* installing to library ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages’ * installing *source* package ‘biglasso’ ... ** package ‘biglasso’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-13 (Debian 13.2.0-25) 13.2.0’ using C++ compiler: ‘g++-13 (Debian 13.2.0-25) 13.2.0’ make[1]: Entering directory '/tmp/RtmpdJxkKd/R.INSTALL2d81b568d87498/biglasso/src' g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -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'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -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'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c binomial.cpp -o binomial.o In file included from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:18, 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 utilities.h:13, from binomial.cpp:1: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/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:27: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template 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& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ binomial.cpp: In function ‘SEXPREC* cdfit_binomial_ssr_approx(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: binomial.cpp:694:34: warning: ‘sumS’ may be used uninitialized [-Wmaybe-uninitialized] 694 | violations = check_rest_set(e1, e2, z, xMat, row_idx, col_idx,center, scale, a, lambda[l], sumS, alpha, s, m, n, p); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ binomial.cpp:544:10: note: ‘sumS’ was declared here 544 | double sumS; // temp result sum of s | ^~~~ g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -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'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c cox.cpp -o 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:18, 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 utilities.h:13, from cox.cpp:1: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/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:27: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template 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& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ cox.cpp: In function ‘_Z9safe_initRSt6vectorIdSaIdEEN4Rcpp4XPtrI9BigMatrixNS3_15PreserveStorageEXadL_ZNS3_25standard_delete_finalizerIS5_EEvPT_EELb0EEEPdSB_S2_iPiRS_IiSaIiEERNS3_6VectorILi14ES6_EESI_iiiSB_SB_SC_._omp_fn.0’: cox.cpp:92:26: warning: ‘xTy’ may be used uninitialized [-Wmaybe-uninitialized] 92 | if(y[i] > 0) xTy += xCol[row_idx[i]]; | ~~~~^~~~~~~~~~~~~~~~~~~ cox.cpp:78:10: note: ‘xTy’ was declared here 78 | double xTy = 0; | ^~~ g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -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'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c gaussian.cpp -o gaussian.o In file included from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:18, 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 utilities.h:13, from gaussian.cpp:1: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/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:27: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template 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& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -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'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c gaussian_simple.cpp -o gaussian_simple.o In file included from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:18, 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 utilities.h:13, from gaussian_simple.cpp:1: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/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:27: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template 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& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ gcc-13 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -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'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -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'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c mgaussian.cpp -o mgaussian.o In file included from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:18, 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 utilities.h:13, from mgaussian.cpp:1: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/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:27: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template 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& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -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'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c utilities.cpp -o utilities.o In file included from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:18, 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 utilities.h:13, from utilities.cpp:10: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/13/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:27: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template 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& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -Wl,-O1 -o biglasso.so RcppExports.o binomial.o cox.o gaussian.o gaussian_simple.o init.o mgaussian.o utilities.o -fopenmp -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 '/tmp/RtmpdJxkKd/R.INSTALL2d81b568d87498/biglasso/src' make[1]: Entering directory '/tmp/RtmpdJxkKd/R.INSTALL2d81b568d87498/biglasso/src' make[1]: Leaving directory '/tmp/RtmpdJxkKd/R.INSTALL2d81b568d87498/biglasso/src' installing to /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-biglasso/00new/biglasso/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 * creating tarball packaged installation of ‘biglasso’ as ‘biglasso_1.6.0_R_x86_64-pc-linux-gnu.tar.gz’ * DONE (biglasso)