* installing *source* package ‘bigPLScox’ ... ** this is package ‘bigPLScox’ version ‘0.8.1’ ** package ‘bigPLScox’ successfully unpacked and MD5 sums checked ** using staged installation ** 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/bigPLScox/src' g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_USE_CURRENT -I'/data/gannet/ripley/R/test-dev/BH/include' -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/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/BH/include' -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/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 big_pls_cox.cpp -o big_pls_cox.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 big_pls_cox.cpp:2: /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/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27, from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:23: /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/BH/include' -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/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 big_pls_cox_fast_big.cpp -o big_pls_cox_fast_big.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 big_pls_cox_fast_big.cpp:2: /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 big_pls_cox_fast_big.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/BH/include' -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/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 big_pls_cox_fast_dense.cpp -o big_pls_cox_fast_dense.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 fast_common.h:5, from big_pls_cox_fast_dense.cpp:2: /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 big_pls_cox_fast_dense.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/BH/include' -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/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 big_pls_cox_gd.cpp -o big_pls_cox_gd.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 big_pls_cox_gd.cpp:2: /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 big_pls_cox_gd.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/BH/include' -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/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 big_pls_cox_transform.cpp -o big_pls_cox_transform.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 big_pls_cox_transform.cpp:2: /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/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27, from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:23: /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/BH/include' -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/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 cox_score_residuals_fast.cpp -o cox_score_residuals_fast.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_USE_CURRENT -I'/data/gannet/ripley/R/test-dev/BH/include' -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/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 deviance_residuals.cpp -o deviance_residuals.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 deviance_residuals.cpp:2: /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/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27, from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:23: /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/BH/include' -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/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 partial_loglik.cpp -o partial_loglik.o g++ -std=gnu++17 -shared -L/usr/local/lib64 -o bigPLScox.so RcppExports.o big_pls_cox.o big_pls_cox_fast_big.o big_pls_cox_fast_dense.o big_pls_cox_gd.o big_pls_cox_transform.o cox_score_residuals_fast.o deviance_residuals.o partial_loglik.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/bigPLScox/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/bigPLScox/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/bigPLScox/src' installing to /data/gannet/ripley/R/packages/tests-devel/bigPLScox.Rcheck/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)