* installing *source* package ‘rMVP’ ...
** this is package ‘rMVP’ version ‘1.4.0’
** package ‘rMVP’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/rMVP/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/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++17 -I"/data/gannet/ripley/R/R-devel/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
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/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 assoc.cpp:1:
/data/gannet/ripley/R/test-dev/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 /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:38,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
from rMVP.h:11:
/usr/include/c++/14/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++/14/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++/14/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++/14/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++/14/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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
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:253:21: required from here
253 | return glm_c<char>(y, X, iXX, xpMat, geno_ind, marker_ind, marker_bycol, step, verbose, threads);
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:95:21: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
95 | 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:255:22: required from here
255 | return glm_c<short>(y, X, iXX, xpMat, geno_ind, marker_ind, marker_bycol, step, verbose, threads);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:95:21: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
95 | 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:257:20: required from here
257 | return glm_c<int>(y, X, iXX, xpMat, geno_ind, marker_ind, marker_bycol, step, verbose, threads);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:95:21: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
95 | 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:259:23: required from here
259 | return glm_c<double>(y, X, iXX, xpMat, geno_ind, marker_ind, marker_bycol, step, verbose, threads);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:95:21: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
95 | 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:432:21: required from here
432 | return mlm_c<char>(y, X, U, vgs, xpMat, geno_ind, marker_ind, marker_bycol, step, verbose, threads);
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:291:21: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
291 | 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:434:22: required from here
434 | return mlm_c<short>(y, X, U, vgs, xpMat, geno_ind, marker_ind, marker_bycol, step, verbose, threads);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:291:21: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
291 | 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:436:20: required from here
436 | return mlm_c<int>(y, X, U, vgs, xpMat, geno_ind, marker_ind, marker_bycol, step, verbose, threads);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:291:21: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
291 | 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:438:23: required from here
438 | return mlm_c<double>(y, X, U, vgs, xpMat, geno_ind, marker_ind, marker_bycol, step, verbose, threads);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:291:21: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
291 | if(y.n_elem != n) throw Rcpp::exception("number of individuals not match.!");
| ~~~~~~~~~^~~~
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: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 /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:38,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
from rMVP.h:11:
/usr/include/c++/14/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++/14/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++/14/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++/14/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++/14/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++/14/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++/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: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++17 -I"/data/gannet/ripley/R/R-devel/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++17 -I"/data/gannet/ripley/R/R-devel/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: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 /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:38,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
from rMVP.h:11:
/usr/include/c++/14/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++/14/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++/14/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++/14/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++/14/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++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/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: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 /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:38,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
from rMVP.h:11:
/usr/include/c++/14/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++/14/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++/14/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++/14/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++/14/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++/14/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) {
| ~~~~^~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o rMVP.so RcppExports.o assoc.o data_converter.o fit_diago.o impute.o kinship.o -fopenmp -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/rMVP/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/rMVP/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/rMVP/src'
installing to /data/gannet/ripley/R/packages/tests-devel/rMVP.Rcheck/00LOCK-rMVP/00new/rMVP/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rMVP)