* installing *source* package ‘rMVP’ ...
** this is package ‘rMVP’ version ‘1.4.5’
** package ‘rMVP’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-CXX20/rMVP/src'
g++ -std=gnu++20 -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include   -DARMA_64BIT_WORD=1 -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include   -DARMA_64BIT_WORD=1 -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c assoc.cpp -o assoc.o
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/shared_ptr.hpp:17,
                 from /data/gannet/ripley/R/test-dev/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from rMVP.h:13,
                 from assoc.cpp:1:
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  294 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/15/memory:80,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:38,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:32,
                 from rMVP.h:11:
/usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/data/gannet/ripley/R/test-dev/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++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/data/gannet/ripley/R/test-dev/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++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/data/gannet/ripley/R/test-dev/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++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/data/gannet/ripley/R/test-dev/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++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/data/gannet/ripley/R/test-dev/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++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
assoc.cpp: In function ‘SEXPREC* glm_c(const arma::vec&, const arma::mat&, const arma::mat&, Rcpp::XPtr<BigMatrix>, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, bool, int, bool, int)’:
assoc.cpp:216:34: error: reference to ‘span’ is ambiguous [-Wtemplate-body]
  216 |                         iXXs(q0, span(0, q0 - 1)) = NeginvB22B21;
      |                                  ^~~~
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:155:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note: candidates are: ‘struct arma::span’
   38 | struct span : public span_base<>
      |        ^~~~
In file included from /usr/include/c++/15/format:51,
                 from /usr/include/c++/15/bits/chrono_io.h:41,
                 from /usr/include/c++/15/chrono:3378,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:53:
/usr/include/c++/15/span:60:11: note:                 ‘template<class _Type, long unsigned int _Extent> class std::span’
   60 |     class span;
      |           ^~~~
assoc.cpp:217:30: error: reference to ‘span’ is ambiguous [-Wtemplate-body]
  217 |                         iXXs(span(0, q0 - 1), q0) = NeginvB22B21.t();
      |                              ^~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note: candidates are: ‘struct arma::span’
   38 | struct span : public span_base<>
      |        ^~~~
/usr/include/c++/15/span:60:11: note:                 ‘template<class _Type, long unsigned int _Extent> class std::span’
   60 |     class span;
      |           ^~~~
assoc.cpp: In function ‘SEXPREC* mlm_c(const arma::vec&, const arma::mat&, const arma::mat&, double, Rcpp::XPtr<BigMatrix>, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, bool, int, bool, int)’:
assoc.cpp:407:34: error: reference to ‘span’ is ambiguous [-Wtemplate-body]
  407 |                         iXXs(q0, span(0, q0 - 1)) = NeginvB22B21;
      |                                  ^~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note: candidates are: ‘struct arma::span’
   38 | struct span : public span_base<>
      |        ^~~~
/usr/include/c++/15/span:60:11: note:                 ‘template<class _Type, long unsigned int _Extent> class std::span’
   60 |     class span;
      |           ^~~~
assoc.cpp:408:30: error: reference to ‘span’ is ambiguous [-Wtemplate-body]
  408 |                         iXXs(span(0, q0 - 1), q0) = NeginvB22B21.t();
      |                              ^~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note: candidates are: ‘struct arma::span’
   38 | struct span : public span_base<>
      |        ^~~~
/usr/include/c++/15/span:60:11: note:                 ‘template<class _Type, long unsigned int _Extent> class std::span’
   60 |     class span;
      |           ^~~~
assoc.cpp: In instantiation of ‘SEXPREC* glm_c(const arma::vec&, const arma::mat&, const arma::mat&, Rcpp::XPtr<BigMatrix>, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, bool, int, bool, int) [with T = char; SEXP = SEXPREC*; arma::vec = arma::Col<double>; arma::mat = arma::Mat<double>]’:
assoc.cpp:258:21:   required from here
  258 |                 return glm_c<char>(y, X, iXX, xpMat, geno_ind, marker_ind, marker_bycol, step, verbose, threads);
      |                        ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:100:21: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
  100 |         if(y.n_elem != n)       throw Rcpp::exception("number of individuals not match!");
      |            ~~~~~~~~~^~~~
assoc.cpp: In instantiation of ‘SEXPREC* glm_c(const arma::vec&, const arma::mat&, const arma::mat&, Rcpp::XPtr<BigMatrix>, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, bool, int, bool, int) [with T = short int; SEXP = SEXPREC*; arma::vec = arma::Col<double>; arma::mat = arma::Mat<double>]’:
assoc.cpp:260:22:   required from here
  260 |                 return glm_c<short>(y, X, iXX, xpMat, geno_ind, marker_ind, marker_bycol, step, verbose, threads);
      |                        ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:100:21: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
  100 |         if(y.n_elem != n)       throw Rcpp::exception("number of individuals not match!");
      |            ~~~~~~~~~^~~~
assoc.cpp: In instantiation of ‘SEXPREC* glm_c(const arma::vec&, const arma::mat&, const arma::mat&, Rcpp::XPtr<BigMatrix>, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, bool, int, bool, int) [with T = int; SEXP = SEXPREC*; arma::vec = arma::Col<double>; arma::mat = arma::Mat<double>]’:
assoc.cpp:262:20:   required from here
  262 |                 return glm_c<int>(y, X, iXX, xpMat, geno_ind, marker_ind, marker_bycol, step, verbose, threads);
      |                        ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:100:21: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
  100 |         if(y.n_elem != n)       throw Rcpp::exception("number of individuals not match!");
      |            ~~~~~~~~~^~~~
assoc.cpp: In instantiation of ‘SEXPREC* glm_c(const arma::vec&, const arma::mat&, const arma::mat&, Rcpp::XPtr<BigMatrix>, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, bool, int, bool, int) [with T = double; SEXP = SEXPREC*; arma::vec = arma::Col<double>; arma::mat = arma::Mat<double>]’:
assoc.cpp:264:23:   required from here
  264 |                 return glm_c<double>(y, X, iXX, xpMat, geno_ind, marker_ind, marker_bycol, step, verbose, threads);
      |                        ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:100:21: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
  100 |         if(y.n_elem != n)       throw Rcpp::exception("number of individuals not match!");
      |            ~~~~~~~~~^~~~
assoc.cpp: In instantiation of ‘SEXPREC* mlm_c(const arma::vec&, const arma::mat&, const arma::mat&, double, Rcpp::XPtr<BigMatrix>, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, bool, int, bool, int) [with T = char; SEXP = SEXPREC*; arma::vec = arma::Col<double>; arma::mat = arma::Mat<double>]’:
assoc.cpp:437:21:   required from here
  437 |                 return mlm_c<char>(y, X, U, vgs, xpMat, geno_ind, marker_ind, marker_bycol, step, verbose, threads);
      |                        ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:296:21: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
  296 |         if(y.n_elem != n)       throw Rcpp::exception("number of individuals not match.!");
      |            ~~~~~~~~~^~~~
assoc.cpp: In instantiation of ‘SEXPREC* mlm_c(const arma::vec&, const arma::mat&, const arma::mat&, double, Rcpp::XPtr<BigMatrix>, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, bool, int, bool, int) [with T = short int; SEXP = SEXPREC*; arma::vec = arma::Col<double>; arma::mat = arma::Mat<double>]’:
assoc.cpp:439:22:   required from here
  439 |                 return mlm_c<short>(y, X, U, vgs, xpMat, geno_ind, marker_ind, marker_bycol, step, verbose, threads);
      |                        ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:296:21: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
  296 |         if(y.n_elem != n)       throw Rcpp::exception("number of individuals not match.!");
      |            ~~~~~~~~~^~~~
assoc.cpp: In instantiation of ‘SEXPREC* mlm_c(const arma::vec&, const arma::mat&, const arma::mat&, double, Rcpp::XPtr<BigMatrix>, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, bool, int, bool, int) [with T = int; SEXP = SEXPREC*; arma::vec = arma::Col<double>; arma::mat = arma::Mat<double>]’:
assoc.cpp:441:20:   required from here
  441 |                 return mlm_c<int>(y, X, U, vgs, xpMat, geno_ind, marker_ind, marker_bycol, step, verbose, threads);
      |                        ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:296:21: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
  296 |         if(y.n_elem != n)       throw Rcpp::exception("number of individuals not match.!");
      |            ~~~~~~~~~^~~~
assoc.cpp: In instantiation of ‘SEXPREC* mlm_c(const arma::vec&, const arma::mat&, const arma::mat&, double, Rcpp::XPtr<BigMatrix>, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, bool, int, bool, int) [with T = double; SEXP = SEXPREC*; arma::vec = arma::Col<double>; arma::mat = arma::Mat<double>]’:
assoc.cpp:443:23:   required from here
  443 |                 return mlm_c<double>(y, X, U, vgs, xpMat, geno_ind, marker_ind, marker_bycol, step, verbose, threads);
      |                        ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:296:21: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
  296 |         if(y.n_elem != n)       throw Rcpp::exception("number of individuals not match.!");
      |            ~~~~~~~~~^~~~
make[1]: *** [/data/gannet/ripley/R/cxx20/etc/Makeconf:201: assoc.o] Error 1
g++ -std=gnu++20 -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include   -DARMA_64BIT_WORD=1 -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c data_converter.cpp -o data_converter.o
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/shared_ptr.hpp:17,
                 from /data/gannet/ripley/R/test-dev/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from rMVP.h:13,
                 from data_converter.cpp:17:
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  294 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/15/memory:80,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:38,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:32,
                 from rMVP.h:11:
/usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/data/gannet/ripley/R/test-dev/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++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/data/gannet/ripley/R/test-dev/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++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/data/gannet/ripley/R/test-dev/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++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/data/gannet/ripley/R/test-dev/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++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/data/gannet/ripley/R/test-dev/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++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/bind/mem_fn.hpp:23,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/mem_fn.hpp:22,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/function/function_template.hpp:16,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/function.hpp:16,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/algorithm/string/split.hpp:16,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/algorithm/string.hpp:23,
                 from data_converter.cpp:19:
/data/gannet/ripley/R/test-dev/BH/include/boost/get_pointer.hpp: At global scope:
/data/gannet/ripley/R/test-dev/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)
      |                                        ^~~~~~~~
/usr/include/c++/15/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:606:32:   required from here
  606 |         return read_bfile<char>(bed_file, xpMat, maxLine, NA_CHAR, threads, verbose);
      |                ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
data_converter.cpp:570:12: warning: variable ‘n_bytes_read’ set but not used [-Wunused-but-set-variable]
  570 |     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:608:33:   required from here
  608 |         return read_bfile<short>(bed_file, xpMat, maxLine, NA_SHORT, threads, verbose);
      |                ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
data_converter.cpp:570:12: warning: variable ‘n_bytes_read’ set but not used [-Wunused-but-set-variable]
  570 |     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:610:31:   required from here
  610 |         return read_bfile<int>(bed_file, xpMat, maxLine, NA_INTEGER, threads, verbose);
      |                ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
data_converter.cpp:570:12: warning: variable ‘n_bytes_read’ set but not used [-Wunused-but-set-variable]
  570 |     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:612:34:   required from here
  612 |         return read_bfile<double>(bed_file, xpMat, maxLine, NA_REAL, threads, verbose);
      |                ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
data_converter.cpp:570:12: warning: variable ‘n_bytes_read’ set but not used [-Wunused-but-set-variable]
  570 |     size_t n_bytes_read = static_cast<size_t>(fread(buffer, 1, 3, fin));
      |            ^~~~~~~~~~~~
g++ -std=gnu++20 -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include   -DARMA_64BIT_WORD=1 -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c fit_diago.cpp -o fit_diago.o
g++ -std=gnu++20 -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include   -DARMA_64BIT_WORD=1 -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c impute.cpp -o impute.o
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/shared_ptr.hpp:17,
                 from /data/gannet/ripley/R/test-dev/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from rMVP.h:13,
                 from impute.cpp:15:
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  294 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/15/memory:80,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:38,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:32,
                 from rMVP.h:11:
/usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/data/gannet/ripley/R/test-dev/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++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/data/gannet/ripley/R/test-dev/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++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/data/gannet/ripley/R/test-dev/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++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/data/gannet/ripley/R/test-dev/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++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/data/gannet/ripley/R/test-dev/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++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++20 -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include   -DARMA_64BIT_WORD=1 -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c kinship.cpp -o kinship.o
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/shared_ptr.hpp:17,
                 from /data/gannet/ripley/R/test-dev/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from rMVP.h:13,
                 from kinship.cpp:5:
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  294 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/15/memory:80,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:38,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:32,
                 from rMVP.h:11:
/usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/data/gannet/ripley/R/test-dev/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++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/data/gannet/ripley/R/test-dev/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++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/data/gannet/ripley/R/test-dev/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++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/data/gannet/ripley/R/test-dev/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++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/data/gannet/ripley/R/test-dev/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++/15/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
kinship.cpp: In instantiation of ‘arma::vec BigRowMean(Rcpp::XPtr<BigMatrix>, bool, size_t, int, Rcpp::Nullable<arma::Col<long long unsigned int> >, bool) [with T = char; arma::vec = arma::Col<double>; size_t = long unsigned int]’:
kinship.cpp:154:26:   required from here
  154 |                 return BigRowMean<char>(xpMat, marker_bycol, step, threads, geno_ind, verbose);
      |                        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kinship.cpp:43:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   43 |                 for (; j < m && cnt < step; j++)
      |                                 ~~~~^~~~~~
kinship.cpp:48:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   48 |                 if (cnt != step) {
      |                     ~~~~^~~~~~~
kinship.cpp: In instantiation of ‘arma::vec BigRowMean(Rcpp::XPtr<BigMatrix>, bool, size_t, int, Rcpp::Nullable<arma::Col<long long unsigned int> >, bool) [with T = short int; arma::vec = arma::Col<double>; size_t = long unsigned int]’:
kinship.cpp:156:27:   required from here
  156 |                 return BigRowMean<short>(xpMat, marker_bycol, step, threads, geno_ind, verbose);
      |                        ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kinship.cpp:43:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   43 |                 for (; j < m && cnt < step; j++)
      |                                 ~~~~^~~~~~
kinship.cpp:48:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   48 |                 if (cnt != step) {
      |                     ~~~~^~~~~~~
kinship.cpp: In instantiation of ‘arma::vec BigRowMean(Rcpp::XPtr<BigMatrix>, bool, size_t, int, Rcpp::Nullable<arma::Col<long long unsigned int> >, bool) [with T = int; arma::vec = arma::Col<double>; size_t = long unsigned int]’:
kinship.cpp:158:25:   required from here
  158 |                 return BigRowMean<int>(xpMat, marker_bycol, step, threads, geno_ind, verbose);
      |                        ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kinship.cpp:43:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   43 |                 for (; j < m && cnt < step; j++)
      |                                 ~~~~^~~~~~
kinship.cpp:48:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   48 |                 if (cnt != step) {
      |                     ~~~~^~~~~~~
kinship.cpp: In instantiation of ‘arma::vec BigRowMean(Rcpp::XPtr<BigMatrix>, bool, size_t, int, Rcpp::Nullable<arma::Col<long long unsigned int> >, bool) [with T = double; arma::vec = arma::Col<double>; size_t = long unsigned int]’:
kinship.cpp:160:28:   required from here
  160 |                 return BigRowMean<double>(xpMat, marker_bycol, step, threads, geno_ind, verbose);
      |                        ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kinship.cpp:43:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   43 |                 for (; j < m && cnt < step; j++)
      |                                 ~~~~^~~~~~
kinship.cpp:48:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   48 |                 if (cnt != step) {
      |                     ~~~~^~~~~~~
make[1]: Target 'all' not remade because of errors.
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-CXX20/rMVP/src'
ERROR: compilation failed for package ‘rMVP’
* removing ‘/data/gannet/ripley/R/packages/tests-CXX20/rMVP.Rcheck/rMVP’