############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL epistasisGA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘epistasisGA’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/bigmemory/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/bigmemory/include' -I/usr/local/include -fPIC -g -O2 -Wall -c epistasisGA.cpp -o epistasisGA.o In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/lexical_cast.hpp:30, from epistasisGA.cpp:2: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/bigmemory/include/bigmemory/BigMatrix.h:10, from epistasisGA.cpp:7: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-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++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25, from /home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from epistasisGA.cpp:1: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/bigmemory/include/bigmemory/BigMatrix.h:10, from epistasisGA.cpp:7: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25, from /home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from epistasisGA.cpp:1: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/bigmemory/include/bigmemory/BigMatrix.h:10, from epistasisGA.cpp:7: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25, from /home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from epistasisGA.cpp:1: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/bigmemory/include/bigmemory/BigMatrix.h:10, from epistasisGA.cpp:7: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25, from /home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from epistasisGA.cpp:1: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/bigmemory/include/bigmemory/BigMatrix.h:10, from epistasisGA.cpp:7: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25, from /home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from epistasisGA.cpp:1: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/bigmemory/include/bigmemory/BigMatrix.h:10, from epistasisGA.cpp:7: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25, from /home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from epistasisGA.cpp:1: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/bigmemory/include/bigmemory/BigMatrix.h:10, from epistasisGA.cpp:7: /home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25, from /home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from epistasisGA.cpp:1: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o epistasisGA.so RcppExports.o epistasisGA.o -llapack -lblas -lgfortran -lm -L/home/biocbuild/R/R-4.3.1/lib -lR installing to /home/biocbuild/R/R-4.3.1/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)