* installing to library ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages’
* installing *source* package ‘bigPLScox’ ...
** this is package ‘bigPLScox’ version ‘0.6.0’
** package ‘bigPLScox’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-10) 14.3.0’
using C++17
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpKd1kia/R.INSTALL14a9ae554f7e0f/bigPLScox/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -DARMA_USE_CURRENT -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/bigmemory/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -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-release-gcc/Work/build/include" -DNDEBUG -DARMA_USE_CURRENT -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/bigmemory/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c big_pls_cox.cpp -o big_pls_cox.o
In file included from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/shared_ptr.hpp:17,
                 from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from big_pls_cox.cpp:2:
/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:23:
/usr/include/c++/14/bits/unique_ptr.h:58:28: note: declared here
   58 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-release-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:58:28: note: declared here
   58 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-release-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:58:28: note: declared here
   58 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-release-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:58:28: note: declared here
   58 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-release-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:58:28: note: declared here
   58 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-release-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-release-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:58:28: note: declared here
   58 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
big_pls_cox.cpp: In instantiation of ‘Rcpp::NumericMatrix {anonymous}::compute_scores_impl(Accessor&, std::size_t, std::size_t, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericMatrix&, const Rcpp::NumericMatrix&, const Rcpp::IntegerVector&) [with Accessor = BigMatrixAccessorWrapper; Rcpp::NumericMatrix = Rcpp::Matrix<14>; std::size_t = long unsigned int; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>]’:
big_pls_cox.cpp:294:29:   required from here
  294 |   return compute_scores_impl(accessor, n, p, means, sds, weights, loadings, comps);
      |          ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
big_pls_cox.cpp:84:22: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   84 |     if (means.size() != p || sds.size() != p) {
      |         ~~~~~~~~~~~~~^~~~
big_pls_cox.cpp:84:41: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   84 |     if (means.size() != p || sds.size() != p) {
      |                              ~~~~~~~~~~~^~~~
big_pls_cox.cpp: In instantiation of ‘Rcpp::NumericMatrix {anonymous}::compute_scores_impl(Accessor&, std::size_t, std::size_t, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericMatrix&, const Rcpp::NumericMatrix&, const Rcpp::IntegerVector&) [with Accessor = NumericMatrixAccessorWrapper; Rcpp::NumericMatrix = Rcpp::Matrix<14>; std::size_t = long unsigned int; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>]’:
big_pls_cox.cpp:307:29:   required from here
  307 |   return compute_scores_impl(accessor, n, p, means, sds, weights, loadings, comps);
      |          ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
big_pls_cox.cpp:84:22: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   84 |     if (means.size() != p || sds.size() != p) {
      |         ~~~~~~~~~~~~~^~~~
big_pls_cox.cpp:84:41: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   84 |     if (means.size() != p || sds.size() != p) {
      |                              ~~~~~~~~~~~^~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -DARMA_USE_CURRENT -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/bigmemory/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c big_pls_cox_gd.cpp -o big_pls_cox_gd.o
In file included from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/shared_ptr.hpp:17,
                 from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from big_pls_cox_gd.cpp:2:
/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:38,
                 from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:32,
                 from big_pls_cox_gd.cpp:1:
/usr/include/c++/14/bits/unique_ptr.h:58:28: note: declared here
   58 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-release-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:58:28: note: declared here
   58 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-release-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:58:28: note: declared here
   58 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-release-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:58:28: note: declared here
   58 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-release-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:58:28: note: declared here
   58 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-release-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-release-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:58:28: note: declared here
   58 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -DARMA_USE_CURRENT -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/bigmemory/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c deviance_residuals.cpp -o deviance_residuals.o
In file included from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/shared_ptr.hpp:17,
                 from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from deviance_residuals.cpp:2:
/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:23:
/usr/include/c++/14/bits/unique_ptr.h:58:28: note: declared here
   58 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-release-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:58:28: note: declared here
   58 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-release-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:58:28: note: declared here
   58 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-release-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:58:28: note: declared here
   58 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-release-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:58:28: note: declared here
   58 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/hornik/tmp/R.check/r-release-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-release-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:58:28: note: declared here
   58 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -DARMA_USE_CURRENT -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/bigmemory/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c partial_loglik.cpp -o partial_loglik.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -Wl,-O1 -o bigPLScox.so RcppExports.o big_pls_cox.o big_pls_cox_gd.o deviance_residuals.o partial_loglik.o -llapack -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpKd1kia/R.INSTALL14a9ae554f7e0f/bigPLScox/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpKd1kia/R.INSTALL14a9ae554f7e0f/bigPLScox/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpKd1kia/R.INSTALL14a9ae554f7e0f/bigPLScox/src'
installing to /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-bigPLScox/00new/bigPLScox/libs
** R
** data
** inst
** 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 (bigPLScox)