* 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++.exe (GCC) 14.3.0'
using C++17
make[1]: Entering directory '/d/temp/2025_11_13_01_50_00_26121/RtmpSYMObq/R.INSTALL75f029961ea0/bigPLScox/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DARMA_USE_CURRENT -I'D:/RCompile/CRANpkg/lib/4.6/BH/include' -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/bigmemory/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
In file included from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo:26,
from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo.h:32,
from RcppExports.cpp:4:
D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
373 | #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
| ^
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DARMA_USE_CURRENT -I'D:/RCompile/CRANpkg/lib/4.6/BH/include' -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/bigmemory/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c big_pls_cox.cpp -o big_pls_cox.o
In file included from D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/shared_ptr.hpp:17,
from D:/RCompile/CRANpkg/lib/4.6/bigmemory/include/bigmemory/BigMatrix.h:10,
from big_pls_cox.cpp:2:
D:/RCompile/CRANpkg/lib/4.6/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 D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/memory:78,
from D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
from D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/smart_ptr/detail/shared_count.hpp:23:
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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()
| ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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()
| ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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 )
| ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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 )
| ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
D:/RCompile/CRANpkg/lib/4.6/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 );
| ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | 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 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 long int'} and 'std::size_t' {aka 'long 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 long int'} and 'std::size_t' {aka 'long 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 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 long int'} and 'std::size_t' {aka 'long 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 long int'} and 'std::size_t' {aka 'long long unsigned int'} [-Wsign-compare]
84 | if (means.size() != p || sds.size() != p) {
| ~~~~~~~~~~~^~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DARMA_USE_CURRENT -I'D:/RCompile/CRANpkg/lib/4.6/BH/include' -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/bigmemory/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c big_pls_cox_gd.cpp -o big_pls_cox_gd.o
In file included from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo:26,
from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo.h:32,
from big_pls_cox_gd.cpp:1:
D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
373 | #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
| ^
In file included from D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/shared_ptr.hpp:17,
from D:/RCompile/CRANpkg/lib/4.6/bigmemory/include/bigmemory/BigMatrix.h:10,
from big_pls_cox_gd.cpp:2:
D:/RCompile/CRANpkg/lib/4.6/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 D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/memory:78,
from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo:38:
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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()
| ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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()
| ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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 )
| ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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 )
| ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
D:/RCompile/CRANpkg/lib/4.6/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 );
| ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DARMA_USE_CURRENT -I'D:/RCompile/CRANpkg/lib/4.6/BH/include' -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/bigmemory/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c deviance_residuals.cpp -o deviance_residuals.o
In file included from D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/shared_ptr.hpp:17,
from D:/RCompile/CRANpkg/lib/4.6/bigmemory/include/bigmemory/BigMatrix.h:10,
from deviance_residuals.cpp:2:
D:/RCompile/CRANpkg/lib/4.6/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 D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/memory:78,
from D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
from D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/smart_ptr/detail/shared_count.hpp:23:
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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()
| ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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()
| ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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 )
| ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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 )
| ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
D:/RCompile/CRANpkg/lib/4.6/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 );
| ^~~~~~~~
D:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.3.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DARMA_USE_CURRENT -I'D:/RCompile/CRANpkg/lib/4.6/BH/include' -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/bigmemory/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c partial_loglik.cpp -o partial_loglik.o
g++ -shared -s -static-libgcc -o bigPLScox.dll tmp.def RcppExports.o big_pls_cox.o big_pls_cox_gd.o deviance_residuals.o partial_loglik.o -LD:/RCompile/recent/R/bin/x64 -lRlapack -LD:/RCompile/recent/R/bin/x64 -lRblas -lgfortran -lquadmath -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2025_11_13_01_50_00_26121/RtmpSYMObq/R.INSTALL75f029961ea0/bigPLScox/src'
make[1]: Entering directory '/d/temp/2025_11_13_01_50_00_26121/RtmpSYMObq/R.INSTALL75f029961ea0/bigPLScox/src'
make[1]: Leaving directory '/d/temp/2025_11_13_01_50_00_26121/RtmpSYMObq/R.INSTALL75f029961ea0/bigPLScox/src'
installing to d:/Rcompile/CRANpkg/lib/4.6/00LOCK-bigPLScox/00new/bigPLScox/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'bigPLScox' as bigPLScox_0.6.0.zip
* DONE (bigPLScox)