* installing to library ‘/home/hornik/tmp/R.check/r-patched-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 '/home/hornik/tmp/scratch/RtmpgmOHaz/R.INSTALL25bc4d67eb056b/simer/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/bind/mem_fn.hpp:23,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/bind/bind.hpp:23,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/bind.hpp:29,
from data_converter.cpp:2:
/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/config/no_tr1/memory.hpp:21,
from /home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/bind.hpp:30:
/home/hornik/tmp/R.check/r-patched-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-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/arg.hpp:25,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/placeholders.hpp:24,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/iterator_range.hpp:13,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/as_literal.hpp:18,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string.hpp:19,
from data_converter.cpp:3:
/home/hornik/tmp/R.check/r-patched-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-patched-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-patched-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-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/shared_ptr.hpp:17,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigmemory/include/bigmemory/BigMatrix.h:10,
from data_converter.cpp:4:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
326 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
/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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
354 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
/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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
365 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
/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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
423 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
/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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
430 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
/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-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
432 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
/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-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/shared_ptr.hpp:17,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigmemory/include/bigmemory/BigMatrix.h:10,
from emma.cpp:2:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
326 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from /usr/include/c++/14/memory:78,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:38,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
from /home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
354 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
/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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
365 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
/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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
423 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
/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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
430 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
/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-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
432 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
/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-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/shared_ptr.hpp:17,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigmemory/include/bigmemory/BigMatrix.h:10,
from genotype.cpp:3:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
326 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from /usr/include/c++/14/memory:78,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:38,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
from /home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
354 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
/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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
365 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
/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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
423 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
/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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
430 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
/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-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
432 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
/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-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/arg.hpp:25,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/placeholders.hpp:24,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/iterator_range.hpp:13,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/as_literal.hpp:18,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string.hpp:19,
from impute.cpp:2:
/home/hornik/tmp/R.check/r-patched-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-patched-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-patched-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-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/bind/mem_fn.hpp:23,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mem_fn.hpp:22,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/function/function_template.hpp:16,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/function.hpp:16,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/split.hpp:16,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string.hpp:23:
/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/function/function_base.hpp:23,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/function/function_template.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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/shared_ptr.hpp:17,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigmemory/include/bigmemory/BigMatrix.h:10,
from impute.cpp:3:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
326 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
/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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
354 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
/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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
365 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
/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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
423 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
/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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
430 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
/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-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
432 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
/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-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/arg.hpp:25,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/placeholders.hpp:24,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/iterator_range.hpp:13,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/as_literal.hpp:18,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string.hpp:19,
from pedigree.cpp:2:
/home/hornik/tmp/R.check/r-patched-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-patched-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-patched-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-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/bind/mem_fn.hpp:23,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mem_fn.hpp:22,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/function/function_template.hpp:16,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/function.hpp:16,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/split.hpp:16,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string.hpp:23:
/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:38,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
from /home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/shared_ptr.hpp:17,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigmemory/include/bigmemory/BigMatrix.h:10,
from pedigree.cpp:3:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
326 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
/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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
354 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
/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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
365 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
/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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
423 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
/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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
430 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
/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-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
432 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
/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-patched-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-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpgmOHaz/R.INSTALL25bc4d67eb056b/simer/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpgmOHaz/R.INSTALL25bc4d67eb056b/simer/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpgmOHaz/R.INSTALL25bc4d67eb056b/simer/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-simer/00new/simer/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘simer’
finding HTML links ... done
GxG.network html
IndPerGen html
annotation html
build.cov html
cal.eff html
checkEnv html
format_time html
generate.map html
generate.pop html
geno.cvt1 html
geno.cvt2 html
genotype html
getfam html
load_if_installed html
logging.initialize html
logging.log html
logging.print html
make_line html
mate.2waycro html
mate.3waycro html
mate.4waycro html
mate html
mate.assort html
mate.backcro html
mate.clone html
mate.dh html
mate.disassort html
mate.randexself html
mate.randmate html
mate.selfpol html
mate.userped html
mkl_env html
param.annot html
param.geno html
param.global html
param.pheno html
param.reprod html
param.sel html
param.simer html
paste_label html
phenotype html
pop.geno html
pop.map html
print_accomplished html
print_bar html
print_info html
remove_bigmatrix html
reproduces html
rule_wrap html
selects html
simer.Data.Bfile2MVP html
simer.Data.Env html
simer.Data.Geno html
simer.Data.Impute html
simer.Data.Json html
simer.Data.Kin html
simer.Data.MVP2Bfile html
simer.Data.MVP2MVP html
simer.Data.Map html
simer.Data.Ped html
simer.Data.Pheno html
simer.Data html
simer.Data.SELIND html
simer.Data.cHIBLUP html
simer html
simer.Version html
write.file html
** 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)