* installing *source* package ‘bigPLSR’ ... ** this is package ‘bigPLSR’ version ‘0.7.2’ ** package ‘bigPLSR’ successfully unpacked and MD5 sums checked ** using staged installation ==> bigPLSR: running configure ==> bigPLSR: CBLAS header NOT found — building without BIGPLSR_USE_CBLAS_SYRK ==> bigPLSR: wrote src/Makevars ** libs specified C++17 using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’ using C++17 make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/bigPLSR/src' g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_USE_CURRENT -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/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -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 -DARMA_USE_CURRENT -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/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -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 cpp_dense_cross.cpp -o cpp_dense_cross.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_USE_CURRENT -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/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -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 cpp_dense_scores.cpp -o cpp_dense_scores.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_USE_CURRENT -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/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -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 irls_binomial.cpp -o irls_binomial.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_USE_CURRENT -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/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -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 kernel_pls.cpp -o kernel_pls.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_USE_CURRENT -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/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -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 kf_pls.cpp -o kf_pls.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 kf_pls.cpp:7: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( 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 kf_pls.cpp:1: /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_USE_CURRENT -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/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -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 kf_pls_state.cpp -o kf_pls_state.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_USE_CURRENT -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/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -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 kpls_double_rkhs.cpp -o kpls_double_rkhs.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 kpls_double_rkhs.cpp:3: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( 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 kpls_double_rkhs.cpp:1: /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ kpls_double_rkhs.cpp: In function ‘Rcpp::List cpp_kpls_rkhs_xy_dense(Rcpp::NumericMatrix, Rcpp::RObject, int, double, std::string, double, int, double, std::string, double, int, double, double, double)’: kpls_double_rkhs.cpp:91:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 91 | if (Ym.nrow() != X.n_rows) stop("rkhs_xy: X and Y must have same number of rows"); | ~~~~~~~~~~^~~~~~~~~~~ kpls_double_rkhs.cpp:95:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 95 | if ((int)yv.size() != X.n_rows) stop("rkhs_xy: y length must equal nrow(X)"); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_USE_CURRENT -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/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -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 kpls_logistic.cpp -o kpls_logistic.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 kpls_logistic.cpp:4: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( 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 kpls_logistic.cpp:1: /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_USE_CURRENT -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/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -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 kpls_rkhs.cpp -o kpls_rkhs.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 kpls_rkhs.cpp:6: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( 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 kpls_rkhs.cpp:1: /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_USE_CURRENT -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/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -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 kpls_sparse.cpp -o kpls_sparse.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 kpls_sparse.cpp:3: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( 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 kpls_sparse.cpp:1: /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_USE_CURRENT -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/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -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 kpls_stream_cols.cpp -o kpls_stream_cols.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 kpls_stream_cols.cpp:3: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( 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 kpls_stream_cols.cpp:1: /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_USE_CURRENT -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/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -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 kpls_stream_xxt.cpp -o kpls_stream_xxt.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 kpls_stream_xxt.cpp:3: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( 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 kpls_stream_xxt.cpp:1: /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_USE_CURRENT -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/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -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 kpls_stubs.cpp -o kpls_stubs.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 kpls_stubs.cpp:4: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( 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 kpls_stubs.cpp:1: /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_USE_CURRENT -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/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -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 pls2_cross_simpls.cpp -o pls2_cross_simpls.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 pls2_cross_simpls.cpp:4: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( 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 pls2_cross_simpls.cpp:3: /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ pls2_cross_simpls.cpp: At global scope: pls2_cross_simpls.cpp:263:35: warning: ‘Rcpp::S4 allocate_big_matrix(std::size_t, std::size_t, const char*)’ declared ‘static’ but never defined [-Wunused-function] 263 | [[maybe_unused]] static inline S4 allocate_big_matrix(std::size_t nrow, std::size_t ncol, const char* name); | ^~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_USE_CURRENT -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/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -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 pls_cpp.cpp -o pls_cpp.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 pls_cpp.cpp:6: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( 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 pls_cpp.cpp:1: /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_USE_CURRENT -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/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -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 pls_nipals.cpp -o pls_nipals.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 pls_nipals.cpp:6: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( 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 pls_nipals.cpp:1: /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -shared -L/usr/local/lib64 -o bigPLSR.so RcppExports.o cpp_dense_cross.o cpp_dense_scores.o irls_binomial.o kernel_pls.o kf_pls.o kf_pls_state.o kpls_double_rkhs.o kpls_logistic.o kpls_rkhs.o kpls_sparse.o kpls_stream_cols.o kpls_stream_xxt.o kpls_stubs.o pls2_cross_simpls.o pls_cpp.o pls_nipals.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/bigPLSR/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/bigPLSR/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/bigPLSR/src' installing to /data/gannet/ripley/R/packages/tests-devel/bigPLSR.Rcheck/00LOCK-bigPLSR/00new/bigPLSR/libs ** R ** data *** moving datasets to lazyload DB ** 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 (bigPLSR)