############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL pqsfinder ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘pqsfinder’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c pqsfinder.cpp -o pqsfinder.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27, from pqsfinder.cpp:13: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/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++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27, from pqsfinder.cpp:13: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/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++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27, from pqsfinder.cpp:13: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27, from pqsfinder.cpp:13: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27, from pqsfinder.cpp:13: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27, from pqsfinder.cpp:13: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27, from pqsfinder.cpp:13: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from pqsfinder.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27, from pqsfinder.cpp:13: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ pqsfinder.cpp: In function ‘void find_all_runs(SEXP, int, std::__cxx11::basic_string::const_iterator, std::__cxx11::basic_string::const_iterator, run_match*, const regex&, const opts_t&, const scoring&, const const_iterator&, size_t, storage&, int&, results&, bool, std::chrono::_V2::system_clock::time_point, int, int, int, int&, bool)’: pqsfinder.cpp:584:53: warning: ‘loop_len’ may be used uninitialized in this function [-Wmaybe-uninitialized] 584 | pqs_storage, int_cnt, res, (loop_len == 0 ? true : zero_loop), | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/cpp_regex_traits.cpp -o boost_regex/cpp_regex_traits.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/cpp_regex_traits.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/cregex.cpp -o boost_regex/cregex.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: /home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/cregex.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/usinstances.cpp -o boost_regex/usinstances.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/icu.cpp -o boost_regex/icu.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/fileiter.cpp -o boost_regex/fileiter.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from boost_regex/fileiter.cpp:28: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from boost_regex/fileiter.cpp:28: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from boost_regex/fileiter.cpp:28: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from boost_regex/fileiter.cpp:28: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from boost_regex/fileiter.cpp:28: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from boost_regex/fileiter.cpp:28: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from boost_regex/fileiter.cpp:28: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from boost_regex/fileiter.cpp:28: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from boost_regex/fileiter.cpp:28: /home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from boost_regex/fileiter.cpp:28: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/regex.cpp -o boost_regex/regex.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: /home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/regex.cpp:24: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: /home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/posix_api.cpp:23: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/c_regex_traits.cpp -o boost_regex/c_regex_traits.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/c_regex_traits.cpp:28: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/c_regex_traits.cpp:28: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/c_regex_traits.cpp:28: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/c_regex_traits.cpp:28: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/c_regex_traits.cpp:28: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/c_regex_traits.cpp:28: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/c_regex_traits.cpp:28: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/c_regex_traits.cpp:28: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/c_regex_traits.cpp:28: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/c_regex_traits.cpp:28: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/c_regex_traits.cpp:28: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/c_regex_traits.cpp:28: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/c_regex_traits.cpp:28: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/c_regex_traits.cpp:28: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/c_regex_traits.cpp:28: /home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/c_regex_traits.cpp:28: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: /home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/wide_posix_api.cpp:25: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/winstances.cpp -o boost_regex/winstances.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/winstances.cpp:30: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/winstances.cpp:30: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/winstances.cpp:30: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/winstances.cpp:30: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/winstances.cpp:30: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/winstances.cpp:30: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/winstances.cpp:30: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/winstances.cpp:30: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/winstances.cpp:30: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/winstances.cpp:30: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/winstances.cpp:30: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/winstances.cpp:30: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/winstances.cpp:30: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/winstances.cpp:30: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/winstances.cpp:30: /home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/winstances.cpp:30: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/w32_regex_traits.cpp -o boost_regex/w32_regex_traits.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/instances.cpp -o boost_regex/instances.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/instances.cpp:30: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/instances.cpp:30: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/instances.cpp:30: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/instances.cpp:30: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/instances.cpp:30: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/instances.cpp:30: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/instances.cpp:30: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/instances.cpp:30: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/instances.cpp:30: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/instances.cpp:30: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/instances.cpp:30: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/instances.cpp:30: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/instances.cpp:30: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/instances.cpp:30: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/instances.cpp:30: /home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31, from boost_regex/instances.cpp:30: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/regex_traits_defaults.cpp -o boost_regex/regex_traits_defaults.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: /home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27, from boost_regex/regex_traits_defaults.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/wc_regex_traits.cpp -o boost_regex/wc_regex_traits.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/wc_regex_traits.cpp:76: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from boost_regex/wc_regex_traits.cpp:23: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/wc_regex_traits.cpp:76: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from boost_regex/wc_regex_traits.cpp:23: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/wc_regex_traits.cpp:76: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from boost_regex/wc_regex_traits.cpp:23: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/wc_regex_traits.cpp:76: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from boost_regex/wc_regex_traits.cpp:23: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/wc_regex_traits.cpp:76: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from boost_regex/wc_regex_traits.cpp:23: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/wc_regex_traits.cpp:76: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from boost_regex/wc_regex_traits.cpp:23: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/wc_regex_traits.cpp:76: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from boost_regex/wc_regex_traits.cpp:23: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26, from boost_regex/wc_regex_traits.cpp:76: /home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from boost_regex/wc_regex_traits.cpp:23: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/regex_raw_buffer.cpp -o boost_regex/regex_raw_buffer.o mkdir -p "/home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-pqsfinder/00new/pqsfinder/lib" ar rs "/home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a" boost_regex/cpp_regex_traits.o boost_regex/cregex.o boost_regex/usinstances.o boost_regex/icu.o boost_regex/fileiter.o boost_regex/regex.o boost_regex/posix_api.o boost_regex/c_regex_traits.o boost_regex/wide_posix_api.o boost_regex/winstances.o boost_regex/w32_regex_traits.o boost_regex/instances.o boost_regex/regex_traits_defaults.o boost_regex/wc_regex_traits.o boost_regex/regex_debug.o boost_regex/static_mutex.o boost_regex/regex_raw_buffer.o ar: creating /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o pqsfinder.so RcppExports.o pqsfinder.o /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-pqsfinder/00new/pqsfinder/libs ** R ** 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 (pqsfinder)