpp/vector/Vector.h:213:60:   required from 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(InputIterator, InputIterator) [with InputIterator = int; int RTYPE = 14; StoragePolicy = Rcpp::PreserveStorage]'
genotype.cpp:58:17:   required from 'Rcpp::NumericVector FilterGeno(Rcpp::XPtr<BigMatrix>, double, Rcpp::IntegerVector, Rcpp::IntegerVector, int) [with T = char; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>]'
genotype.cpp:75:68:   required from here
D:/Compiler/rtools40/mingw32/include/c++/8.3.0/bits/stl_iterator_base_funcs.h:138:5: error: no type named 'difference_type' in 'struct std::iterator_traits<int>'
make[1]: *** [D:/RCompile/recent/R-4.1.3/etc/i386/Makeconf:245: genotype.o] Error 1
make[1]: Leaving directory '/d/temp/RtmpM1ikGn/R.INSTALL16bac76fc795e/simer/src-i386'
ERROR: compilation failed for package 'simer'
* removing 'd:/Rcompile/CRANpkg/lib/4.1/simer'