############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL epistasisGA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘epistasisGA’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/bigmemory/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/bigmemory/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c epistasisGA.cpp -o epistasisGA.o In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from /home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.21-bioc/R/site-library/bigmemory/include/bigmemory/BigMatrix.h:10, from epistasisGA.cpp:7: /home/biocbuild/bbs-3.21-bioc/R/site-library/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/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include/armadillo:38, from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58, from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from epistasisGA.cpp:1: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /home/biocbuild/bbs-3.21-bioc/R/site-library/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/biocbuild/bbs-3.21-bioc/R/site-library/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/biocbuild/bbs-3.21-bioc/R/site-library/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/biocbuild/bbs-3.21-bioc/R/site-library/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/biocbuild/bbs-3.21-bioc/R/site-library/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/biocbuild/bbs-3.21-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/bbs-3.21-bioc/R/site-library/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++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o epistasisGA.so RcppExports.o epistasisGA.o -llapack -L/home/biocbuild/bbs-3.21-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-epistasisGA/00new/epistasisGA/libs ** R ** data ** 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 (epistasisGA)