* using log directory 'd:/Rcompile/CRANpkg/local/4.1/simer.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'simer/DESCRIPTION' ... OK * this is package 'simer' version '0.9.0.2' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'simer' can be installed ... ERROR Installation failed. See 'd:/Rcompile/CRANpkg/local/4.1/simer.Rcheck/00install.out' for details. * DONE The installation logfile: * installing *source* package 'simer' ... ** package 'simer' successfully unpacked and MD5 sums checked ** using staged installation ** libs *** arch - i386 make[1]: Entering directory '/d/temp/Rtmpu2uk0g/R.INSTALLfc68b482bb0/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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr 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 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 + 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_::************ ^ 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( 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 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 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && 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 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& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( 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 class auto_ptr; ^~~~~~~~ data_converter.cpp: In instantiation of 'void read_bfile(std::__cxx11::string, Rcpp::XPtr, long int, double, int, bool) [with T = char; std::__cxx11::string = std::__cxx11::basic_string]': 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(fread(buffer, 1, 3, fin)); ^~~~~~~~~~~~ data_converter.cpp: In instantiation of 'void read_bfile(std::__cxx11::string, Rcpp::XPtr, long int, double, int, bool) [with T = short int; std::__cxx11::string = std::__cxx11::basic_string]': 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, long int, double, int, bool) [with T = int; std::__cxx11::string = std::__cxx11::basic_string]': 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, long int, double, int, bool) [with T = double; std::__cxx11::string = std::__cxx11::basic_string]': 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( 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/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 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 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/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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & 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/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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && 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/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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & 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/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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && 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/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 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& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( 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/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 class auto_ptr; ^~~~~~~~ genotype.cpp: In instantiation of 'Rcpp::NumericVector FilterGeno(Rcpp::XPtr, 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, 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, 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, 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, double, Rcpp::IntegerVector, Rcpp::IntegerVector, int) [with T = char; arma::mat = arma::Mat; 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, double, Rcpp::IntegerVector, Rcpp::IntegerVector, int) [with T = short int; arma::mat = arma::Mat; 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, double, Rcpp::IntegerVector, Rcpp::IntegerVector, int) [with T = int; arma::mat = arma::Mat; 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, double, Rcpp::IntegerVector, Rcpp::IntegerVector, int) [with T = double; arma::mat = arma::Mat; 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, Rcpp::IntegerMatrix, Rcpp::Nullable >, 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, Rcpp::IntegerMatrix, Rcpp::Nullable >, 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, Rcpp::IntegerMatrix, Rcpp::Nullable >, 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, Rcpp::IntegerMatrix, Rcpp::Nullable >, 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, Rcpp::XPtr, Rcpp::Nullable >, 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, Rcpp::XPtr, Rcpp::Nullable >, 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, Rcpp::XPtr, Rcpp::Nullable >, 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, Rcpp::XPtr, Rcpp::Nullable >, 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, Rcpp::XPtr, 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, Rcpp::XPtr, 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, Rcpp::XPtr, 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, Rcpp::XPtr, 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::Vector(InputIterator, InputIterator) [with InputIterator = int; int RTYPE = 14; StoragePolicy = Rcpp::PreserveStorage]': genotype.cpp:58:17: required from 'Rcpp::NumericVector FilterGeno(Rcpp::XPtr, 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/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 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 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::Vector(InputIterator, InputIterator) [with InputIterator = int; int RTYPE = 14; StoragePolicy = Rcpp::PreserveStorage]' genotype.cpp:58:17: required from 'Rcpp::NumericVector FilterGeno(Rcpp::XPtr, 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' make[1]: *** [D:/RCompile/recent/R-4.1.3/etc/i386/Makeconf:245: genotype.o] Error 1 make[1]: Leaving directory '/d/temp/Rtmpu2uk0g/R.INSTALLfc68b482bb0/simer/src-i386' ERROR: compilation failed for package 'simer' * removing 'd:/Rcompile/CRANpkg/lib/4.1/simer'