* 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++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/tmp/RtmpEfR6aN/R.INSTALL83a051f811c06/simer/src'
g++-14 -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++-14 -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++/14/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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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
166 | return read_bfile<char>(bed_file, xpMat, maxLine, NA_CHAR, threads, verbose);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
168 | return read_bfile<short>(bed_file, xpMat, maxLine, NA_SHORT, threads, verbose);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 = int; std::string = std::__cxx11::basic_string<char>]’:
data_converter.cpp:170:27: required from here
170 | return read_bfile<int>(bed_file, xpMat, maxLine, NA_INTEGER, threads, verbose);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 = double; std::string = std::__cxx11::basic_string<char>]’:
data_converter.cpp:172:30: required from here
172 | return read_bfile<double>(bed_file, xpMat, maxLine, NA_REAL, threads, verbose);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~
g++-14 -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++/14/memory:78,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:38,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
from emma.cpp:1:
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
g++-14 -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++/14/memory:78,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:38,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
from genotype.cpp:1:
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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
75 | return FilterGeno<char>(xpMat, NA_CHAR, rowIdx, colIdx, threads);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
77 | return FilterGeno<short>(xpMat, NA_SHORT, rowIdx, colIdx, threads);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
79 | return FilterGeno<int>(xpMat, NA_INTEGER, rowIdx, colIdx, threads);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
81 | return FilterGeno<double>(xpMat, NA_REAL, rowIdx, colIdx, threads);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
117 | return CalGenoFreq<char>(xpMat, NA_CHAR, rowIdx, colIdx, threads);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
119 | return CalGenoFreq<short>(xpMat, NA_SHORT, rowIdx, colIdx, threads);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
121 | return CalGenoFreq<int>(xpMat, NA_INTEGER, rowIdx, colIdx, threads);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
123 | return CalGenoFreq<double>(xpMat, NA_REAL, rowIdx, colIdx, threads);
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
399 | return Mat2BigMat<char>(xpMat, mat, colIdx, op, threads);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
401 | return Mat2BigMat<short>(xpMat, mat, colIdx, op, threads);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
403 | return Mat2BigMat<int>(xpMat, mat, colIdx, op, threads);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
405 | return Mat2BigMat<double>(xpMat, mat, colIdx, op, threads);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
462 | return BigMat2BigMat<char>(xpMat, xpmat, colIdx, op, threads);
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
464 | return BigMat2BigMat<short>(xpMat, xpmat, colIdx, op, threads);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
466 | return BigMat2BigMat<int>(xpMat, xpmat, colIdx, op, threads);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
468 | return BigMat2BigMat<double>(xpMat, xpmat, colIdx, op, threads);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
546 | return GenoMixer<char>(xpMat, xpmat, sirIdx, damIdx, nBlock, op, threads);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
548 | return GenoMixer<short>(xpMat, xpmat, sirIdx, damIdx, nBlock, op, threads);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
550 | return GenoMixer<int>(xpMat, xpmat, sirIdx, damIdx, nBlock, op, threads);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
552 | return GenoMixer<double>(xpMat, xpmat, sirIdx, damIdx, nBlock, op, threads);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++-14 -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++/14/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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++-14 -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++/14/memory:78,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:38,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
from pedigree.cpp:1:
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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:239:35: required from here
239 | return PedigreeCorrector<char>(xpMat, rawGenoID, rawPed, candSirID, candDamID, exclThres, assignThres, birthDate, threads, verbose);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pedigree.cpp:84:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
84 | for (size_t i = 0; i < candSirIDUse.size(); i++)
| ~~^~~~~~~~~~~~~~~~~~~~~
pedigree.cpp:89:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
89 | 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:241:36: required from here
241 | return PedigreeCorrector<short>(xpMat, rawGenoID, rawPed, candSirID, candDamID, exclThres, assignThres, birthDate, threads, verbose);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pedigree.cpp:84:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
84 | for (size_t i = 0; i < candSirIDUse.size(); i++)
| ~~^~~~~~~~~~~~~~~~~~~~~
pedigree.cpp:89:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
89 | 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:243:34: required from here
243 | return PedigreeCorrector<int>(xpMat, rawGenoID, rawPed, candSirID, candDamID, exclThres, assignThres, birthDate, threads, verbose);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pedigree.cpp:84:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
84 | for (size_t i = 0; i < candSirIDUse.size(); i++)
| ~~^~~~~~~~~~~~~~~~~~~~~
pedigree.cpp:89:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
89 | 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:245:37: required from here
245 | return PedigreeCorrector<double>(xpMat, rawGenoID, rawPed, candSirID, candDamID, exclThres, assignThres, birthDate, threads, verbose);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pedigree.cpp:84:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
84 | for (size_t i = 0; i < candSirIDUse.size(); i++)
| ~~^~~~~~~~~~~~~~~~~~~~~
pedigree.cpp:89:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
89 | for (size_t i = 0; i < candDamIDUse.size(); i++)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++-14 -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 '/tmp/RtmpEfR6aN/R.INSTALL83a051f811c06/simer/src'
make[1]: Entering directory '/tmp/RtmpEfR6aN/R.INSTALL83a051f811c06/simer/src'
make[1]: Leaving directory '/tmp/RtmpEfR6aN/R.INSTALL83a051f811c06/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
* DONE (simer)