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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL epistasisGA
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘epistasisGA’ ...
** this is package ‘epistasisGA’ version ‘1.10.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/bigmemory/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/bigmemory/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c epistasisGA.cpp -o epistasisGA.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.21-bioc/R/site-library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.21-bioc/R/site-library/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++/13/memory:78,
                 from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include/current/armadillo:38,
                 from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:32,
                 from epistasisGA.cpp:1:
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/biocbuild/bbs-3.21-bioc/R/site-library/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++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/biocbuild/bbs-3.21-bioc/R/site-library/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++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/biocbuild/bbs-3.21-bioc/R/site-library/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++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/biocbuild/bbs-3.21-bioc/R/site-library/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++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/biocbuild/bbs-3.21-bioc/R/site-library/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/biocbuild/bbs-3.21-bioc/R/site-library/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++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
epistasisGA.cpp: In function ‘Rcpp::List chrom_fitness_score(Rcpp::IntegerMatrix, Rcpp::IntegerMatrix, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, int, int, double, double, bool)’:
epistasisGA.cpp:970:26: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  970 |          !arma::is_finite(n_case_high_risk) | !arma::is_finite(n_comp_high_risk)){
      |           ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include/current/armadillo:518:
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
  167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
      | ^~~~~~~~~
epistasisGA.cpp:970:63: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  970 |          !arma::is_finite(n_case_high_risk) | !arma::is_finite(n_comp_high_risk)){
      |                                                ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
  167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
      | ^~~~~~~~~
epistasisGA.cpp:1045:77: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
 1045 |     if ( (fitness_score <= 0) | R_isnancpp(fitness_score) | !arma::is_finite(fitness_score) ){
      |                                                              ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
  167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
      | ^~~~~~~~~
epistasisGA.cpp: In function ‘Rcpp::List GxE_fitness_score_mvlm(Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericMatrix, arma::uvec, arma::vec, arma::vec, arma::vec, int, int)’:
epistasisGA.cpp:1382:64: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
 1382 |             if ( (s <= 0) | (R_isnancpp(s)) | (!arma::is_finite(s)) | any(H_Einv_diag <= 0)){
      |                                                 ~~~~~~~~~~~~~~~^~~
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
  167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
      | ^~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o epistasisGA.so RcppExports.o epistasisGA.o -llapack -L/home/biocbuild/bbs-3.21-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-epistasisGA/00new/epistasisGA/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (epistasisGA)