* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘simer’ ...
** package ‘simer’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpvSJldH/R.INSTALL1cace4567b6824/simer/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigmemory/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigmemory/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c data_converter.cpp -o data_converter.o
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/bind/bind.hpp:26,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/bind.hpp:29,
                 from data_converter.cpp:2:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/13/memory:78,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/get_pointer.hpp:14:
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/bind/detail/requires_cxx11.hpp:9,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/bind/bind.hpp:24:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/config/pragma_message.hpp:24:34: 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.’
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/bind.hpp:36:1: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/arg.hpp:25,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/range/as_literal.hpp:18,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/algorithm/string.hpp:19,
                 from data_converter.cpp:3:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/shared_ptr.hpp:17,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from data_converter.cpp:4:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
data_converter.cpp: In instantiation of ‘void read_bfile(std::string, Rcpp::XPtr<BigMatrix>, long int, double, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>]’:
data_converter.cpp:166:28:   required from here
data_converter.cpp:131:10: warning: variable ‘n_bytes_read’ set but not used [-Wunused-but-set-variable]
  131 |   size_t n_bytes_read = static_cast<size_t>(fread(buffer, 1, 3, fin));
      |          ^~~~~~~~~~~~
data_converter.cpp: In instantiation of ‘void read_bfile(std::string, Rcpp::XPtr<BigMatrix>, long int, double, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>]’:
data_converter.cpp:168:29:   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::string, Rcpp::XPtr<BigMatrix>, long int, double, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>]’:
data_converter.cpp:170:27:   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::string, Rcpp::XPtr<BigMatrix>, long int, double, int, bool) [with T = double; std::string = std::__cxx11::basic_string<char>]’:
data_converter.cpp:172:30:   required from here
data_converter.cpp:131:10: warning: variable ‘n_bytes_read’ set but not used [-Wunused-but-set-variable]
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigmemory/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c emma.cpp -o emma.o
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/shared_ptr.hpp:17,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from emma.cpp:2:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/13/memory:78,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigmemory/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c genotype.cpp -o genotype.o
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/shared_ptr.hpp:17,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from genotype.cpp:3:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/13/memory:78,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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:75:28:   required from here
genotype.cpp:61:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   61 |   for (j = 0; j < colIdx.size(); j++) {
      |                               ^
genotype.cpp:62:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   62 |     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:77:29:   required from here
genotype.cpp:61:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   61 |   for (j = 0; j < colIdx.size(); j++) {
      |                               ^
genotype.cpp:62:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   62 |     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:79:27:   required from here
genotype.cpp:61:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   61 |   for (j = 0; j < colIdx.size(); j++) {
      |                               ^
genotype.cpp:62:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   62 |     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:81:30:   required from here
genotype.cpp:61:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   61 |   for (j = 0; j < colIdx.size(); j++) {
      |                               ^
genotype.cpp:62:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   62 |     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:117:29:   required from here
genotype.cpp:97:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   97 |   for (i = 0; i < rowIdx.size(); i++) {
      |                               ^
genotype.cpp:98:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   98 |     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:119:30:   required from here
genotype.cpp:97:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   97 |   for (i = 0; i < rowIdx.size(); i++) {
      |                               ^
genotype.cpp:98:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   98 |     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:121:28:   required from here
genotype.cpp:97:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   97 |   for (i = 0; i < rowIdx.size(); i++) {
      |                               ^
genotype.cpp:98:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   98 |     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:123:31:   required from here
genotype.cpp:97:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   97 |   for (i = 0; i < rowIdx.size(); i++) {
      |                               ^
genotype.cpp:98:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   98 |     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:399:28:   required from here
genotype.cpp:374:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  374 |   if (m != pMat->nrow()) {
      |       ~~^~~~~~~~~~~~~~~
genotype.cpp:377:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  377 |   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:401:29:   required from here
genotype.cpp:374:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  374 |   if (m != pMat->nrow()) {
      |       ~~^~~~~~~~~~~~~~~
genotype.cpp:377:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  377 |   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:403:27:   required from here
genotype.cpp:374:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  374 |   if (m != pMat->nrow()) {
      |       ~~^~~~~~~~~~~~~~~
genotype.cpp:377:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  377 |   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:405:30:   required from here
genotype.cpp:374:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  374 |   if (m != pMat->nrow()) {
      |       ~~^~~~~~~~~~~~~~~
genotype.cpp:377:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  377 |   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:462:31:   required from here
genotype.cpp:428:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  428 |   if (m != pMat->nrow()) {
      |       ~~^~~~~~~~~~~~~~~
genotype.cpp:431:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  431 |   if (op + n > pMat->ncol()) {
      |       ~~~~~~~^~~~~~~~~~~~~~
genotype.cpp:440:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  440 |   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:464:32:   required from here
genotype.cpp:428:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  428 |   if (m != pMat->nrow()) {
      |       ~~^~~~~~~~~~~~~~~
genotype.cpp:431:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  431 |   if (op + n > pMat->ncol()) {
      |       ~~~~~~~^~~~~~~~~~~~~~
genotype.cpp:440:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  440 |   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:466:30:   required from here
genotype.cpp:428:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  428 |   if (m != pMat->nrow()) {
      |       ~~^~~~~~~~~~~~~~~
genotype.cpp:431:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  431 |   if (op + n > pMat->ncol()) {
      |       ~~~~~~~^~~~~~~~~~~~~~
genotype.cpp:440:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  440 |   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:468:33:   required from here
genotype.cpp:428:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  428 |   if (m != pMat->nrow()) {
      |       ~~^~~~~~~~~~~~~~~
genotype.cpp:431:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  431 |   if (op + n > pMat->ncol()) {
      |       ~~~~~~~^~~~~~~~~~~~~~
genotype.cpp:440:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  440 |   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:546:27:   required from here
genotype.cpp:490:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  490 |   if (m != pMat->nrow()) {
      |       ~~^~~~~~~~~~~~~~~
genotype.cpp:493:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  493 |   if (op + n > pMat->ncol()) {
      |       ~~~~~~~^~~~~~~~~~~~~~
genotype.cpp:507:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  507 |   for (i = 0; i < nBlock; i++) {
      |               ~~^~~~~~~~
genotype.cpp:512:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  512 |   for (i = 1; i < nBlock; i++) {
      |               ~~^~~~~~~~
genotype.cpp:518:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  518 |   for (j = 0; j < pmat->ncol(); j++) {
      |                              ^
genotype.cpp:525:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  525 |   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:548:28:   required from here
genotype.cpp:490:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  490 |   if (m != pMat->nrow()) {
      |       ~~^~~~~~~~~~~~~~~
genotype.cpp:493:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  493 |   if (op + n > pMat->ncol()) {
      |       ~~~~~~~^~~~~~~~~~~~~~
genotype.cpp:507:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  507 |   for (i = 0; i < nBlock; i++) {
      |               ~~^~~~~~~~
genotype.cpp:512:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  512 |   for (i = 1; i < nBlock; i++) {
      |               ~~^~~~~~~~
genotype.cpp:518:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  518 |   for (j = 0; j < pmat->ncol(); j++) {
      |                              ^
genotype.cpp:525:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  525 |   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:550:26:   required from here
genotype.cpp:490:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  490 |   if (m != pMat->nrow()) {
      |       ~~^~~~~~~~~~~~~~~
genotype.cpp:493:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  493 |   if (op + n > pMat->ncol()) {
      |       ~~~~~~~^~~~~~~~~~~~~~
genotype.cpp:507:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  507 |   for (i = 0; i < nBlock; i++) {
      |               ~~^~~~~~~~
genotype.cpp:512:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  512 |   for (i = 1; i < nBlock; i++) {
      |               ~~^~~~~~~~
genotype.cpp:518:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  518 |   for (j = 0; j < pmat->ncol(); j++) {
      |                              ^
genotype.cpp:525:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  525 |   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:552:29:   required from here
genotype.cpp:490:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  490 |   if (m != pMat->nrow()) {
      |       ~~^~~~~~~~~~~~~~~
genotype.cpp:493:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  493 |   if (op + n > pMat->ncol()) {
      |       ~~~~~~~^~~~~~~~~~~~~~
genotype.cpp:507:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  507 |   for (i = 0; i < nBlock; i++) {
      |               ~~^~~~~~~~
genotype.cpp:512:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  512 |   for (i = 1; i < nBlock; i++) {
      |               ~~^~~~~~~~
genotype.cpp:518:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘index_type’ {aka ‘long int’} [-Wsign-compare]
  518 |   for (j = 0; j < pmat->ncol(); j++) {
      |                              ^
genotype.cpp:525:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  525 |   for (k = 0; k < nBlock; k++) {
      |                   ^~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigmemory/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c impute.cpp -o impute.o
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/arg.hpp:25,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/range/as_literal.hpp:18,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/algorithm/string.hpp:19,
                 from impute.cpp:2:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mem_fn.hpp:22,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/function/detail/prologue.hpp:19,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/function.hpp:30,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/algorithm/string.hpp:23:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/13/memory:78,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/function/function_base.hpp:34,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/function/detail/prologue.hpp:18:
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/shared_ptr.hpp:17,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from impute.cpp:3:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
impute.cpp: In function ‘bool hasNABed(std::string, int, long int, int, bool)’:
impute.cpp:101:43: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  101 |       for (size_t x = 0; x < 4 && (c + x) < ind; x++) {
      |                                   ~~~~~~~~^~~~~
impute.cpp:97:14: warning: unused variable ‘r’ [-Wunused-variable]
   97 |       size_t r = (block_start + j) / n;
      |              ^
impute.cpp:82:10: warning: variable ‘n_bytes_read’ set but not used [-Wunused-but-set-variable]
   82 |   size_t n_bytes_read = static_cast<size_t>(fread(buffer, 1, 3, fin));
      |          ^~~~~~~~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigmemory/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c pedigree.cpp -o pedigree.o
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/arg.hpp:25,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/range/as_literal.hpp:18,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/algorithm/string.hpp:19,
                 from pedigree.cpp:2:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mem_fn.hpp:22,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/function/detail/prologue.hpp:19,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/function.hpp:30,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/algorithm/string.hpp:23:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/13/memory:78,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/function/function_base.hpp:34,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/function/detail/prologue.hpp:18:
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/shared_ptr.hpp:17,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from pedigree.cpp:3:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
pedigree.cpp: In instantiation of ‘Rcpp::DataFrame PedigreeCorrector(Rcpp::XPtr<BigMatrix>, Rcpp::StringVector, Rcpp::DataFrame, Rcpp::Nullable<Rcpp::Vector<16> >, Rcpp::Nullable<Rcpp::Vector<16> >, double, double, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, int, bool) [with T = char; Rcpp::DataFrame = Rcpp::DataFrame_Impl<Rcpp::PreserveStorage>; Rcpp::StringVector = Rcpp::Vector<16>]’:
pedigree.cpp:251:35:   required from here
pedigree.cpp:86:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   86 |     for (size_t i = 0; i < candSirIDUse.size(); i++)
      |                        ~~^~~~~~~~~~~~~~~~~~~~~
pedigree.cpp:91:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   91 |     for (size_t i = 0; i < candDamIDUse.size(); i++)
      |                        ~~^~~~~~~~~~~~~~~~~~~~~
pedigree.cpp: In instantiation of ‘Rcpp::DataFrame PedigreeCorrector(Rcpp::XPtr<BigMatrix>, Rcpp::StringVector, Rcpp::DataFrame, Rcpp::Nullable<Rcpp::Vector<16> >, Rcpp::Nullable<Rcpp::Vector<16> >, double, double, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, int, bool) [with T = short int; Rcpp::DataFrame = Rcpp::DataFrame_Impl<Rcpp::PreserveStorage>; Rcpp::StringVector = Rcpp::Vector<16>]’:
pedigree.cpp:253:36:   required from here
pedigree.cpp:86:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   86 |     for (size_t i = 0; i < candSirIDUse.size(); i++)
      |                        ~~^~~~~~~~~~~~~~~~~~~~~
pedigree.cpp:91:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   91 |     for (size_t i = 0; i < candDamIDUse.size(); i++)
      |                        ~~^~~~~~~~~~~~~~~~~~~~~
pedigree.cpp: In instantiation of ‘Rcpp::DataFrame PedigreeCorrector(Rcpp::XPtr<BigMatrix>, Rcpp::StringVector, Rcpp::DataFrame, Rcpp::Nullable<Rcpp::Vector<16> >, Rcpp::Nullable<Rcpp::Vector<16> >, double, double, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, int, bool) [with T = int; Rcpp::DataFrame = Rcpp::DataFrame_Impl<Rcpp::PreserveStorage>; Rcpp::StringVector = Rcpp::Vector<16>]’:
pedigree.cpp:255:34:   required from here
pedigree.cpp:86:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   86 |     for (size_t i = 0; i < candSirIDUse.size(); i++)
      |                        ~~^~~~~~~~~~~~~~~~~~~~~
pedigree.cpp:91:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   91 |     for (size_t i = 0; i < candDamIDUse.size(); i++)
      |                        ~~^~~~~~~~~~~~~~~~~~~~~
pedigree.cpp: In instantiation of ‘Rcpp::DataFrame PedigreeCorrector(Rcpp::XPtr<BigMatrix>, Rcpp::StringVector, Rcpp::DataFrame, Rcpp::Nullable<Rcpp::Vector<16> >, Rcpp::Nullable<Rcpp::Vector<16> >, double, double, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, int, bool) [with T = double; Rcpp::DataFrame = Rcpp::DataFrame_Impl<Rcpp::PreserveStorage>; Rcpp::StringVector = Rcpp::Vector<16>]’:
pedigree.cpp:257:37:   required from here
pedigree.cpp:86:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   86 |     for (size_t i = 0; i < candSirIDUse.size(); i++)
      |                        ~~^~~~~~~~~~~~~~~~~~~~~
pedigree.cpp:91:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   91 |     for (size_t i = 0; i < candDamIDUse.size(); i++)
      |                        ~~^~~~~~~~~~~~~~~~~~~~~
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o simer.so RcppExports.o data_converter.o emma.o genotype.o impute.o pedigree.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpvSJldH/R.INSTALL1cace4567b6824/simer/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpvSJldH/R.INSTALL1cace4567b6824/simer/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpvSJldH/R.INSTALL1cace4567b6824/simer/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-simer/00new/simer/libs
** R
** data
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* creating tarball
packaged installation of ‘simer’ as ‘simer_0.9.0.4_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (simer)